Set output log file
Split up model into pieces using selection_method Choices are [‘by_chain’, ‘by_segment’,’all’, ‘boxes’] by_chain: each chain is a selection @@ -1352,7 +1352,7 @@
Extract tlso_group_info from aniso records in model
Set output log file
Set output log file
Bases: object
Bases: object
Print out a list of all issues that have been identified.
Show statistics for a proposed element identity.
Show atomic properties that are independent of the suspected identity.
Examines the environment around a single atom to determine if it is actually a misidentified metal ion.
no_final is used internally, when candidates is not Auto, to try all of the @@ -629,7 +629,7 @@
Iterates through all of the waters in a model, examining the maps and local environment to check their identity and suggest likely ions where appropriate.
@@ -895,7 +895,7 @@Prints out information about an entire model’s scattering statistics, such as mean map heights and b-factors for carbons and waters.
Examines one site in the model and determines if it was correctly modelled, returning a boolean indicating correctness.
Iterate over all the ions built into the model by this module and double check their correctness. Looks for tell-tale signs such as negative peaks in the mFo-DFc and anomalous difference maps, abnormal b-factor, and diff --git a/mmtbx/mmtbx.ions.svm.html b/mmtbx/mmtbx.ions.svm.html index 76fd03ad..7de1d9d4 100644 --- a/mmtbx/mmtbx.ions.svm.html +++ b/mmtbx/mmtbx.ions.svm.html @@ -315,7 +315,7 @@
Uses a SVM to analyze all of a model’s water sites and decide whether to re-assign them as ions.
Shows information about a SVM’s prediction of a site’s identity.
Shows a brief description of a SVM’s prediction of a site’s identity, for use in output as a table.
Convert any elemental ions in the PDB hierarchy to water, resetting the occupancy and scaling the B-factor. The atom segids will be set to the old resname. NOTE: this does not change the corresponding scatterer in the xray diff --git a/mmtbx/mmtbx.maps.html b/mmtbx/mmtbx.maps.html index 9b94171a..6d0728bb 100644 --- a/mmtbx/mmtbx.maps.html +++ b/mmtbx/mmtbx.maps.html @@ -118,7 +118,7 @@
Bases: object
Afonine et al. (2014). FEM: Feature Enhanced Map
@@ -465,7 +465,7 @@Bases: object
Bases: object
Automation wrapper for calculating standard 2mFo-DFc, mFo-DFc, and optional anomalous difference map coefficients, starting from an X-ray structure and diff --git a/mmtbx/mmtbx.refinement.html b/mmtbx/mmtbx.refinement.html index d34c2869..18d0e18b 100644 --- a/mmtbx/mmtbx.refinement.html +++ b/mmtbx/mmtbx.refinement.html @@ -1263,7 +1263,7 @@
Bases: object
Encapsulates all operations required to convert the original data to a different symmetry as suggested by Xtriage.
Bases: object
Given a target ligand and a list of reference ligands, return the RMSD(s) for any ligand determined to be approximately equivalent. (Usually there will be just one of these, but this allows for alternate conformations.)
@@ -5347,12 +5347,12 @@Comprehensive output with individual outlier lists, plus summary.
pdb_truncate_to_ala", "iotbx.reflection_file_reader - generic reflection file input", "iotbx.shelx", "iotbx.xds", "libtbx - low-level utilities and infrastructure for CCTBX", "libtbx.easy_mp: functions for painless parallelization of Python code", "libtbx.program_template: Standard Program Template for CCTBX Programs", "mmtbx - macromolecular crystallography", "mmtbx.building package", "mmtbx.bulk_solvent package", "mmtbx.cablam package", "mmtbx.cablam.fingerprints package", "mmtbx.chemical_components package", "mmtbx.command_line package", "mmtbx.conformation_dependent_library package", "mmtbx.den package", "mmtbx.density_modification package", "mmtbx.disorder package", "mmtbx.dynamics package", "mmtbx.f_model", "mmtbx.geometry package", "mmtbx.geometry_restraints package", "mmtbx.hydrogens package", "mmtbx.ias package", "mmtbx.ions package", "mmtbx.ions.build module", "mmtbx.ions.environment module", "mmtbx.ions.geometry module", "mmtbx.ions.halides module", "mmtbx.ions.identify module", "mmtbx.ions.svm package", "mmtbx.ions.svm.dump_sites module", "mmtbx.ions.svm.utils module", "mmtbx.ions.utils module", "mmtbx.kinemage package", "mmtbx.ligands package", "mmtbx.maps package", "mmtbx.masks package", "mmtbx.max_lik package", "mmtbx.monomer_library package", "mmtbx.ncs", "mmtbx.pdbtools - model manipulation utilities", "mmtbx.polygon package", "mmtbx.real_space package", "mmtbx.refinement package", "mmtbx.refinement.ensemble_refinement package", "mmtbx.refinement.real_space package", "mmtbx.rotamer package", "mmtbx.rsr package", "mmtbx.scaling package", "mmtbx.secondary_structure package", "mmtbx.secondary_structure.build package", "mmtbx.solvent package", "mmtbx.tls package", "mmtbx.torsion_restraints package", "mmtbx.twinning package", "mmtbx.utils package", "mmtbx.validation package", "mmtbx.validation.molprobity package", "mmtbx.wwpdb package", "mmtbx", "scitbx - general-purpose scientific programming infrastructure", "scitbx.array_family.flex", "scitbx.lbfgs", "scitbx.lstbx", "scitbx.matrix", "Tour of the cctbx", "xfel", "xfel package", "xfel.cftbx package", "xfel.cftbx.detector package", "xfel.clustering package", "xfel.command_line package", "xfel.cxi package", "xfel.cxi.cspad_ana package", "xfel.cxi.gfx package", "xfel.cxi.merging package", "xfel.cxi.postrefine package", "xfel.metrology package", "xfel.metrology.legacy_scale package", "xfel.mono_simulation package"], "titleterms": {"": 261, "2000": 262, "A": 335, "At": 335, "The": [148, 198, 335], "absenc": 318, "absence_likelihood": 318, "absolute_sc": 318, "accessori": [264, 268], "act": 335, "adp_refin": 313, "adp_restraint": [2, 3, 4], "adp_symmetry_constraint": 79, "adptbx": 5, "all": 326, "all_ax": [80, 205], "altloc": 289, "altloc_weight": 283, "analysi": 326, "analyze_adp": 81, "analyze_model": 286, "analyze_peptid": 326, "anomalous_scatterer_group": 313, "antiparallel_beta": 280, "antiparallel_beta_bridg": 280, "api": [264, 265, 266, 268, 271, 272, 282, 288, 310, 331, 332, 333, 334], "architectur": 274, "argument": 268, "arrai": [148, 331], "array_famili": [6, 7, 331, 335], "asa": 289, "aspect": 148, "asu_galleri": [206, 207, 208, 209, 210, 211], "atom": 326, "attenuation_coeffici": 47, "auto_submit": 341, "average_spot": 342, "average_tbx": 343, "backbon": 286, "balanc": 335, "base": 326, "base_pair": 319, "basic": 273, "basic_analys": 318, "beach": 335, "beam": 257, "beta": 326, "bfg": 154, "bond_angle_registri": 283, "bondlength_default": 308, "boost": 0, "boost_adaptbx": [0, 261], "bottom": 335, "box": 335, "bravais_typ": 166, "brehm_diederich": [9, 147, 341], "bridg": 335, "browse_set": 212, "build": [262, 277, 294, 320, 335], "build_hydrogen": 291, "bulk_solv": 278, "bulk_solvent_and_sc": 278, "burzlaff_zimmermann_dewolff": 24, "c": [264, 326], "c_beta": 290, "cablam": [279, 280], "cablam_align": 279, "cablam_fingerprint": 279, "cablam_math": 279, "cablam_r": 279, "cablam_train": 279, "cablam_valid": 279, "cartesian_dynam": 287, "cbf_averag": 341, "cctbx": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 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"wavelength_unit": 20, "web": [204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231], "web_link": 211, "weight": 315, "weighting_schem": 255, "weights_param": 313, "welcom": 261, "window": 262, "work": [148, 331], "wrapper": 0, "writer": 263, "wwpdb": 328, "wx_detector": 344, "wx_tardy_pdb": 313, "wyckoff": 231, "xd": [258, 272], "xes_finalis": [341, 343], "xes_histogram": [341, 343], "xfel": [261, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349], "xrai": [232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255], "xray_scatt": 76, "xray_structur": 21, "xtal_screen": 304, "xtriag": 318}})
\ No newline at end of file
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module": [[326, "module-mmtbx.validation.waters"]], "mmtbx.wwpdb package": [[328, "mmtbx-wwpdb-package"]], "mmtbx.wwpdb.rcsb_web_services module": [[328, "module-mmtbx.wwpdb.rcsb_web_services"]], "mmtbx.wwpdb.standard_geometry_cif module": [[328, "module-mmtbx.wwpdb.standard_geometry_cif"]], "mmtbx.wwpdb.utils module": [[328, "module-mmtbx.wwpdb.utils"]], "parallel_map: parallel map() function for multiple architectures": [[274, "parallel-map-parallel-map-function-for-multiple-architectures"]], "pool_map: parallel map() function for Unix/Linux systems": [[274, "pool-map-parallel-map-function-for-unix-linux-systems"]], "scitbx": [[261, "scitbx"]], "scitbx - general-purpose scientific programming infrastructure": [[330, "scitbx-general-purpose-scientific-programming-infrastructure"]], "scitbx.array_family.flex": [[331, "scitbx-array-family-flex"], [335, "scitbx-array-family-flex"]], "scitbx.lbfgs": [[332, "scitbx-lbfgs"]], "scitbx.lstbx": [[333, "scitbx-lstbx"]], "scitbx.matrix": [[334, "module-scitbx.matrix"]], "sgtbx - Space Group Toolbox": [[260, "sgtbx-space-group-toolbox"]], "singleframe.SingleFrame": [[340, "singleframe-singleframe"]], "smtbx": [[261, "smtbx"]], "v0_getting_started.py": [[269, "v0-getting-started-py"]], "v1_loop_over_atoms.py": [[269, "v1-loop-over-atoms-py"]], "v2_simple.py": [[269, "v2-simple-py"]], "v3_better.py": [[269, "v3-better-py"]], "v4_with_bells_and_whistles.py": [[269, "v4-with-bells-and-whistles-py"]], "xfel": [[261, "xfel"], [336, "xfel"]], "xfel package": [[337, "xfel-package"]], "xfel.cftbx package": [[338, "xfel-cftbx-package"]], "xfel.cftbx.detector package": [[339, "xfel-cftbx-detector-package"]], "xfel.cftbx.detector.cspad_cbf_tbx module": [[339, "module-xfel.cftbx.detector.cspad_cbf_tbx"]], "xfel.cftbx.detector.cspad_detector module": [[339, "xfel-cftbx-detector-cspad-detector-module"]], "xfel.cftbx.detector.generic_detector module": [[339, "xfel-cftbx-detector-generic-detector-module"]], "xfel.cftbx.detector.metrology module": [[339, "xfel-cftbx-detector-metrology-module"]], "xfel.cftbx.detector.metrology2phil module": [[339, "module-xfel.cftbx.detector.metrology2phil"]], "xfel.clustering package": [[340, "xfel-clustering-package"]], "xfel.clustering.cluster module": [[340, "module-xfel.clustering.cluster"]], "xfel.clustering.cluster_groups module": [[340, "module-xfel.clustering.cluster_groups"]], "xfel.clustering.singleframe module": [[340, "module-xfel.clustering.singleframe"]], "xfel.command_line package": [[341, "xfel-command-line-package"]], "xfel.command_line.auto_submit module": [[341, "module-xfel.command_line.auto_submit"]], "xfel.command_line.brehm_diederichs module": [[341, "module-xfel.command_line.brehm_diederichs"]], "xfel.command_line.cbf_average module": [[341, "module-xfel.command_line.cbf_average"]], "xfel.command_line.cluster_42 module": [[341, "xfel-command-line-cluster-42-module"]], "xfel.command_line.cluster_intensity_statistics module": [[341, "xfel-command-line-cluster-intensity-statistics-module"]], "xfel.command_line.cluster_per_frame_wilson module": [[341, "xfel-command-line-cluster-per-frame-wilson-module"]], "xfel.command_line.cluster_unit_cell module": [[341, "xfel-command-line-cluster-unit-cell-module"]], "xfel.command_line.cluster_visualise_orientations module": [[341, "xfel-command-line-cluster-visualise-orientations-module"]], "xfel.command_line.convert_gain_map module": [[341, "module-xfel.command_line.convert_gain_map"]], "xfel.command_line.convert_gain_map_cbf module": [[341, "module-xfel.command_line.convert_gain_map_cbf"]], "xfel.command_line.cxi_apply_metrology module": [[341, "module-xfel.command_line.cxi_apply_metrology"]], "xfel.command_line.cxi_cspad_pinwheel module": [[341, "module-xfel.command_line.cxi_cspad_pinwheel"]], "xfel.command_line.cxi_diff module": [[341, "module-xfel.command_line.cxi_diff"]], "xfel.command_line.cxi_display_metrology module": [[341, "module-xfel.command_line.cxi_display_metrology"]], "xfel.command_line.cxi_generate_circular_gain_mask module": [[341, "module-xfel.command_line.cxi_generate_circular_gain_mask"]], "xfel.command_line.cxi_image2pickle module": [[341, "xfel-command-line-cxi-image2pickle-module"]], "xfel.command_line.cxi_index module": [[341, "module-xfel.command_line.cxi_index"]], "xfel.command_line.cxi_lsf module": [[341, "module-xfel.command_line.cxi_lsf"]], "xfel.command_line.cxi_merge module": [[341, "module-xfel.command_line.cxi_merge"]], "xfel.command_line.cxi_optical2cbfheader module": [[341, "module-xfel.command_line.cxi_optical2cbfheader"]], "xfel.command_line.cxi_pbs module": [[341, "module-xfel.command_line.cxi_pbs"]], "xfel.command_line.cxi_pickle2cbf module": [[341, "module-xfel.command_line.cxi_pickle2cbf"]], "xfel.command_line.cxi_plotcv module": [[341, "module-xfel.command_line.cxi_plotcv"]], "xfel.command_line.cxi_psana module": [[341, "module-xfel.command_line.cxi_psana"]], "xfel.command_line.cxi_pyana module": [[341, "module-xfel.command_line.cxi_pyana"]], "xfel.command_line.cxi_spots module": [[341, "module-xfel.command_line.cxi_spots"]], "xfel.command_line.cxi_stream_to_pickle module": [[341, "module-xfel.command_line.cxi_stream_to_pickle"]], "xfel.command_line.cxi_view module": [[341, "module-xfel.command_line.cxi_view"]], "xfel.command_line.cxi_xmerge module": [[341, "module-xfel.command_line.cxi_xmerge"]], "xfel.command_line.get_next_trial_id module": [[341, "xfel-command-line-get-next-trial-id-module"]], "xfel.command_line.grid_index module": [[341, "xfel-command-line-grid-index-module"]], "xfel.command_line.histogram_finalise module": [[341, "module-xfel.command_line.histogram_finalise"]], "xfel.command_line.list_db_metadata module": [[341, "module-xfel.command_line.list_db_metadata"]], "xfel.command_line.make_mask module": [[341, "module-xfel.command_line.make_mask"]], "xfel.command_line.metrology module": [[341, "module-xfel.command_line.metrology"]], "xfel.command_line.monitor_detectors module": [[341, "module-xfel.command_line.monitor_detectors"]], "xfel.command_line.monitor_trials module": [[341, "module-xfel.command_line.monitor_trials"]], "xfel.command_line.overlay_spectra module": [[341, "module-xfel.command_line.overlay_spectra"]], "xfel.command_line.plot_to_subpixel module": [[341, "module-xfel.command_line.plot_to_subpixel"]], "xfel.command_line.postrefine module": [[341, "module-xfel.command_line.postrefine"]], "xfel.command_line.print_pickle module": [[341, "module-xfel.command_line.print_pickle"]], "xfel.command_line.quadrants module": [[341, "module-xfel.command_line.quadrants"]], "xfel.command_line.radial_average module": [[341, "module-xfel.command_line.radial_average"]], "xfel.command_line.smooth_spectrum module": [[341, "module-xfel.command_line.smooth_spectrum"]], "xfel.command_line.subtract_background module": [[341, "module-xfel.command_line.subtract_background"]], "xfel.command_line.trial_stats module": [[341, "module-xfel.command_line.trial_stats"]], "xfel.command_line.view_pixel_histograms module": [[341, "module-xfel.command_line.view_pixel_histograms"]], "xfel.command_line.xes_finalise module": [[341, "module-xfel.command_line.xes_finalise"]], "xfel.command_line.xes_histograms module": [[341, "module-xfel.command_line.xes_histograms"]], "xfel.cxi package": [[342, "xfel-cxi-package"]], "xfel.cxi.average_spots module": [[342, "module-xfel.cxi.average_spots"]], "xfel.cxi.completeness_plot module": [[342, "xfel-cxi-completeness-plot-module"]], "xfel.cxi.correction_vector_plot module": [[342, "module-xfel.cxi.correction_vector_plot"]], "xfel.cxi.cspad_ana package": [[343, "xfel-cxi-cspad-ana-package"]], "xfel.cxi.cspad_ana.average_tbx module": [[343, "module-xfel.cxi.cspad_ana.average_tbx"]], "xfel.cxi.cspad_ana.common_mode module": [[343, "module-xfel.cxi.cspad_ana.common_mode"]], "xfel.cxi.cspad_ana.cspad_tbx module": [[343, "module-xfel.cxi.cspad_ana.cspad_tbx"]], "xfel.cxi.cspad_ana.display_calib module": [[343, "module-xfel.cxi.cspad_ana.display_calib"]], "xfel.cxi.cspad_ana.histogram_finalise module": [[343, "module-xfel.cxi.cspad_ana.histogram_finalise"]], "xfel.cxi.cspad_ana.hitfinder_tbx module": [[343, "module-xfel.cxi.cspad_ana.hitfinder_tbx"]], "xfel.cxi.cspad_ana.mod_average module": [[343, "module-xfel.cxi.cspad_ana.mod_average"]], "xfel.cxi.cspad_ana.mod_average_cbf module": [[343, "xfel-cxi-cspad-ana-mod-average-cbf-module"]], "xfel.cxi.cspad_ana.mod_cbf_hitfind module": [[343, "xfel-cxi-cspad-ana-mod-cbf-hitfind-module"]], "xfel.cxi.cspad_ana.mod_cbf_index module": [[343, "xfel-cxi-cspad-ana-mod-cbf-index-module"]], "xfel.cxi.cspad_ana.mod_cspad_cbf module": [[343, "xfel-cxi-cspad-ana-mod-cspad-cbf-module"]], "xfel.cxi.cspad_ana.mod_cspad_cbf_dump module": [[343, "xfel-cxi-cspad-ana-mod-cspad-cbf-dump-module"]], "xfel.cxi.cspad_ana.mod_daq_status module": [[343, "module-xfel.cxi.cspad_ana.mod_daq_status"]], "xfel.cxi.cspad_ana.mod_dump module": [[343, "module-xfel.cxi.cspad_ana.mod_dump"]], "xfel.cxi.cspad_ana.mod_dump_bitmap module": [[343, "module-xfel.cxi.cspad_ana.mod_dump_bitmap"]], "xfel.cxi.cspad_ana.mod_event_info module": [[343, "module-xfel.cxi.cspad_ana.mod_event_info"]], "xfel.cxi.cspad_ana.mod_filter module": [[343, "module-xfel.cxi.cspad_ana.mod_filter"]], "xfel.cxi.cspad_ana.mod_hdf5 module": [[343, "module-xfel.cxi.cspad_ana.mod_hdf5"]], "xfel.cxi.cspad_ana.mod_hitfind module": [[343, "module-xfel.cxi.cspad_ana.mod_hitfind"]], "xfel.cxi.cspad_ana.mod_illumination_filter module": [[343, "module-xfel.cxi.cspad_ana.mod_illumination_filter"]], "xfel.cxi.cspad_ana.mod_ledge module": [[343, "xfel-cxi-cspad-ana-mod-ledge-module"]], "xfel.cxi.cspad_ana.mod_mar module": [[343, "module-xfel.cxi.cspad_ana.mod_mar"]], "xfel.cxi.cspad_ana.mod_param module": [[343, "module-xfel.cxi.cspad_ana.mod_param"]], "xfel.cxi.cspad_ana.mod_pickle2cbf_dump module": [[343, "xfel-cxi-cspad-ana-mod-pickle2cbf-dump-module"]], "xfel.cxi.cspad_ana.mod_pulnix_dump module": [[343, "module-xfel.cxi.cspad_ana.mod_pulnix_dump"]], "xfel.cxi.cspad_ana.mod_radial_average module": [[343, "module-xfel.cxi.cspad_ana.mod_radial_average"]], "xfel.cxi.cspad_ana.mod_spectra module": [[343, "xfel-cxi-cspad-ana-mod-spectra-module"]], "xfel.cxi.cspad_ana.mod_spectra_view module": [[343, "xfel-cxi-cspad-ana-mod-spectra-view-module"]], "xfel.cxi.cspad_ana.mod_view module": [[343, "xfel-cxi-cspad-ana-mod-view-module"]], "xfel.cxi.cspad_ana.mod_xes module": [[343, "module-xfel.cxi.cspad_ana.mod_xes"]], "xfel.cxi.cspad_ana.parse_calib module": [[343, "module-xfel.cxi.cspad_ana.parse_calib"]], "xfel.cxi.cspad_ana.pixel_histograms module": [[343, "module-xfel.cxi.cspad_ana.pixel_histograms"]], "xfel.cxi.cspad_ana.xes_finalise module": [[343, "module-xfel.cxi.cspad_ana.xes_finalise"]], "xfel.cxi.cspad_ana.xes_histograms module": [[343, "module-xfel.cxi.cspad_ana.xes_histograms"]], "xfel.cxi.cxi_cc module": [[342, "module-xfel.cxi.cxi_cc"]], "xfel.cxi.display_powder_arcs module": [[342, "module-xfel.cxi.display_powder_arcs"]], "xfel.cxi.display_spots module": [[342, "module-xfel.cxi.display_spots"]], "xfel.cxi.gfx package": [[344, "xfel-cxi-gfx-package"]], "xfel.cxi.gfx.status_plot module": [[344, "module-xfel.cxi.gfx.status_plot"]], "xfel.cxi.gfx.trials_plot module": [[344, "module-xfel.cxi.gfx.trials_plot"]], "xfel.cxi.gfx.wx_detectors module": [[344, "module-xfel.cxi.gfx.wx_detectors"]], "xfel.cxi.integrate_image_api module": [[342, "module-xfel.cxi.integrate_image_api"]], "xfel.cxi.merging package": [[345, "xfel-cxi-merging-package"]], "xfel.cxi.merging.general_fcalc module": [[345, "xfel-cxi-merging-general-fcalc-module"]], "xfel.cxi.merging.phil_validation module": [[345, "xfel-cxi-merging-phil-validation-module"]], "xfel.cxi.merging.refine module": [[345, "xfel-cxi-merging-refine-module"]], "xfel.cxi.merging_database module": [[342, "xfel-cxi-merging-database-module"]], "xfel.cxi.merging_database_fs module": [[342, "xfel-cxi-merging-database-fs-module"]], "xfel.cxi.merging_database_sqlite3 module": [[342, "xfel-cxi-merging-database-sqlite3-module"]], "xfel.cxi.postrefine package": [[346, "xfel-cxi-postrefine-package"]], "xfel.cxi.postrefine.justsum module": [[346, "xfel-cxi-postrefine-justsum-module"]], "xfel.cxi.postrefine.mod_energy module": [[346, "xfel-cxi-postrefine-mod-energy-module"]], "xfel.cxi.postrefine.mod_graddesc module": [[346, "xfel-cxi-postrefine-mod-graddesc-module"]], "xfel.cxi.postrefine.mod_leastsqr module": [[346, "xfel-cxi-postrefine-mod-leastsqr-module"]], "xfel.cxi.postrefine.mod_normal_eqns module": [[346, "xfel-cxi-postrefine-mod-normal-eqns-module"]], "xfel.cxi.postrefine.mod_partiality module": [[346, "xfel-cxi-postrefine-mod-partiality-module"]], "xfel.cxi.postrefine.mod_pdb module": [[346, "xfel-cxi-postrefine-mod-pdb-module"]], "xfel.cxi.postrefine.mod_polar module": [[346, "xfel-cxi-postrefine-mod-polar-module"]], "xfel.cxi.postrefine.mod_results module": [[346, "xfel-cxi-postrefine-mod-results-module"]], "xfel.cxi.postrefine.mod_util module": [[346, "xfel-cxi-postrefine-mod-util-module"]], "xfel.cxi.postrefine.postrefine module": [[346, "xfel-cxi-postrefine-postrefine-module"]], "xfel.cxi.postrefine.probe module": [[346, "xfel-cxi-postrefine-probe-module"]], "xfel.cxi.postrefine.probe_best module": [[346, "xfel-cxi-postrefine-probe-best-module"]], "xfel.cxi.postrefine.read_serial_and_img module": [[346, "xfel-cxi-postrefine-read-serial-and-img-module"]], "xfel.cxi.postrefine.test_energy_model module": [[346, "xfel-cxi-postrefine-test-energy-model-module"]], "xfel.cxi.postrefine.test_rs module": [[346, "xfel-cxi-postrefine-test-rs-module"]], "xfel.cxi.strong_zulu module": [[342, "module-xfel.cxi.strong_zulu"]], "xfel.cxi.util module": [[342, "module-xfel.cxi.util"]], "xfel.detector_formats module": [[337, 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"mmtbx.density_modification.density_modification.active_indices", false]], "ad_hoc_single_atom_residue (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.ad_hoc_single_atom_residue", false]], "add() (cctbx.development.structure_factor_utils.collector method)": [[44, "cctbx.development.structure_factor_utils.collector.add", false]], "add() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.add", false]], "add() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.add", false]], "add() (cctbx.web.asu_gallery.jv_index.symbol_table method)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table.add", false]], "add() (dxtbx.model.scan.scanfactory static method)": [[257, "dxtbx.model.scan.ScanFactory.add", false]], "add() (mmtbx.geometry.altloc.indexer method)": [[289, "mmtbx.geometry.altloc.Indexer.add", false]], "add() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.add", false]], "add() (mmtbx.geometry.topology.molecule method)": [[289, "mmtbx.geometry.topology.Molecule.add", false]], "add() (mmtbx.refinement.real_space.fit_residue.monitor method)": [[315, "mmtbx.refinement.real_space.fit_residue.monitor.add", false]], "add() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.add", false]], "add() (mmtbx.refinement.rigid_body.rigid_body_shift_accumulator method)": [[313, "mmtbx.refinement.rigid_body.rigid_body_shift_accumulator.add", false]], "add() (mmtbx.utils.states method)": [[325, "mmtbx.utils.states.add", false]], "add_angle_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_angle_proxies", false]], "add_angle_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_angle_proxies", false]], "add_angles_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_angles_in_place", false]], "add_arg_like_h() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_arg_like_h", false]], "add_atom() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.add_atom", false]], "add_atoms_in() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.add_atoms_in", false]], "add_bond() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.add_bond", false]], "add_bond_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_bond_proxies", false]], "add_bond_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_bond_proxies", false]], "add_box() (mmtbx.maps.composite_omit_map.omit_regions method)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.add_box", false]], "add_buffer() (cctbx.crystal.direct_space_asu.direct_space_asu method)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu.add_buffer", false]], "add_buffer() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_buffer", false]], "add_ca_ha1_and_ha2() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ca_ha1_and_ha2", false]], "add_ca_ha1_or_ha2() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ca_ha1_or_ha2", false]], "add_cc() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_cc", false]], "add_cc_list() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_cc_list", false]], "add_cell() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.add_cell", false]], "add_cells() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.add_cells", false]], "add_chain_residue_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_chain_residue_id", false]], "add_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_chi_torsion_restraints_in_place", false]], "add_chirality_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_chirality_proxies", false]], "add_chirality_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_chirality_proxies", false]], "add_column() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.add_column", false]], "add_columns() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.add_columns", false]], "add_coordinate_restraints() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.add_coordinate_restraints", false]], "add_crystal_symmetry_to_model_if_necessary() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.add_crystal_symmetry_to_model_if_necessary", false]], "add_cycle() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.add_cycle", false]], "add_default_options() (mmtbx.validation.molprobity.molprobityparser method)": [[327, "mmtbx.validation.molprobity.MolProbityParser.add_default_options", false]], "add_dihedral_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_dihedral_proxies", false]], "add_dihedral_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_dihedral_proxies", false]], "add_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_dihedrals_in_place", false]], "add_empty() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.add_empty", false]], "add_fan() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.add_fan", false]], "add_frame() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.add_frame", false]], "add_gradients() (in module cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.add_gradients", false]], "add_hhh() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_hhh", false]], "add_identity_op() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_identity_op", false]], "add_identity_op() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_identity_op", false]], "add_if_missing() (libtbx.group_args method)": [[273, "libtbx.group_args.add_if_missing", false]], "add_if_not_duplicated() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.add_if_not_duplicated", false]], "add_if_not_duplicated() (cctbx.geometry_restraints.chirality_proxy_registry method)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry.add_if_not_duplicated", false]], "add_if_not_duplicated() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.add_if_not_duplicated", false]], "add_if_not_duplicated() (cctbx.geometry_restraints.parallelity_proxy_registry method)": [[131, "cctbx.geometry_restraints.parallelity_proxy_registry.add_if_not_duplicated", false]], "add_if_not_duplicated() (cctbx.geometry_restraints.planarity_proxy_registry method)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry.add_if_not_duplicated", false]], "add_label() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.add_label", false]], "add_limitation() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.add_limitation", false]], "add_lone_pairs_for_peptyde_o() (in module mmtbx.ias)": [[292, "mmtbx.ias.add_lone_pairs_for_peptyde_o", false]], "add_map_from_fourier_coefficients() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.add_map_from_fourier_coefficients", false]], "add_map_manager() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.add_map_manager", false]], "add_map_manager_by_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.add_map_manager_by_id", false]], "add_miller_array() (iotbx.cif.miller_arrays_as_cif_block method)": [[264, "iotbx.cif.miller_arrays_as_cif_block.add_miller_array", false]], "add_model() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.add_model", false]], "add_model_by_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.add_model_by_id", false]], "add_ncs_object() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.add_ncs_object", false]], "add_new_bond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_new_bond_restraints_in_place", false]], "add_new_hbond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_new_hbond_restraints_in_place", false]], "add_new_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.add_new_solvent", false]], "add_nodes_to_query_if_needed_in_place() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.add_nodes_to_query_if_needed_in_place", false]], "add_note() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_note", false]], "add_occupancy_selection() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.add_occupancy_selection", false]], "add_operator() (mmtbx.ncs.ligands.group_operators method)": [[309, "mmtbx.ncs.ligands.group_operators.add_operator", false]], "add_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.add_outlier", false]], "add_pairs() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.add_pairs", false]], "add_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_parallelities_in_place", false]], "add_parallelity_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_parallelity_proxies", false]], "add_parallelity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_parallelity_proxies", false]], "add_planarities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_planarities_in_place", false]], "add_planarity_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.add_planarity_proxies", false]], "add_planarity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.add_planarity_proxies", false]], "add_plane() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_plane", false]], "add_planes() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.add_planes", false]], "add_point_group_type() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.add_point_group_type", false]], "add_position() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.add_position", false]], "add_positions() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.add_positions", false]], "add_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.add_reference_coordinate_restraints_in_place", false]], "add_residue() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.add_residue", false]], "add_residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_residues_in_common_list", false]], "add_ring_h() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.add_ring_h", false]], "add_rmsd_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.add_rmsd_list", false]], "add_rotamer_restraints() (in module mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.add_rotamer_restraints", false]], "add_row() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.add_row", false]], "add_scatterer() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.add_scatterer", false]], "add_scatterer() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.add_scatterer", false]], "add_scatterers() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.add_scatterers", false]], "add_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.add_scatterers", false]], "add_selected() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.add_selected", false]], "add_selected() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.add_selected", false]], "add_selected() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.add_selected", false]], "add_selected() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.add_selected", false]], "add_source_info() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.add_source_info", false]], "add_spring() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.add_spring", false]], "add_tiles_to_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.add_tiles_to_cbf", false]], "add_to_info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.add_to_info", false]], "add_to_validation_counts() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.add_to_validation_counts", false]], "add_tuples_int() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.add_tuples_int", false]], "add_water() (mmtbx.validation.experimental.real_space method)": [[326, "mmtbx.validation.experimental.real_space.add_water", false]], "add_wavelength_info() (mmtbx.scaling.make_param.phil_lego method)": [[318, "mmtbx.scaling.make_param.phil_lego.add_wavelength_info", false]], "adjust_class() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.adjust_class", false]], "adjust_cosine() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.adjust_cosine", false]], "adjust_fraction() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.adjust_fraction", false]], "adjust_magnification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.adjust_magnification", false]], "adjust_magnification() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.adjust_magnification", false]], "adjust_occupancy() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.adjust_occupancy", false]], "adjust_u_iso() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.adjust_u_iso", false]], "adjust_weight_sample_rate() (mmtbx.refinement.real_space.individual_sites.refinery method)": [[315, "mmtbx.refinement.real_space.individual_sites.refinery.adjust_weight_sample_rate", false]], "adopt_den_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_den_manager", false]], "adopt_init_args() (in module libtbx)": [[273, "libtbx.adopt_init_args", false]], "adopt_optional_init_args() (in module libtbx)": [[273, "libtbx.adopt_optional_init_args", false]], "adopt_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_reference_coordinate_restraints_in_place", false]], "adopt_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.adopt_reference_dihedral_manager", false]], "adopt_set() (cctbx.miller.array method)": [[148, "cctbx.miller.array.adopt_set", false]], "adopt_xray_structure() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.adopt_xray_structure", false]], "adp_aniso_restraints (class in cctbx.adp_restraints)": [[2, "cctbx.adp_restraints.adp_aniso_restraints", false]], "adp_refinement() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.adp_refinement", false]], "adp_similarity_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.adp_similarity_deviation", false]], "adp_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.adp_stats", false]], "af_shared_atom (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.af_shared_atom", false]], "afix_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.afix_parser", false]], "aggregator (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Aggregator", false]], "algebraic() (cctbx.sgtbx.harker.plane_fractional method)": [[177, "cctbx.sgtbx.harker.plane_fractional.algebraic", false]], "algorithm() (cctbx.xray.structure_factors.manager.managed_calculation_base method)": [[250, "cctbx.xray.structure_factors.manager.managed_calculation_base.algorithm", false]], "algorithm2 (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.algorithm2", false]], "align_chain() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.align_chain", false]], "align_model() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.align_model", false]], "all (mmtbx.validation.model_properties.model_statistics attribute)": [[326, "mmtbx.validation.model_properties.model_statistics.all", false]], "all() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.all", false]], "all() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all", false]], "all() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all", false]], "all() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all", false]], "all() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all", false]], "all() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all", false]], "all() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.all", false]], "all() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all", false]], "all() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all", false]], "all() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all", false]], "all() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all", false]], "all() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.all", false]], "all() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.all", false]], "all() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.all", false]], "all() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.all", false]], "all_approx_equal() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_approx_equal", false]], "all_approx_equal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_approx_equal", false]], "all_approx_equal_relatively() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_approx_equal_relatively", false]], "all_approx_equal_relatively() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_approx_equal_relatively", false]], "all_associated_i_seqs() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.all_associated_i_seqs", false]], "all_atoms_are_in_main_conf() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.all_atoms_are_in_main_conf", false]], "all_bonds() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.all_bonds", false]], "all_cells() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.all_cells", false]], "all_cut_points() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.all_cut_points", false]], "all_eq() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all_eq", false]], "all_eq() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_eq", false]], "all_eq() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_eq", false]], "all_eq() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_eq", false]], "all_eq() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_eq", false]], "all_eq() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_eq", false]], "all_eq() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_eq", false]], "all_eq() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all_eq", false]], "all_frames_intensity_stats() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.all_frames_intensity_stats", false]], "all_ge() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_ge", false]], "all_ge() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_ge", false]], "all_ge() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_ge", false]], "all_ge() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_ge", false]], "all_ge() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_ge", false]], "all_gt() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_gt", false]], "all_gt() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_gt", false]], "all_gt() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_gt", false]], "all_gt() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_gt", false]], "all_gt() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_gt", false]], "all_le() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_le", false]], "all_le() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_le", false]], "all_le() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_le", false]], "all_le() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_le", false]], "all_le() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_le", false]], "all_lt() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_lt", false]], "all_lt() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_lt", false]], "all_lt() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_lt", false]], "all_lt() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_lt", false]], "all_lt() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_lt", false]], "all_master_params() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.all_master_params", false]], "all_ne() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.all_ne", false]], "all_ne() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.all_ne", false]], "all_ne() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.all_ne", false]], "all_ne() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.all_ne", false]], "all_ne() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.all_ne", false]], "all_ne() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.all_ne", false]], "all_ne() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.all_ne", false]], "all_ne() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.all_ne", false]], "all_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.all_points", false]], "all_selection() (cctbx.miller.set method)": [[148, "cctbx.miller.set.all_selection", false]], "all_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.all_selection", false]], "all_site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all_site_cluster_analysis", false]], "all_size (scitbx.array_family.flex.smart_selection property)": [[331, "scitbx.array_family.flex.smart_selection.all_size", false]], "all_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.all_with_effective_resolution", false]], "alpha_beta (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta", false]], "alpha_beta() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.alpha_beta", false]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta.alpha_beta", false]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta_calc method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc.alpha_beta", false]], "alpha_beta() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.alpha_beta", false]], "alpha_beta() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.alpha_beta", false]], "alpha_beta() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.alpha_beta", false]], "alpha_beta() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.alpha_beta", false]], "alpha_beta_calc (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc", false]], "alpha_beta_est_manager (class in mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager", false]], "alpha_beta_f() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.alpha_beta_f", false]], "alpha_beta_for_each_reflection() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.alpha_beta_for_each_reflection", false]], "alpha_beta_w() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.alpha_beta_w", false]], "alphas() (iotbx.shelx.hklf.reader method)": [[271, "iotbx.shelx.hklf.reader.alphas", false]], "alt_atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.alt_atom_id", false]], "alternate (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Alternate", false]], "alternate_conformations_as_multiple_models() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.alternate_conformations_as_multiple_models", false]], "alternative_find_best_cell (class in cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell", false]], "altid_for() (in module mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.altid_for", false]], "altloc (iotbx.pdb.hierarchy.atom_group property)": [[268, "iotbx.pdb.hierarchy.atom_group.altloc", false]], "altloc (iotbx.pdb.hierarchy.atom_with_labels property)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.altloc", false]], "altloc (iotbx.pdb.hierarchy.conformer property)": [[268, "iotbx.pdb.hierarchy.conformer.altloc", false]], "altloc (mmtbx.disorder.analyze_model.atom_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.altloc", false]], "altloc (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.altloc", false]], "altloc (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.altloc", false]], "altloc (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.altloc", false]], "altloc (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.altloc", false]], "altloc (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.altloc", false]], "altloc (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.altloc", false]], "altloc (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.altloc", false]], "altloc (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.altloc", false]], "altloc (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.altloc", false]], "altloc (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.altloc", false]], "altloc (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.altloc", false]], "altloc (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.altloc", false]], "altloc (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.altloc", false]], "altloc (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.altloc", false]], "altloc (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.altloc", false]], "altloc (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.altloc", false]], "altloc (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.altloc", false]], "altloc (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.altloc", false]], "altloc() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.altloc", false]], "altloc_averaged_calculation() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.altloc_averaged_calculation", false]], "altloc_indices() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.altloc_indices", false]], "altloc_strategy_from_atom() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.altloc_strategy_from_atom", false]], "altlocs_present() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.altlocs_present", false]], "amore_alpha_beta_gamma (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma", false]], "amore_alpha_beta_gamma_as_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_as_matrix", false]], "amore_alpha_beta_gamma_from_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_from_matrix", false]], "amore_alpha_beta_gamma_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma_normalize", false]], "amore_kappa_l_m_n (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n", false]], "amore_kappa_l_m_n_as_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_as_matrix", false]], "amore_kappa_l_m_n_from_matrix() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_from_matrix", false]], "amore_kappa_l_m_n_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n_normalize", false]], "amplitude (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.amplitude", false]], "amplitude_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitude_normalisations", false]], "amplitude_normalisations() (cctbx.miller.set method)": [[148, "cctbx.miller.set.amplitude_normalisations", false]], "amplitude_quasi_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitude_quasi_normalisations", false]], "amplitude_unit_weighting (class in cctbx.xray.weighting_schemes)": [[255, "cctbx.xray.weighting_schemes.amplitude_unit_weighting", false]], "amplitudes() (cctbx.miller.array method)": [[148, "cctbx.miller.array.amplitudes", false]], "amplitudes() (mmtbx.maps.map_coeffs_mtz_label_manager method)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager.amplitudes", false]], "analyse() (mmtbx.scaling.pair_analyses.reindexing method)": [[318, "mmtbx.scaling.pair_analyses.reindexing.analyse", false]], "analyze() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.analyze", false]], "analyze_absences (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.analyze_absences", false]], "analyze_aniso_correction() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.analyze_aniso_correction", false]], "analyze_intensity_statistics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.analyze_intensity_statistics", false]], "analyze_intensity_statistics() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.analyze_intensity_statistics", false]], "analyze_measurability (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.analyze_measurability", false]], "analyze_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.analyze_redundancies", false]], "analyze_resolution_limits (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits", false]], "analyze_substructure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_substructure", false]], "analyze_water() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_water", false]], "analyze_water() (mmtbx.ions.svm.manager method)": [[299, "mmtbx.ions.svm.manager.analyze_water", false]], "analyze_waters() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.analyze_waters", false]], "analyze_waters() (mmtbx.ions.svm.manager method)": [[299, "mmtbx.ions.svm.manager.analyze_waters", false]], "angle (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.angle", false]], "angle() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.angle", false]], "angle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.angle", false]], "angle() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.angle", false]], "angle() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.angle", false]], "angle_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.angle_counters", false]], "angle_delta_deg() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.angle_delta_deg", false]], "angle_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations", false]], "angle_deviations_weighted() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations_weighted", false]], "angle_deviations_z() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.angle_deviations_z", false]], "angle_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.angle_list", false]], "angle_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.angle_outlier_as_kinemage", false]], "angle_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.angle_proxy_registry", false]], "angle_rmsd (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.angle_rmsd", false]], "angles (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.angles", false]], "angles (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.angles", false]], "angles (mmtbx.validation.rna_validate.rna_validation attribute)": [[326, "mmtbx.validation.rna_validate.rna_validation.angles", false]], "anglesforaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.anglesForAA", false]], "anglesforrot (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.anglesForRot", false]], "angstroms_to_ev (xfel.clustering.singleframe.singleframe attribute)": [[340, "xfel.clustering.singleframe.SingleFrame.ANGSTROMS_TO_EV", false]], "aniso_b_min (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_b_min", false]], "aniso_b_ratio (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_b_ratio", false]], "aniso_range_of_b (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.aniso_range_of_b", false]], "aniso_ratio_p_value() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.aniso_ratio_p_value", false]], "anisotropic_correction() (in module mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.anisotropic_correction", false]], "anisotropic_correction() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.anisotropic_correction", false]], "anisotropic_scaling() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.anisotropic_scaling", false]], "anneal() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.anneal", false]], "annealing_callback (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.annealing_callback", false]], "ano_scaling (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.ano_scaling", false]], "anom (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.anom", false]], "anom_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id6", false], [295, "mmtbx.ions.environment.ScatteringEnvironment.anom_density", false]], "anom_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.ANOM_PEAK", false]], "anomalous (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.anomalous", false]], "anomalous (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.anomalous", false]], "anomalous_completeness() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_completeness", false]], "anomalous_differences() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_differences", false]], "anomalous_flag (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.anomalous_flag", false]], "anomalous_flag() (cctbx.miller.set method)": [[148, "cctbx.miller.set.anomalous_flag", false]], "anomalous_map() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.anomalous_map", false]], "anomalous_probability_plot() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_probability_plot", false]], "anomalous_reflection_intensity_primitive_cell() (in module cctbx.sgtbx.subgroups)": [[187, "cctbx.sgtbx.subgroups.anomalous_reflection_intensity_primitive_cell", false]], "anomalous_residual (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.anomalous_residual", false]], "anomalous_scatterer_group (class in cctbx.xray.scatterer)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group", false]], "anomalous_signal() (cctbx.miller.array method)": [[148, "cctbx.miller.array.anomalous_signal", false]], "anonymize_ions() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.anonymize_ions", false]], "any (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.any", false]], "any_compatible_crystal_symmetry() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_compatible_crystal_symmetry", false]], "any_compatible_unit_cell() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_compatible_unit_cell", false]], "any_file() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.any_file", false]], "any_file_fast() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.any_file_fast", false]], "any_file_fast_input (class in iotbx.file_reader)": [[265, "iotbx.file_reader.any_file_fast_input", false]], "any_file_input (class in iotbx.file_reader)": [[265, "iotbx.file_reader.any_file_input", false]], "any_generator_set (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.any_generator_set", false]], "any_generator_set() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.any_generator_set", false]], "any_reflection_file (class in iotbx.reflection_file_reader)": [[270, "iotbx.reflection_file_reader.any_reflection_file", false]], "append() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.append", false]], "append() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.append", false]], "append() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.append", false]], "append() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.append", false]], 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"scitbx.array_family.flex.sym_mat3_double.append", false]], "append() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.append", false]], "append() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.append", false]], "append() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.append", false]], "append_atom() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.append_atom", false]], "append_atom_group() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.append_atom_group", false]], "append_atom_with_other_parent() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.append_atom_with_other_parent", false]], "append_chain() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.append_chain", false]], "append_custom_proxy() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.append_custom_proxy", false]], "append_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_emsley8k_proxies", false]], "append_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_emsley_proxies", false]], "append_fixed_site() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.append_fixed_site", false]], "append_model() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.append_model", false]], "append_neighbours() (mmtbx.geometry.asa.separatecheckerbuilder static method)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder.append_neighbours", false]], "append_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_oldfield_proxies", false]], "append_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.append_phi_psi_2_proxies", false]], "append_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.append_reference_coordinate_restraints_in_place", false]], "append_residue_group() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.append_residue_group", false]], "append_residue_group() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.append_residue_group", false]], "apply_aniso_b_cart_to_f_array_info() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.apply_aniso_b_cart_to_f_array_info", false]], "apply_atom_selection() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.apply_atom_selection", false]], "apply_back_b_iso() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.apply_back_b_iso", false]], "apply_back_trace_of_overall_exp_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.apply_back_trace_of_overall_exp_scale_matrix", false]], "apply_back_trace_of_overall_exp_scale_matrix() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.apply_back_trace_of_overall_exp_scale_matrix", false]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.apply_change_in_place", false]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.apply_change_in_place", false]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.apply_change_in_place", false]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.apply_change_in_place", false]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.apply_change_in_place", false]], "apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.apply_change_in_place", false]], "apply_change_of_basis() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_change_of_basis", false]], "apply_change_of_basis() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.apply_change_of_basis", false]], "apply_chem_mod_list() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.apply_chem_mod_list", false]], "apply_cob_to_vector() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.apply_cob_to_vector", false]], "apply_debye_waller_factors() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_debye_waller_factors", false]], "apply_default_filter() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.apply_default_filter", false]], "apply_eucl_ops() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.apply_eucl_ops", false]], "apply_final() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.apply_final", false]], "apply_gaussian_noise() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.apply_gaussian_noise", false]], "apply_glyco_link_using_proxies_and_atoms() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.apply_glyco_link_using_proxies_and_atoms", false]], "apply_ligand_ncs (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.apply_ligand_ncs", false]], "apply_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.apply_mask", false]], "apply_mask_inplace() (mmtbx.utils.extract_box_around_model_and_map method)": [[325, "mmtbx.utils.extract_box_around_model_and_map.apply_mask_inplace", false]], "apply_mask_to_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.apply_mask_to_map", false]], "apply_mask_to_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.apply_mask_to_maps", false]], "apply_mod() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.apply_mod", false]], "apply_mod() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.apply_mod", false]], "apply_ncs_to_dv_results() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.apply_ncs_to_dv_results", false]], "apply_ncs_to_sites() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.apply_ncs_to_sites", false]], "apply_new_sites_to_hierarchies() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.apply_new_sites_to_hierarchies", false]], "apply_new_sites_to_xray_structure() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.apply_new_sites_to_xray_structure", false]], "apply_overall_scale() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.apply_overall_scale", false]], "apply_phil_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.apply_phil_str", false]], "apply_rigid_body_shift() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_rigid_body_shift", false]], "apply_rigid_body_shift_obj() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_rigid_body_shift_obj", false]], "apply_rotation_translation() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.apply_rotation_translation", false]], "apply_rt() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.apply_rt", false]], "apply_scale_to_original_data() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.apply_scale_to_original_data", false]], "apply_scaling() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_scaling", false]], "apply_shelxl_extinction_correction() (cctbx.miller.array method)": [[148, "cctbx.miller.array.apply_shelxl_extinction_correction", false]], "apply_shift() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_shift", false]], "apply_shifts() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.apply_shifts", false]], "apply_shifts() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.apply_shifts", false]], "apply_shifts() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.apply_shifts", false]], "apply_shifts() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.apply_shifts", false]], "apply_sign_correction() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.apply_sign_correction", false]], "apply_special_position_ops_d_target_d_site() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_special_position_ops_d_target_d_site", false]], "apply_spectral_scaling() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.apply_spectral_scaling", false]], "apply_sub_pixel_metrology() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.apply_sub_pixel_metrology", false]], "apply_symmetry() (cctbx.neutron.scatterer method)": [[152, "cctbx.neutron.scatterer.apply_symmetry", false]], "apply_symmetry() (cctbx.neutron.structure method)": [[152, "cctbx.neutron.structure.apply_symmetry", false]], "apply_symmetry_sites() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.apply_symmetry_sites", false]], "apply_symmetry_u_stars() (cctbx.xray.structure.structure method)": [[238, 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(scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.assign", false]], "assign() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.assign", false]], "assign() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.assign", false]], "assign() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.assign", false]], "assign() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.assign", false]], "assign_charge() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_charge", false]], "assign_directly() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_directly", false]], "assign_from_monomer_mapping() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.assign_from_monomer_mapping", false]], "assign_r_free_flags_by_shells() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.assign_r_free_flags_by_shells", false]], "assign_random_r_free_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.assign_random_r_free_flags", false]], "assistant (class in cctbx.miller.reindexing)": [[150, "cctbx.miller.reindexing.assistant", false]], "asu (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.asu", false]], "asu_001() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_001", false]], "asu_002() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_002", false]], "asu_003() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_003", false]], "asu_004() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_004", false]], "asu_005() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_005", false]], "asu_006() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_006", false]], "asu_007() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_007", false]], "asu_008() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_008", false]], "asu_009() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_009", false]], "asu_01() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_01", false]], "asu_010() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_010", false]], "asu_011() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_011", false]], "asu_012() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_012", false]], "asu_013() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_013", false]], "asu_014() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_014", false]], "asu_015() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_015", false]], "asu_016() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_016", false]], "asu_017() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_017", false]], "asu_018() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_018", false]], "asu_019() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_019", false]], "asu_02() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_02", false]], "asu_020() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_020", false]], "asu_021() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_021", false]], "asu_022() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_022", false]], "asu_023() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_023", false]], "asu_024() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_024", false]], "asu_025() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_025", false]], "asu_026() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_026", false]], "asu_027() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_027", false]], "asu_028() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_028", false]], "asu_029() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_029", false]], "asu_03() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_03", false]], "asu_030() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_030", false]], "asu_031() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_031", false]], "asu_032() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_032", false]], "asu_033() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_033", false]], "asu_034() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_034", false]], "asu_035() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_035", false]], "asu_036() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_036", false]], "asu_037() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_037", false]], "asu_038() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_038", false]], "asu_039() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_039", false]], "asu_04() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_04", false]], "asu_040() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_040", false]], "asu_041() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_041", false]], "asu_042() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_042", false]], "asu_043() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_043", false]], "asu_044() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_044", false]], "asu_045() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_045", false]], "asu_046() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_046", false]], "asu_047() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_047", false]], "asu_048() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_048", false]], "asu_049() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_049", false]], "asu_05() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_05", false]], "asu_050() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_050", false]], "asu_051() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_051", false]], "asu_052() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_052", false]], "asu_053() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_053", false]], "asu_054() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_054", false]], "asu_055() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_055", false]], "asu_056() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_056", false]], "asu_057() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_057", false]], "asu_058() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_058", false]], "asu_059() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_059", false]], "asu_06() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_06", false]], "asu_060() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_060", false]], "asu_061() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_061", false]], "asu_062() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_062", false]], "asu_063() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_063", false]], "asu_064() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_064", false]], "asu_065() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_065", false]], "asu_066() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_066", false]], "asu_067() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_067", false]], "asu_068() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_068", false]], "asu_069() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_069", false]], "asu_07() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_07", false]], "asu_070() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_070", false]], "asu_071() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_071", false]], "asu_072() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_072", false]], "asu_073() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_073", false]], "asu_074() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_074", false]], "asu_075() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_075", false]], "asu_076() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_076", false]], "asu_077() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_077", false]], "asu_078() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_078", false]], "asu_079() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_079", false]], "asu_08() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_08", false]], "asu_080() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_080", false]], "asu_081() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_081", false]], "asu_082() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_082", false]], "asu_083() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_083", false]], "asu_084() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_084", false]], "asu_085() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_085", false]], "asu_086() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_086", false]], "asu_087() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_087", false]], "asu_088() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_088", false]], "asu_089() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_089", false]], "asu_09() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_09", false]], "asu_090() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_090", false]], "asu_091() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_091", false]], "asu_092() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_092", false]], "asu_093() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_093", false]], "asu_094() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_094", false]], "asu_095() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_095", false]], "asu_096() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_096", false]], "asu_097() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_097", false]], "asu_098() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_098", false]], "asu_099() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_099", false]], "asu_10() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_10", false]], "asu_100() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_100", false]], "asu_101() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_101", false]], "asu_102() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_102", false]], "asu_103() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_103", false]], "asu_104() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_104", false]], "asu_105() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_105", false]], "asu_106() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_106", false]], "asu_107() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_107", false]], "asu_108() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_108", false]], "asu_109() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_109", false]], "asu_11() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_11", false]], "asu_110() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_110", false]], "asu_111() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_111", false]], "asu_112() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_112", false]], "asu_113() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_113", false]], "asu_114() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_114", false]], "asu_115() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_115", false]], "asu_116() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_116", false]], "asu_117() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_117", false]], "asu_118() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_118", false]], "asu_119() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_119", false]], "asu_12() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_12", false]], "asu_120() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_120", false]], "asu_121() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_121", false]], "asu_122() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_122", false]], "asu_123() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_123", false]], "asu_124() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_124", false]], "asu_125() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_125", false]], "asu_126() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_126", false]], "asu_127() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_127", false]], "asu_128() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_128", false]], "asu_129() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_129", false]], "asu_13() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_13", false]], "asu_130() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_130", false]], "asu_131() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_131", false]], "asu_132() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_132", false]], "asu_133() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_133", false]], "asu_134() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_134", false]], "asu_135() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_135", false]], "asu_136() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_136", false]], "asu_137() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_137", false]], "asu_138() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_138", false]], "asu_139() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_139", false]], "asu_14() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_14", false]], "asu_140() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_140", false]], "asu_141() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_141", false]], "asu_142() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_142", false]], "asu_143() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_143", false]], "asu_144() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_144", false]], "asu_145() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_145", false]], "asu_146() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_146", false]], "asu_147() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_147", false]], "asu_148() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_148", false]], "asu_149() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_149", false]], "asu_15() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_15", false]], "asu_150() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_150", false]], "asu_151() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_151", false]], "asu_152() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_152", false]], "asu_153() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_153", false]], "asu_154() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_154", false]], "asu_155() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_155", false]], "asu_156() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_156", false]], "asu_157() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_157", false]], "asu_158() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_158", false]], "asu_159() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_159", false]], "asu_16() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_16", false]], "asu_160() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_160", false]], "asu_161() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_161", false]], "asu_162() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_162", false]], "asu_163() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_163", false]], "asu_164() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_164", false]], "asu_165() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_165", false]], "asu_166() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_166", false]], "asu_167() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_167", false]], "asu_168() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_168", false]], "asu_169() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_169", false]], "asu_17() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.asu_17", false]], "asu_170() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_170", false]], "asu_171() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_171", false]], "asu_172() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_172", false]], "asu_173() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_173", false]], "asu_174() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_174", false]], "asu_175() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_175", false]], "asu_176() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_176", false]], "asu_177() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_177", false]], "asu_178() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_178", false]], "asu_179() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_179", false]], "asu_180() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_180", false]], "asu_181() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_181", false]], "asu_182() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_182", false]], "asu_183() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_183", false]], "asu_184() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_184", false]], "asu_185() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_185", false]], "asu_186() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_186", false]], "asu_187() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_187", false]], "asu_188() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_188", false]], "asu_189() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_189", false]], "asu_190() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_190", false]], "asu_191() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_191", false]], "asu_192() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_192", false]], "asu_193() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_193", false]], "asu_194() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_194", false]], "asu_195() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_195", false]], "asu_196() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_196", false]], "asu_197() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_197", false]], "asu_198() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_198", false]], "asu_199() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_199", false]], "asu_200() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_200", false]], "asu_201() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_201", false]], "asu_202() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_202", false]], "asu_203() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_203", false]], "asu_204() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_204", false]], "asu_205() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_205", false]], "asu_206() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_206", false]], "asu_207() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_207", false]], "asu_208() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_208", false]], "asu_209() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_209", false]], "asu_210() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_210", false]], "asu_211() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_211", false]], "asu_212() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_212", false]], "asu_213() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_213", false]], "asu_214() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_214", false]], "asu_215() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_215", false]], "asu_216() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_216", false]], "asu_217() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_217", false]], "asu_218() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_218", false]], "asu_219() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_219", false]], "asu_220() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_220", false]], "asu_221() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_221", false]], "asu_222() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_222", false]], "asu_223() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_223", false]], "asu_224() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_224", false]], "asu_225() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_225", false]], "asu_226() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_226", false]], "asu_227() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_227", false]], "asu_228() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_228", false]], "asu_229() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_229", false]], "asu_230() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.asu_230", false]], "asu_as_jvx() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.asu_as_jvx", false]], "asu_map_from_fmodel() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.asu_map_from_fmodel", false]], "asu_mapping_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.asu_mapping_for", false]], "asu_mappings() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.asu_mappings", false]], "asu_mappings() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.asu_mappings", false]], "asu_mappings() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.asu_mappings", false]], "asu_mask (class in mmtbx.masks)": [[306, "mmtbx.masks.asu_mask", false]], "asu_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.asu_polygons", false]], "asu_show_() (in module cctbx.sgtbx.direct_space_asu.proto)": [[173, "cctbx.sgtbx.direct_space_asu.proto.asu_show_", false]], "asucontent (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ASUContent", false]], "asymmetric_unit_in_p1() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.asymmetric_unit_in_p1", false]], "at_first_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.at_first_index", false]], "atom (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.atom", false]], "atom (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Atom", false]], "atom (class in mmtbx.ias)": [[292, "mmtbx.ias.atom", false]], "atom (class in mmtbx.validation)": [[326, "mmtbx.validation.atom", false]], "atom (mmtbx.geometry.clash.atomdescriptor property)": [[289, "mmtbx.geometry.clash.AtomDescriptor.atom", false]], "atom (mmtbx.ions.environment.atom_contact attribute)": [[295, "id15", false], [295, "mmtbx.ions.environment.atom_contact.atom", false]], "atom (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id0", false], [295, "mmtbx.ions.environment.ChemicalEnvironment.atom", false]], "atom_as_str() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.atom_as_str", false]], "atom_base (class in mmtbx.validation)": [[326, "mmtbx.validation.atom_base", false]], "atom_bfactor (class in mmtbx.validation.model_properties)": [[326, "mmtbx.validation.model_properties.atom_bfactor", false]], "atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_by_id", false]], "atom_contact (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.atom_contact", false]], "atom_curves (class in cctbx.maptbx)": [[139, "cctbx.maptbx.atom_curves", false]], "atom_dict() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.atom_dict", false]], "atom_for (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.atom_for", false]], "atom_group (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.atom_group", false]], "atom_group (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.atom_group", false]], "atom_group_as_hierarchy() (in module mmtbx.building)": [[277, "mmtbx.building.atom_group_as_hierarchy", false]], "atom_group_id_str() (mmtbx.validation.atom_base method)": [[326, "mmtbx.validation.atom_base.atom_group_id_str", false]], "atom_group_id_str() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.atom_group_id_str", false]], "atom_group_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy", false]], "atom_groups() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.atom_groups", false]], "atom_groups() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.atom_groups", false]], "atom_groups() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.atom_groups", false]], "atom_groups() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.atom_groups", false]], "atom_groups() (mmtbx.disorder.analyze_model.residue_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.atom_groups", false]], "atom_groups_size() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.atom_groups_size", false]], "atom_i_seq() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_i_seq", false]], "atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.atom_id", false]], "atom_id_no_altloc() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.atom_id_no_altloc", false]], "atom_ids() (mmtbx.monomer_library.cif_types.chem_comp_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_bond.atom_ids", false]], "atom_ids() 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[[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_name_interpretation", false]], "atom_names_given (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_names_given", false]], "atom_names_mappings (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.atom_names_mappings", false]], "atom_occupancy (class in mmtbx.validation.model_properties)": [[326, "mmtbx.validation.model_properties.atom_occupancy", false]], "atom_pair() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.atom_pair", false]], "atom_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.atom_parser", false]], "atom_radius_as_central_peak_width() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.atom_radius_as_central_peak_width", false]], "atom_scat() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.atom_scat", false]], "atom_selection (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.atom_selection", false]], "atom_selection (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.atom_selection", false]], "atom_selection (mmtbx.validation.atoms attribute)": [[326, "mmtbx.validation.atoms.atom_selection", false]], "atom_selection (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.atom_selection", false]], "atom_selection (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.atom_selection", false]], "atom_selection (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.atom_selection", false]], "atom_selection (mmtbx.validation.entity attribute)": [[326, "mmtbx.validation.entity.atom_selection", false]], "atom_selection (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.atom_selection", false]], "atom_selection (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.atom_selection", false]], "atom_selection (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.atom_selection", false]], "atom_selection (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.atom_selection", false]], "atom_selection (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.atom_selection", false]], "atom_selection (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.atom_selection", false]], "atom_selection (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.atom_selection", false]], "atom_selection (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.atom_selection", false]], "atom_selection (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.atom_selection", false]], "atom_selection (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.atom_selection", false]], "atom_selection (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.atom_selection", false]], "atom_selection (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.atom_selection", false]], "atom_selection (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.atom_selection", false]], "atom_selection (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.atom_selection", false]], "atom_selection (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.atom_selection", false]], "atom_selection (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.atom_selection", false]], "atom_selection (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.atom_selection", false]], "atom_selection (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.atom_selection", false]], "atom_selection (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.atom_selection", false]], "atom_selection (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.atom_selection", false]], "atom_selection (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.atom_selection", false]], "atom_selection (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.atom_selection", false]], "atom_selection() (in module mmtbx.utils)": [[325, "mmtbx.utils.atom_selection", false]], "atom_selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.atom_selection", false]], "atom_selection_cache() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.atom_selection_cache", false]], "atom_selection_string() (mmtbx.validation.clashscore.nqh_flip method)": [[326, "mmtbx.validation.clashscore.nqh_flip.atom_selection_string", false]], "atom_selection_string() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.atom_selection_string", false]], "atom_type_flags (class in mmtbx.ions)": [[293, "mmtbx.ions.atom_type_flags", false]], "atom_types (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id1", false], [299, "mmtbx.ions.svm.svm_prediction.atom_types", false]], "atom_weight() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.atom_weight", false]], "atom_with_labels (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.atom_with_labels", false]], "atomdescriptor (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.AtomDescriptor", false]], "atomic_number() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.atomic_number", false]], "atomic_number_list() (cctbx.eltbx.attenuation_coefficient.nist_elements method)": [[47, "cctbx.eltbx.attenuation_coefficient.nist_elements.atomic_number_list", false]], "atomic_weights() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.atomic_weights", false]], "atomname_token (class in iotbx.shelx.tokens)": [[271, "iotbx.shelx.tokens.atomname_token", false]], "atomproperties (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.AtomProperties", false]], "atoms (class in mmtbx.validation)": [[326, "mmtbx.validation.atoms", false]], "atoms (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.atoms", false]], "atoms (mmtbx.geometry.topology.molecule property)": [[289, "mmtbx.geometry.topology.Molecule.atoms", false]], "atoms (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.atoms", false]], "atoms() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.atoms", false]], "atoms() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.atoms", false]], "atoms() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.atoms", false]], "atoms() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.atoms", false]], "atoms() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.atoms", false]], "atoms() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.atoms", false]], "atoms() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.atoms", false]], "atoms() (iotbx.pdb.hierarchy.residue method)": [[268, "iotbx.pdb.hierarchy.residue.atoms", false]], "atoms() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.atoms", false]], "atoms() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.atoms", false]], "atoms() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.atoms", false]], "atoms() (mmtbx.disorder.analyze_model.atom_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.atom_group_proxy.atoms", false]], "atoms() (mmtbx.geometry.clash.model method)": [[289, "mmtbx.geometry.clash.Model.atoms", false]], "atoms_below_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_below_fofc_map_level", false]], "atoms_below_two_fofc_map_level() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_below_two_fofc_map_level", false]], "atoms_info (mmtbx.validation.atoms attribute)": [[326, "mmtbx.validation.atoms.atoms_info", false]], "atoms_info (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.atoms_info", false]], "atoms_info (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.atoms_info", false]], "atoms_info (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.atoms_info", false]], "atoms_info (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.atoms_info", false]], "atoms_info (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.atoms_info", false]], "atoms_info (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.atoms_info", false]], "atoms_info (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.atoms_info", false]], "atoms_info (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.atoms_info", false]], "atoms_info (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.atoms_info", false]], "atoms_outside_density() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.atoms_outside_density", false]], "atoms_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.atoms_proxy", false]], "atoms_reset_serial() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.atoms_reset_serial", false]], "atoms_size() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.atoms_size", false]], "atoms_size() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.atoms_size", false]], "atoms_size() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.atoms_size", false]], "atoms_size() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.atoms_size", false]], "atoms_size() (iotbx.pdb.hierarchy.residue method)": [[268, "iotbx.pdb.hierarchy.residue.atoms_size", false]], "atoms_size() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.atoms_size", false]], "atoms_size() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.atoms_size", false]], "atoms_to_observations_ratio() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.atoms_to_observations_ratio", false]], "atoms_with_i_seq_mismatch() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.atoms_with_i_seq_mismatch", false]], "atoms_with_labels() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.atoms_with_labels", false]], "atoms_with_labels() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.atoms_with_labels", false]], "atoms_with_labels() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.atoms_with_labels", false]], "atomsforangle (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.atomsForAngle", false]], "atomsmovewithangle (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.atomsMoveWithAngle", false]], "auto_anomalous() (cctbx.miller.set method)": [[148, "cctbx.miller.set.auto_anomalous", false]], "autotype (class in libtbx)": [[273, "libtbx.AutoType", false]], "average_all() (mmtbx.scaling.fa_estimation.cns_fa_driver 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(mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.b_factor_cutoff", false]], "b_factor_sharpening_by_map_kurtosis_maximization() (in module mmtbx.maps)": [[305, "mmtbx.maps.b_factor_sharpening_by_map_kurtosis_maximization", false]], "b_histogram (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_histogram", false]], "b_iso (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id7", false], [295, "mmtbx.ions.environment.ScatteringEnvironment.b_iso", false]], "b_iso (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.b_iso", false]], "b_iso (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.b_iso", false]], "b_iso (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.b_iso", false]], "b_iso (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.b_iso", false]], "b_iso (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.b_iso", false]], "b_iso (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.b_iso", false]], "b_iso (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.b_iso", false]], "b_iso (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.b_iso", false]], "b_iso (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.b_iso", false]], "b_iso() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.b_iso", false]], "b_iso_mean (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.b_iso_mean", false]], "b_iso_mean() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.b_iso_mean", false]], "b_iso_min_max_mean() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.b_iso_min_max_mean", false]], "b_iso_or_b_equiv() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.b_iso_or_b_equiv", false]], "b_max (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_max", false]], "b_mean (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_mean", false]], "b_mean_hoh (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id8", false], [295, "mmtbx.ions.environment.ScatteringEnvironment.b_mean_hoh", false]], "b_min (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.b_min", false]], "b_part() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.b_part", false]], "b_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.b_sol", false]], "b_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.b_sols", false]], "b_update() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.b_update", false]], "back() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.back", false]], "back() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.back", false]], "back() (scitbx.array_family.flex.double method)": [[331, 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"scitbx.array_family.flex.vec3_int.back", false]], "backrub_angle (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.backrub_angle", false]], "backrub_move() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.backrub_move", false]], "backrub_residue (class in mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.backrub_residue", false]], "bad_adps (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.bad_adps", false]], "bad_coord_atom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_coord_atom", false]], "bad_coord_atom (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_COORD_ATOM", false]], "bad_coord_residue (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_coord_residue", false]], "bad_coord_residue (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_COORD_RESIDUE", false]], "bad_fpp (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_FPP", false]], "bad_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_geom", false]], "bad_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_GEOMETRY", false]], "bad_halide (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_halide", false]], "bad_halide (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_HALIDE", false]], "bad_hydrogens (mmtbx.utils.detect_hydrogen_nomenclature_problem attribute)": [[325, "mmtbx.utils.detect_hydrogen_nomenclature_problem.bad_hydrogens", false]], "bad_valence (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_valence", false]], "bad_valences (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_VALENCES", false]], "bad_vectors (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.bad_vectors", false]], "bad_vectors (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.BAD_VECTORS", false]], "base() (cctbx.web.cgi_utils.server_info method)": [[213, "cctbx.web.cgi_utils.server_info.base", false]], "base_pair_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.base_pair_selection", false]], "base_pair_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.base_pair_selections", false]], "base_symbol() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.base_symbol", false]], "base_symbol_cpp() (in module 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[[343, "xfel.cxi.cspad_ana.mod_param.mod_param.beginjob", false]], "beginjob() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.beginjob", false]], "beginjob() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.beginjob", false]], "beginjob() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.beginjob", false]], "best() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.best", false]], "best_approximation() (in module cctbx.eltbx.xray_scattering)": [[76, "cctbx.eltbx.xray_scattering.best_approximation", false]], "best_bravais__() (cctbx.crystal.burzlaff_zimmermann_dewolff.latticecharacter method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter.best_bravais__", false]], "best_by_cc() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.best_by_CC", false]], "best_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.best_cell", false]], "best_partition_representatives() (cctbx.sgtbx.cosets.left_decomposition_point_groups_only method)": [[167, "cctbx.sgtbx.cosets.left_decomposition_point_groups_only.best_partition_representatives", false]], "best_superpositions_on_other() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.best_superpositions_on_other", false]], "beta_ideal (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.beta_ideal", false]], "beta_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.beta_selection", false]], "beta_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.beta_selections", false]], "bijvoet_ratios() (cctbx.miller.array method)": [[148, "cctbx.miller.array.bijvoet_ratios", false]], "bin2index() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.bin2index", false]], "bin2index_limit() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.bin2index_limit", false]], "bin_generator_equal_range() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bin_generator_equal_range", false]], "bin_generator_equal_size() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bin_generator_equal_size", false]], "binary_filter() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.binary_filter", false]], "binned_correlation() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.binned_correlation", false]], "binned_data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.binned_data", false]], "binner (class in cctbx.miller)": [[148, "cctbx.miller.binner", false]], "binner() (cctbx.miller.set method)": [[148, "cctbx.miller.set.binner", false]], "bivariate_histogram() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.bivariate_histogram", false]], "block (class in iotbx.cif.model)": [[264, "iotbx.cif.model.block", false]], "blue_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.blue_color_model", false]], "bond (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.bond", false]], "bond_angle_registry (class in mmtbx.conformation_dependent_library.bond_angle_registry)": [[283, "mmtbx.conformation_dependent_library.bond_angle_registry.bond_angle_registry", false]], "bond_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.bond_counters", false]], "bond_density (class in mmtbx.ias)": [[292, "mmtbx.ias.bond_density", false]], "bond_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations", false]], "bond_deviations_weighted() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations_weighted", false]], "bond_deviations_z() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.bond_deviations_z", false]], "bond_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.bond_list", false]], "bond_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.bond_outlier_as_kinemage", false]], "bond_rmsd (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.bond_rmsd", false]], "bond_simple_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry", false]], "bonds (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.bonds", false]], "bonds (mmtbx.geometry.topology.compound property)": [[289, "mmtbx.geometry.topology.Compound.bonds", false]], "bonds (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.bonds", false]], "bonds (mmtbx.validation.rna_validate.rna_validation attribute)": [[326, "mmtbx.validation.rna_validate.rna_validation.bonds", false]], "bookkeeping_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.bookkeeping_section", false]], "bool (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.bool", false]], "bool_element_size (scitbx.array_family.flex.smart_selection attribute)": [[331, "scitbx.array_family.flex.smart_selection.bool_element_size", false]], "bool_md5() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.bool_md5", false]], "box_all_maps_around_density_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_density_and_shift_origin", false]], "box_all_maps_around_mask_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_mask_and_shift_origin", false]], "box_all_maps_around_model_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_model_and_shift_origin", false]], "box_all_maps_around_unique_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_around_unique_and_shift_origin", false]], "box_all_maps_with_bounds_and_shift_origin() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.box_all_maps_with_bounds_and_shift_origin", false]], "box_around_selection() (mmtbx.maps.write_xplor_map_file method)": [[305, "mmtbx.maps.write_xplor_map_file.box_around_selection", false]], "box_build_refine_base (class in mmtbx.building)": [[277, "mmtbx.building.box_build_refine_base", false]], "box_iterator() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.box_iterator", false]], "box_map_coefficients() (mmtbx.utils.extract_box_around_model_and_map method)": [[325, "mmtbx.utils.extract_box_around_model_and_map.box_map_coefficients", false]], "box_map_coefficients_as_fft_map() (mmtbx.utils.extract_box_around_model_and_map method)": [[325, "mmtbx.utils.extract_box_around_model_and_map.box_map_coefficients_as_fft_map", false]], "box_max() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.box_max", false]], "box_min() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.box_min", false]], "box_refinement_manager (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager", false]], "boxes (class in cctbx.maptbx)": [[139, "cctbx.maptbx.boxes", false]], "boxes (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.boxes", false]], "boxes_by_dimension (class in cctbx.maptbx)": [[139, "cctbx.maptbx.boxes_by_dimension", false]], "bracketed_link() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.bracketed_link", false]], "bravais_lattice (class in cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.bravais_lattice", false]], "break_indices() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.break_indices", false]], "brick() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.brick", false]], "britton_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests.britton_frac", false]], "britton_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.britton_test", false]], "browse() (cctbx.examples.location_part.symmetries_with_nonzero_location_parts method)": [[98, "cctbx.examples.location_part.symmetries_with_nonzero_location_parts.browse", false]], "bs_ave (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.bs_ave", false]], "build_all_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies", false]], "build_angle_start_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_angle_start_by_tor_id", false]], "build_bfgs_memory() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.build_bfgs_memory", false]], "build_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_chain_proxies", false]], "build_conformation_dependent_angle_proxies() (in module mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.build_conformation_dependent_angle_proxies", false]], "build_crystal_structures() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.build_crystal_structures", false]], "build_den_proxies() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.build_den_proxies", false]], "build_den_restraints() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.build_den_restraints", false]], "build_dict() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.build_dict", false]], "build_dod_and_od() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_dod_and_od", false]], "build_edge_list() (in module cctbx.eltbx.distance_based_connectivity)": [[64, "cctbx.eltbx.distance_based_connectivity.build_edge_list", false]], "build_i_q_packed_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_i_q_packed_by_tor_id", false]], "build_it() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.build_it", false]], "build_miller_arrays() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.build_miller_arrays", false]], "build_miller_set() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.build_miller_set", false]], "build_name_hash() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.build_name_hash", false]], "build_name_hash() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.build_name_hash", false]], "build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.build_reticular_twin_laws", false]], "build_rotamer_tor_atom_ids_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils)": [[308, "mmtbx.monomer_library.rotamer_utils.build_rotamer_tor_atom_ids_by_tor_id", false]], "build_scatterers() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.build_scatterers", false]], "build_selections() (mmtbx.secondary_structure.proteins.find_helices_simple method)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple.build_selections", false]], "build_set() (in module cctbx.miller)": [[148, "cctbx.miller.build_set", false]], "build_simple_two_way_bond_sets() (in module cctbx.crystal.distance_based_connectivity)": [[28, "cctbx.crystal.distance_based_connectivity.build_simple_two_way_bond_sets", false]], "build_up() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method)": [[333, "scitbx.lstbx.normal_eqns.non_linear_ls_mixin.build_up", false]], "build_up() (scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls method)": [[333, "scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls.build_up", false]], "build_water_hydrogens_from_map() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_water_hydrogens_from_map", false]], "build_water_hydrogens_from_map2() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.build_water_hydrogens_from_map2", false]], "build_xray_structure_with_carbon_along_x() (in module cctbx.examples.fft_map_electron_density_around_atom)": [[88, "cctbx.examples.fft_map_electron_density_around_atom.build_xray_structure_with_carbon_along_x", false]], "bulk_solvent (class in mmtbx.masks)": [[306, "mmtbx.masks.bulk_solvent", false]], "bulk_solvent_and_scale() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.bulk_solvent_and_scale", false]], "bulk_solvent_and_scales (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales", false]], "bulk_solvent_mask() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.bulk_solvent_mask", false]], "bulk_solvent_mask() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.bulk_solvent_mask", false]], "bulk_solvent_scaling() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.bulk_solvent_scaling", false]], "by_index_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.by_index_selection", false]], "c (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.c", false]], "c_alpha (class in mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.c_alpha", false]], "c_beta_deviations (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.c_beta_deviations", false]], "c_obs (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.c_obs", false]], "c_obs (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.c_obs", false]], "ca() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.ca", false]], "cache_restraint() (iotbx.shelx.parsers.restraint_parser method)": [[271, "iotbx.shelx.parsers.restraint_parser.cache_restraint", false]], "calc_correlation() 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"cctbx.crystal.calculate_angles", false]], "calculate_base_for_coordinates() (in module mmtbx.geometry.shared_types)": [[289, "mmtbx.geometry.shared_types.calculate_base_for_coordinates", false]], "calculate_cell_content() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.calculate_cell_content", false]], "calculate_contents() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.calculate_contents", false]], "calculate_dihedrals (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_dihedrals", false]], "calculate_distances (class in cctbx.crystal)": [[23, "cctbx.crystal.calculate_distances", false]], "calculate_exp_i_two_phi_peaks() (in module cctbx.examples.phase_o_phrenia)": [[104, "cctbx.examples.phase_o_phrenia.calculate_exp_i_two_phi_peaks", false]], "calculate_ideal_and_deviation (class in mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation", false]], "calculate_mean_intensities() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.calculate_mean_intensities", false]], "calculate_rms() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.calculate_rms", false]], "calculate_shortest_diff() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.calculate_shortest_diff", false]], "calculate_shortest_diffs() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.calculate_shortest_diffs", false]], "calculate_shortest_dist() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.calculate_shortest_dist", false]], "calculate_solvent_mask() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.calculate_solvent_mask", false]], "calculate_structure_content() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.calculate_structure_content", false]], "calculate_valence() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.calculate_valence", false]], "calculate_valences() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.calculate_valences", false]], "calculated (cctbx.xray.weighting_schemes.shelx_weighting property)": [[255, "cctbx.xray.weighting_schemes.shelx_weighting.calculated", false]], "calib2sections() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.calib2sections", false]], "calib2tensor3() (in module xfel.cxi.cspad_ana.parse_calib)": [[343, "xfel.cxi.cspad_ana.parse_calib.calib2tensor3", false]], "call_back() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.call_back", false]], "callback_after_step() (cctbx.examples.unit_cell_refinement.refinery method)": [[127, 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false]], "capacity() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.capacity", false]], "capacity() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.capacity", false]], "carbonyl_oxygen_angle() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.carbonyl_oxygen_angle", false]], "cart_to_grid_units() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.cart_to_grid_units", false]], "cartesian_dynamics (class in mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics", false]], "cartesian_polygon() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.cartesian_polygon", false]], "case (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.Case", false]], "cast_map_coeff_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.cast_map_coeff_params", false]], "cb_op() (cctbx.crystal.find_best_cell.find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.find_best_cell.cb_op", false]], "cb_op() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.cb_op", false]], "cb_op_as_rational() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.cb_op_as_rational", false]], "cb_op_as_rational() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.cb_op_as_rational", false]], "cb_ops (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.cb_ops", false]], "cb_ops_in_niggli_setting() (cctbx.crystal.reindex.reindexing_operators method)": [[30, "cctbx.crystal.reindex.reindexing_operators.cb_ops_in_niggli_setting", false]], "cb_update() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.cb_update", false]], "cb_update() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.cb_update", false]], "cbcaa() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.cbcaa", false]], "cbeta (class in mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.cbeta", false]], "cbeta_dev() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.cbeta_dev", false]], "cbeta_outliers() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.cbeta_outliers", false]], "cbetadev (class in mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.cbetadev", false]], "cbetadev (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.cbetadev", false]], "cbf_file_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.cbf_file_to_basis_dict", false]], "cc (mmtbx.validation.experimental.residue_real_space property)": [[326, "mmtbx.validation.experimental.residue_real_space.cc", false]], "cc (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.cc", false]], "cc (mmtbx.validation.waters.water property)": [[326, "mmtbx.validation.waters.water.cc", false]], "cc() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.cc", false]], "cc() (xfel.metrology.quadrant.one_panel method)": [[347, "xfel.metrology.quadrant.one_panel.CC", false]], "cc() (xfel.metrology.quadrant.one_sensor method)": [[347, "xfel.metrology.quadrant.one_sensor.CC", false]], "cc_anom() (cctbx.miller.array method)": [[148, "cctbx.miller.array.cc_anom", false]], "cc_model_map() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.cc_model_map", false]], "cc_one_half() (cctbx.miller.array method)": [[148, "cctbx.miller.array.cc_one_half", false]], "cc_one_half_outer (mmtbx.scaling.xtriage.merging_statistics property)": [[318, "mmtbx.scaling.xtriage.merging_statistics.cc_one_half_outer", false]], "cc_one_half_sigma_tau() (cctbx.miller.array method)": [[148, "cctbx.miller.array.cc_one_half_sigma_tau", false]], "cc_peak() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.cc_peak", false]], "cc_to_other_map_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.cc_to_other_map_manager", false]], "ccp4_alpha_beta_gamma_fcalc_fobs (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs", false]], "ccp4_alpha_beta_gamma_fobs_fcalc (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc", false]], "ccp4_map() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.ccp4_map", false]], "ccp4_partial_charge (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, 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"module-cctbx.development.electron_density_sampling", false]], "cctbx.development.fmt_utils": [[37, "module-cctbx.development.fmt_utils", false]], "cctbx.development.make_cns_input": [[38, "module-cctbx.development.make_cns_input", false]], "cctbx.development.make_settings": [[39, "module-cctbx.development.make_settings", false]], "cctbx.development.random_structure": [[40, "module-cctbx.development.random_structure", false]], "cctbx.development.run_shelx": [[41, "module-cctbx.development.run_shelx", false]], "cctbx.development.run_shelx76": [[42, "module-cctbx.development.run_shelx76", false]], "cctbx.development.space_group_option_parser": [[43, "module-cctbx.development.space_group_option_parser", false]], "cctbx.development.structure_factor_utils": [[44, "module-cctbx.development.structure_factor_utils", false]], "cctbx.dmtbx": [[45, "module-cctbx.dmtbx", false]], "cctbx.eltbx": [[46, "module-cctbx.eltbx", false]], "cctbx.eltbx.attenuation_coefficient": [[47, "module-cctbx.eltbx.attenuation_coefficient", false]], "cctbx.eltbx.chemical_elements": [[48, "module-cctbx.eltbx.chemical_elements", false]], "cctbx.eltbx.covalent_radii": [[49, "module-cctbx.eltbx.covalent_radii", false]], "cctbx.eltbx.development": [[50, "module-cctbx.eltbx.development", false]], "cctbx.eltbx.development.combine_fits": [[51, "module-cctbx.eltbx.development.combine_fits", false]], "cctbx.eltbx.development.create_n_gaussian_raw_cpp": [[52, "module-cctbx.eltbx.development.create_n_gaussian_raw_cpp", false]], "cctbx.eltbx.development.e_scattering_plots": [[53, "module-cctbx.eltbx.development.e_scattering_plots", false]], "cctbx.eltbx.development.format_gaussian_fits": [[54, "module-cctbx.eltbx.development.format_gaussian_fits", false]], "cctbx.eltbx.development.hydrogen_plots": [[55, "module-cctbx.eltbx.development.hydrogen_plots", false]], "cctbx.eltbx.development.itvc_approx": [[56, "module-cctbx.eltbx.development.itvc_approx", false]], "cctbx.eltbx.development.itvc_cross_validation": [[57, "module-cctbx.eltbx.development.itvc_cross_validation", false]], "cctbx.eltbx.development.itvc_fits": [[58, "module-cctbx.eltbx.development.itvc_fits", false]], "cctbx.eltbx.development.itvc_section61_io": [[60, "module-cctbx.eltbx.development.itvc_section61_io", false]], "cctbx.eltbx.development.kissel_fits": [[61, "module-cctbx.eltbx.development.kissel_fits", false]], "cctbx.eltbx.development.kissel_io": [[62, "module-cctbx.eltbx.development.kissel_io", false]], "cctbx.eltbx.development.rez_rez_grant": [[63, "module-cctbx.eltbx.development.rez_rez_grant", false]], "cctbx.eltbx.distance_based_connectivity": [[64, "module-cctbx.eltbx.distance_based_connectivity", false]], "cctbx.eltbx.e_scattering": [[65, "module-cctbx.eltbx.e_scattering", false]], "cctbx.eltbx.formula": [[66, "module-cctbx.eltbx.formula", false]], "cctbx.eltbx.fp_fdp": [[67, "module-cctbx.eltbx.fp_fdp", false]], "cctbx.eltbx.gaussian_fit": [[68, "module-cctbx.eltbx.gaussian_fit", false]], "cctbx.eltbx.henke": [[69, "module-cctbx.eltbx.henke", false]], "cctbx.eltbx.icsd_radii": [[70, "module-cctbx.eltbx.icsd_radii", false]], "cctbx.eltbx.neutron": [[71, "module-cctbx.eltbx.neutron", false]], "cctbx.eltbx.sasaki": [[72, "module-cctbx.eltbx.sasaki", false]], "cctbx.eltbx.tiny_pse": [[73, "module-cctbx.eltbx.tiny_pse", false]], "cctbx.eltbx.van_der_waals_radii": [[74, "module-cctbx.eltbx.van_der_waals_radii", false]], "cctbx.eltbx.wavelengths": [[75, "module-cctbx.eltbx.wavelengths", false]], "cctbx.eltbx.xray_scattering": [[76, "module-cctbx.eltbx.xray_scattering", false]], "cctbx.euclidean_model_matching": [[77, "module-cctbx.euclidean_model_matching", false]], "cctbx.examples": [[78, "module-cctbx.examples", false]], "cctbx.examples.adp_symmetry_constraints": [[79, "module-cctbx.examples.adp_symmetry_constraints", false]], "cctbx.examples.all_axes": [[80, "module-cctbx.examples.all_axes", false]], "cctbx.examples.analyze_adp": [[81, "module-cctbx.examples.analyze_adp", false]], "cctbx.examples.change_hand_p31": [[82, "module-cctbx.examples.change_hand_p31", false]], "cctbx.examples.convert_ccp4_symop_lib": [[83, "module-cctbx.examples.convert_ccp4_symop_lib", false]], "cctbx.examples.cr2o3_consistency_checks": [[84, "module-cctbx.examples.cr2o3_consistency_checks", false]], "cctbx.examples.cr2o3_primitive_cell": [[85, "module-cctbx.examples.cr2o3_primitive_cell", false]], "cctbx.examples.exp_i_alpha_derivatives": [[86, "module-cctbx.examples.exp_i_alpha_derivatives", false]], "cctbx.examples.f_model_example": [[87, "module-cctbx.examples.f_model_example", false]], "cctbx.examples.fft_map_electron_density_around_atom": [[88, "module-cctbx.examples.fft_map_electron_density_around_atom", false]], "cctbx.examples.find_distances_using_cpp_objects": [[89, "module-cctbx.examples.find_distances_using_cpp_objects", false]], "cctbx.examples.find_sys_abs_equiv_space_groups": [[90, "module-cctbx.examples.find_sys_abs_equiv_space_groups", false]], "cctbx.examples.g_exp_i_alpha_derivatives": [[91, "module-cctbx.examples.g_exp_i_alpha_derivatives", false]], "cctbx.examples.g_exp_i_partial_derivatives": [[92, "module-cctbx.examples.g_exp_i_partial_derivatives", false]], "cctbx.examples.getting_started": [[93, "module-cctbx.examples.getting_started", false]], "cctbx.examples.hirshfeld_test": [[94, "module-cctbx.examples.hirshfeld_test", false]], "cctbx.examples.le_page_1982_vs_lebedev_2005": [[95, "module-cctbx.examples.le_page_1982_vs_lebedev_2005", false]], "cctbx.examples.lebedev_2005_perturbation": [[96, "module-cctbx.examples.lebedev_2005_perturbation", false]], "cctbx.examples.list_non_principal_continuous_shifts": [[97, "module-cctbx.examples.list_non_principal_continuous_shifts", false]], "cctbx.examples.location_part": [[98, "module-cctbx.examples.location_part", false]], "cctbx.examples.map_skewness": [[99, "module-cctbx.examples.map_skewness", false]], "cctbx.examples.maximum_subgroups": [[100, "module-cctbx.examples.maximum_subgroups", false]], "cctbx.examples.miller_common_sets": [[101, "module-cctbx.examples.miller_common_sets", false]], "cctbx.examples.miller_transform": [[102, "module-cctbx.examples.miller_transform", false]], "cctbx.examples.neutron_structure_factors": [[103, "module-cctbx.examples.neutron_structure_factors", false]], "cctbx.examples.phase_o_phrenia": [[104, "module-cctbx.examples.phase_o_phrenia", false]], "cctbx.examples.quartz_structure": [[105, "module-cctbx.examples.quartz_structure", false]], "cctbx.examples.random_f_calc": [[106, "module-cctbx.examples.random_f_calc", false]], "cctbx.examples.random_puckers": [[107, "module-cctbx.examples.random_puckers", false]], "cctbx.examples.reduced_cell_two_folds": [[108, "module-cctbx.examples.reduced_cell_two_folds", false]], "cctbx.examples.site_symmetry_constraints": [[109, "module-cctbx.examples.site_symmetry_constraints", false]], "cctbx.examples.site_symmetry_table": [[110, "module-cctbx.examples.site_symmetry_table", false]], "cctbx.examples.space_group_matrices": [[111, "module-cctbx.examples.space_group_matrices", false]], "cctbx.examples.space_subgroups": [[112, "module-cctbx.examples.space_subgroups", false]], "cctbx.examples.steve_collins": [[113, "module-cctbx.examples.steve_collins", false]], "cctbx.examples.structure_factor_calculus": [[114, "module-cctbx.examples.structure_factor_calculus", false]], "cctbx.examples.structure_factor_calculus.site_derivatives": [[115, "module-cctbx.examples.structure_factor_calculus.site_derivatives", false]], "cctbx.examples.structure_factor_calculus.sites_derivatives": [[116, "module-cctbx.examples.structure_factor_calculus.sites_derivatives", false]], "cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives": [[117, "module-cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives", false]], "cctbx.examples.structure_factor_calculus.u_star_derivatives": [[118, "module-cctbx.examples.structure_factor_calculus.u_star_derivatives", false]], "cctbx.examples.structure_factor_derivatives": [[119, "module-cctbx.examples.structure_factor_derivatives", false]], "cctbx.examples.structure_factor_derivatives_2": [[120, "module-cctbx.examples.structure_factor_derivatives_2", false]], "cctbx.examples.structure_factor_derivatives_3": [[121, "module-cctbx.examples.structure_factor_derivatives_3", false]], "cctbx.examples.structure_factor_derivatives_4": [[122, "module-cctbx.examples.structure_factor_derivatives_4", false]], "cctbx.examples.sub_group_graph": [[123, "module-cctbx.examples.sub_group_graph", false]], "cctbx.examples.symops_530": [[124, "module-cctbx.examples.symops_530", false]], "cctbx.examples.trigonal_r_vs_tetragonal_i": [[125, "module-cctbx.examples.trigonal_r_vs_tetragonal_i", false]], "cctbx.examples.unit_cell_minimizers": [[126, "module-cctbx.examples.unit_cell_minimizers", false]], "cctbx.examples.unit_cell_refinement": [[127, "module-cctbx.examples.unit_cell_refinement", false]], "cctbx.french_wilson": [[129, "module-cctbx.french_wilson", false]], "cctbx.geometry": [[130, "module-cctbx.geometry", false]], "cctbx.geometry_restraints": [[131, "module-cctbx.geometry_restraints", false]], "cctbx.geometry_restraints.energies": [[132, "module-cctbx.geometry_restraints.energies", false]], "cctbx.geometry_restraints.flags": [[133, "module-cctbx.geometry_restraints.flags", false]], "cctbx.geometry_restraints.lbfgs": [[134, "module-cctbx.geometry_restraints.lbfgs", false]], "cctbx.geometry_restraints.manager": [[135, "module-cctbx.geometry_restraints.manager", false]], "cctbx.macro_mol": [[137, "module-cctbx.macro_mol", false]], "cctbx.macro_mol.rotation_parameters": [[138, "module-cctbx.macro_mol.rotation_parameters", false]], "cctbx.maptbx": [[139, "module-cctbx.maptbx", false]], "cctbx.maptbx.mem": [[140, "module-cctbx.maptbx.mem", false]], "cctbx.maptbx.real_space_refinement_simple": [[142, "module-cctbx.maptbx.real_space_refinement_simple", false]], "cctbx.masks": [[144, "module-cctbx.masks", false]], "cctbx.math_module": [[145, "module-cctbx.math_module", false]], "cctbx.merging": [[146, "module-cctbx.merging", false]], "cctbx.merging.brehm_diederichs": [[147, "module-cctbx.merging.brehm_diederichs", false]], "cctbx.miller": [[148, "module-cctbx.miller", false]], "cctbx.miller.display": [[149, "module-cctbx.miller.display", false]], "cctbx.miller.reindexing": [[150, "module-cctbx.miller.reindexing", false]], "cctbx.multipolar": [[151, "module-cctbx.multipolar", false]], "cctbx.neutron": [[152, "module-cctbx.neutron", false]], "cctbx.omz": [[153, "module-cctbx.omz", false]], "cctbx.omz.bfgs": [[154, "module-cctbx.omz.bfgs", false]], "cctbx.omz.cif_refine": [[155, "module-cctbx.omz.cif_refine", false]], "cctbx.omz.cod_refine": [[156, "module-cctbx.omz.cod_refine", false]], "cctbx.omz.cod_select_and_pickle": [[157, "module-cctbx.omz.cod_select_and_pickle", false]], "cctbx.omz.dev": [[158, "module-cctbx.omz.dev", false]], "cctbx.omz.eval_iso_vs_refined": [[159, "module-cctbx.omz.eval_iso_vs_refined", false]], "cctbx.omz.pdb_dev": [[160, "module-cctbx.omz.pdb_dev", false]], "cctbx.omz.tardy_adaptor": [[161, "module-cctbx.omz.tardy_adaptor", false]], "cctbx.r_free_utils": [[162, "module-cctbx.r_free_utils", false]], "cctbx.run_examples": [[163, "module-cctbx.run_examples", false]], "cctbx.run_tests": [[164, "module-cctbx.run_tests", false]], "cctbx.sgtbx": [[165, "module-cctbx.sgtbx", false]], "cctbx.sgtbx.bravais_types": [[166, "module-cctbx.sgtbx.bravais_types", false]], "cctbx.sgtbx.cosets": [[167, "module-cctbx.sgtbx.cosets", false]], "cctbx.sgtbx.direct_space_asu": [[168, "module-cctbx.sgtbx.direct_space_asu", false]], "cctbx.sgtbx.direct_space_asu.check_redundancies": [[169, "module-cctbx.sgtbx.direct_space_asu.check_redundancies", false]], 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false]], "change_symmetry() (cctbx.miller.array method)": [[148, "cctbx.miller.array.change_symmetry", false]], "change_symmetry() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.change_symmetry", false]], "character_tests() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.character_tests", false]], "charge (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.charge", false]], "charge (mmtbx.ions.environment.atom_contact attribute)": [[295, "id16", false], [295, "mmtbx.ions.environment.atom_contact.charge", false]], "charge (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.charge", false]], "charge_as_int() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.charge_as_int", false]], "charge_as_int() (mmtbx.ions.metal_parameters method)": [[293, 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"mmtbx.validation.clashscore.check_and_add_hydrogen", false]], "check_and_report_reduce_failure() (in module mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.check_and_report_reduce_failure", false]], "check_and_set_crystal_symmetry() (in module mmtbx.utils)": [[325, "mmtbx.utils.check_and_set_crystal_symmetry", false]], "check_anisou() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.check_anisou", false]], "check_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_asu", false]], "check_at_bond_vector() (in module mmtbx.ias)": [[292, "mmtbx.ias.check_at_bond_vector", false]], "check_comp() (in module mmtbx.monomer_library.cif_triage)": [[308, "mmtbx.monomer_library.cif_triage.check_comp", false]], "check_compatibility_with_sampling_grid() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_compatibility_with_sampling_grid", false]], "check_condition() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check_condition", false]], "check_conditions() (mmtbx.scaling.absences.analyze_absences method)": [[318, "mmtbx.scaling.absences.analyze_absences.check_conditions", false]], "check_correlation() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_correlation", false]], "check_den_pair_consistency() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.check_den_pair_consistency", false]], "check_file_type() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.check_file_type", false]], "check_files() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.check_files", false]], "check_first_last() (cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table method)": [[193, "cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table.check_first_last", false]], "check_for_acid() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_for_acid", false]], "check_for_pathological_input_data() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.check_for_pathological_input_data", false]], "check_for_peptide_links() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.check_for_peptide_links", false]], "check_fpp_ratio() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.check_fpp_ratio", false]], "check_image() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.check_image", false]], "check_ion_environment() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.check_ion_environment", false]], "check_key_is_unique() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.check_key_is_unique", false]], "check_mask() (mmtbx.scaling.absences.absences method)": [[318, "mmtbx.scaling.absences.absences.check_mask", false]], "check_model_and_set_to_match_map_if_necessary() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.check_model_and_set_to_match_map_if_necessary", false]], "check_multiplicities() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.check_multiplicities", false]], "check_phase_restrictions() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_phase_restrictions", false]], "check_pixel_histogram_fit() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.check_pixel_histogram_fit", false]], "check_r1() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.check_r1", false]], "check_regression() (in module cctbx.development.structure_factor_utils)": [[44, "cctbx.development.structure_factor_utils.check_regression", false]], "check_sites_match() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.check_sites_match", false]], "check_size() (cctbx.xray.structure_factors.gradients_base.gradients_base method)": [[247, "cctbx.xray.structure_factors.gradients_base.gradients_base.check_size", false]], "check_stop_file() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.check_stop_file", false]], "check_strong_wolfe() (cctbx.omz.dev.xfgc_info method)": [[158, "cctbx.omz.dev.xfgc_info.check_strong_wolfe", false]], "check_supported() (in module mmtbx.ions)": [[293, "mmtbx.ions.check_supported", false]], "check_table_name() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.check_table_name", false]], "check_u_cart() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.check_u_cart", false]], "check_valence() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_valence", false]], "check_valence_and_acid() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.check_valence_and_acid", false]], "chem_comp (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp", false]], "chem_comp (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.chem_comp", false]], "chem_comp_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_angle", false]], "chem_comp_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_atom", false]], "chem_comp_atom (class in mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom", false]], "chem_comp_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_bond", false]], "chem_comp_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_chir", false]], "chem_comp_deriv (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_deriv", false]], "chem_comp_plane_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_plane_atom", false]], "chem_comp_rotamer_info (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_rotamer_info", false]], "chem_comp_synonym (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_synonym", false]], "chem_comp_synonym_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_synonym_atom", false]], "chem_comp_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tor", false]], "chem_comp_tree (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_comp_tree", false]], "chem_env (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.chem_env", false]], "chem_link (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link", false]], "chem_link_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_angle", false]], "chem_link_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_bond", false]], "chem_link_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_chir", false]], "chem_link_plane (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_plane", false]], "chem_link_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_link_tor", false]], "chem_mod (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod", false]], "chem_mod_angle (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle", false]], "chem_mod_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_atom", false]], "chem_mod_bond (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond", false]], "chem_mod_chir (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir", false]], "chem_mod_ids (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chem_mod_ids", false]], "chem_mod_plane_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom", false]], "chem_mod_tor (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor", false]], "chem_mod_tree (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree", false]], "chem_plane (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.chem_plane", false]], "chemical_id_search() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.chemical_id_search", false]], "chemicalenvironment (class in mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.ChemicalEnvironment", false]], "chemistry (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id1", false], [295, "mmtbx.ions.environment.ChemicalEnvironment.chemistry", false]], "chemlex() (in module cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.chemlex", false]], "chi_angles (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.chi_angles", false]], "chi_angles (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.chi_angles", false]], "chi_angles() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.chi_angles", false]], "chir_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.chir_list", false]], "chiral_outlier_as_kinemage() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.chiral_outlier_as_kinemage", false]], "chiralities (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.chiralities", false]], "chiralities (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.chiralities", false]], "chirality (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.chirality", false]], "chirality_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.chirality_counters", false]], "chirality_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.chirality_deviations", false]], "chirality_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.chirality_proxy_registry", false]], "chisperaa (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.chisPerAA", false]], "choose_best_set() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.choose_best_set", false]], "choose_h_for_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.choose_h_for_water", false]], "chunk_selections() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.chunk_selections", false]], "cif (class in iotbx.cif.model)": [[264, "iotbx.cif.model.cif", false]], "cif_file_names (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.cif_file_names", false]], "cif_input (class in iotbx.pdb.mmcif)": [[268, "iotbx.pdb.mmcif.cif_input", false]], "cif_keywords() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.cif_keywords", false]], "cif_object (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.cif_object", false]], "cif_objects (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.cif_objects", false]], "cif_output_holder (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.cif_output_holder", false]], "cif_symmetry_code() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.cif_symmetry_code", false]], "circ_len() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_len", false]], "circ_mean() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_mean", false]], "circ_stddev() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.circ_stddev", false]], "clampinclusive() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.clampInclusive", false]], "clash (class in mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.clash", false]], "clash_dict (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clash_dict", false]], "clash_dict_b_cutoff (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clash_dict_b_cutoff", false]], "clash_guard() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.clash_guard", false]], "clashcalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCalculation", false]], "clashcollection (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCollection", false]], "clashcountcalculation (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashCountCalculation", false]], "clashes (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.clashes", false]], "clashing_with() (mmtbx.geometry.clash.asucontent method)": [[289, "mmtbx.geometry.clash.ASUContent.clashing_with", false]], "clashingpair (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashingPair", false]], "clashpoint (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ClashPoint", false]], "clashscore (class in mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.clashscore", false]], "clashscore (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clashscore", false]], "clashscore (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.clashscore", false]], "clashscore() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.clashscore", false]], "clashscore_b_cutoff (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.clashscore_b_cutoff", false]], "class_ (iotbx.shelx.tokens.residue_token attribute)": [[271, "iotbx.shelx.tokens.residue_token.class_", false]], "classic_lbfgs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.classic_lbfgs", false]], "classification (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.classification", false]], "classification (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.classification", false]], "classification (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.classification", false]], "clean_up() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.clean_up", false]], "clean_up_ions() (in module mmtbx.ions.build)": [[294, "mmtbx.ions.build.clean_up_ions", false]], "clear() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.clear", false]], "clear() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.clear", false]], "clear() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.clear", false]], "clear() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.clear", false]], "clear() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.clear", false]], "clear() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.clear", false]], "clear() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.clear", false]], "clear() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.clear", false]], "clear() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.clear", false]], "clear() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.clear", false]], "clear() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.clear", false]], "clear() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.clear", false]], "clear() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.clear", false]], "clear_binner() (cctbx.miller.set method)": [[148, "cctbx.miller.set.clear_binner", false]], "clear_label_asym_id_lookups() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.clear_label_asym_id_lookups", false]], "clear_labels() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.clear_labels", false]], "clear_up_cosets() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.clear_up_cosets", false]], "close_contact (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.close_contact", false]], "close_contact (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.CLOSE_CONTACT", false]], "closest_distances() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.closest_distances", false]], "closest_rational() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.closest_rational", false]], "closest_to_mean() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.closest_to_mean", false]], "cluster (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.cluster", false]], "cluster (class in xfel.clustering.cluster)": [[340, "xfel.clustering.cluster.Cluster", false]], "cluster_erosion() (in module cctbx.crystal)": [[23, "cctbx.crystal.cluster_erosion", false]], "cluster_height_fraction() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.cluster_height_fraction", false]], "cluster_height_fraction() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.cluster_height_fraction", false]], "cluster_site_info (class in cctbx.maptbx)": [[139, "cctbx.maptbx.cluster_site_info", false]], 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(mmtbx.twinning.probabalistic_detwinning.detwin method)": [[324, "mmtbx.twinning.probabalistic_detwinning.detwin.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (xfel.metrology.flatfile.optimise_rectangle method)": [[347, "xfel.metrology.flatfile.optimise_rectangle.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (xfel.metrology.flatfile.optimise_rectangle_2 method)": [[347, "xfel.metrology.flatfile.optimise_rectangle_2.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (xfel.metrology.flatfile.optimise_rectangle_3 method)": [[347, "xfel.metrology.flatfile.optimise_rectangle_3.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.compute_functional_and_gradients", false]], "compute_gradient() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_gradient", false]], "compute_gradient_fd() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method)": [[318, "mmtbx.scaling.pair_analyses.f_double_prime_ratio.compute_gradient_fd", false]], "compute_maha_l() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.compute_maha_l", false]], "compute_map() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.compute_map", false]], "compute_map() (mmtbx.refinement.real_space.structure_monitor method)": 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method)": [[318, "mmtbx.scaling.twin_analyses.wilson_moments.compute_ratios", false]], "compute_refined_matches() (in module cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.compute_refined_matches", false]], "compute_step() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step", false]], "compute_step_just_grads() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step_just_grads", false]], "compute_step_using_curvs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.compute_step_using_curvs", false]], "compute_target() (cctbx.geometry_restraints.lbfgs.lbfgs method)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs.compute_target", false]], "compute_target() (cctbx.xray.minimization.lbfgs method)": [[234, "cctbx.xray.minimization.lbfgs.compute_target", false]], "compute_target() (mmtbx.refinement.minimization.lbfgs method)": [[313, "mmtbx.refinement.minimization.lbfgs.compute_target", false]], "compute_target() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.compute_target", false]], "compute_target() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.compute_target", false]], "compute_target() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.compute_target", false]], "compute_transform_grad() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.compute_transform_grad", false]], "compute_xplor_maps() (in module mmtbx.maps)": [[305, "mmtbx.maps.compute_xplor_maps", false]], "concatenate() (cctbx.miller.array method)": [[148, "cctbx.miller.array.concatenate", false]], "concatenate() (cctbx.miller.set method)": [[148, "cctbx.miller.set.concatenate", false]], "concatenate() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.concatenate", false]], "concatenate() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.concatenate", false]], "concatenate() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.concatenate", false]], "concatenate() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.concatenate", false]], "concatenate() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.concatenate", false]], "concatenate() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.concatenate", false]], "concatenate() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.concatenate", false]], "concatenate() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.concatenate", false]], "concatenate() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.concatenate", false]], "concatenate() (scitbx.array_family.flex.sym_mat3_double method)": [[331, 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"mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.conf_altloc", false]], "confid() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.confid", false]], "conformation_dependent_restraints (class in mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints", false]], "conformation_scorer (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer", false]], "conformer (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.conformer", false]], "conformer_i_seq (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.conformer_i_seq", false]], "conformers() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.conformers", false]], "conformers() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.conformers", false]], "conjugate() (cctbx.miller.array method)": [[148, "cctbx.miller.array.conjugate", false]], "connected_segment_from() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.connected_segment_from", false]], "connected_segments() (mmtbx.geometry.topology.compound method)": [[289, "mmtbx.geometry.topology.Compound.connected_segments", false]], "connectivity_annotation_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.connectivity_annotation_section", false]], "connectivity_annotation_section() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.connectivity_annotation_section", false]], "connectivity_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.connectivity_section", false]], "connectivity_section() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.connectivity_section", false]], "consensus_model() 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"cctbx.sgtbx.special_op_simplified_term.constant", false]], "constraints (iotbx.shelx.parsers.afix_parser attribute)": [[271, "iotbx.shelx.parsers.afix_parser.constraints", false]], "construct_complete_residues() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.construct_complete_residues", false]], "construct_complete_sidechain() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.construct_complete_sidechain", false]], "construct_fourth() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.construct_fourth", false]], "construct_geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.construct_geometry_restraints_manager", false]], "construct_hierarchy() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.construct_hierarchy", false]], "construct_hierarchy() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.construct_hierarchy", false]], "construct_hierarchy_biomt_expanded() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.construct_hierarchy_BIOMT_expanded", false]], "construct_hierarchy_mtrix_expanded() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.construct_hierarchy_MTRIX_expanded", false]], "construct_miller_set() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.construct_miller_set", false]], "construct_nice_cb_op() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.construct_nice_cb_op", false]], "construct_non_crystallographic_conserving_bonds_and_angles() (in module cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.construct_non_crystallographic_conserving_bonds_and_angles", false]], "construct_rational_point_group() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, 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"contiguous_ss_selections() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.contiguous_ss_selections", false]], "contour_plot_deprecated_does_not_apply_subpixel_metrology() (xfel.mono_simulation.mono_treatment.refinement method)": [[349, "xfel.mono_simulation.mono_treatment.refinement.contour_plot_DEPRECATED_DOES_NOT_APPLY_SUBPIXEL_METROLOGY", false]], "convergence_as_shift_over_esd (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit attribute)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit.convergence_as_shift_over_esd", false]], "conversion_info() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.conversion_info", false]], "convert() (mmtbx.monomer_library.pdb_interpretation.conformer_i_seq method)": [[308, "mmtbx.monomer_library.pdb_interpretation.conformer_i_seq.convert", false]], "convert_2x2() (in module xfel.command_line.convert_gain_map)": [[341, 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"mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_kin2Dcont", false]], "convert_dict_to_scilab() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_scilab", false]], "convert_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.convert_histogram_data", false]], "convert_lib_atom() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_atom", false]], "convert_lib_synonym() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_synonym", false]], "convert_lib_vdw() (mmtbx.monomer_library.server.ener_lib method)": [[308, "mmtbx.monomer_library.server.ener_lib.convert_lib_vdw", false]], "convert_link_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_link_list", false]], "convert_link_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_link_list", false]], "convert_list_block() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_list_block", false]], "convert_met_to_semet() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.convert_met_to_semet", false]], "convert_mod_list() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.convert_mod_list", false]], "convert_mod_list() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.convert_mod_list", false]], "convert_multi_word_text_to_forward_compatible() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.convert_multi_word_text_to_forward_compatible", false]], "convert_semet_to_met() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.convert_semet_to_met", false]], "convert_tlso_group_info_to_lists() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.convert_tlso_group_info_to_lists", false]], "convert_to_anisotropic() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.convert_to_anisotropic", false]], "convert_to_histogram() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.convert_to_histogram", false]], "convert_to_isotropic() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.convert_to_isotropic", false]], "convert_to_non_anomalous() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.convert_to_non_anomalous", false]], "convert_to_non_anomalous_if_ratio_pairs_lone_less_than() (cctbx.miller.array method)": [[148, "cctbx.miller.array.convert_to_non_anomalous_if_ratio_pairs_lone_less_than", false]], "converter_base (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.converter_base", false]], "coord_geom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.coord_geom", false]], "coordinate_adaptor() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.coordinate_adaptor", false]], "coordinate_degrees_of_freedom_counts() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.coordinate_degrees_of_freedom_counts", false]], "coordinate_of() (mmtbx.geometry.indexing.structure_indexer static method)": [[289, "mmtbx.geometry.indexing.structure_indexer.coordinate_of", false]], "coordinate_offset() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.coordinate_offset", false]], "coordinate_shifts (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts", false]], "coordinates() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.coordinates", false]], "coordinates_from_form() (in module cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.coordinates_from_form", false]], "coording_geometry (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.COORDING_GEOMETRY", false]], "coot_todo() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.coot_todo", false]], "coot_todo() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.coot_todo", false]], "copy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.copy", false]], "copy() (cctbx.miller.set method)": [[148, "cctbx.miller.set.copy", false]], "copy() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.copy", false]], "copy() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.copy", false]], "copy() (libtbx.group_args method)": [[273, "libtbx.group_args.copy", false]], "copy_cbf_header() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.copy_cbf_header", false]], "copy_rot_trans() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.copy_rot_trans", false]], "copy_selected() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.copy_selected", false]], "copy_selected() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.copy_selected", false]], "copy_to_byte_str() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.copy_to_byte_str", false]], "copy_to_byte_str() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.copy_to_byte_str", false]], "copy_to_byte_str() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.copy_to_byte_str", false]], "copy_to_byte_str() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.copy_to_byte_str", false]], "copy_to_scatterers_in_place() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.copy_to_scatterers_in_place", false]], "copy_vector_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.copy_vector_list", false]], "core_parameters (class in scitbx.lbfgs)": [[332, "scitbx.lbfgs.core_parameters", false]], "corners() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.corners", false]], "corners_asic() (xfel.cxi.cspad_ana.parse_calib.section method)": [[343, "xfel.cxi.cspad_ana.parse_calib.Section.corners_asic", false]], "correct_hydrogen_geometries() (in module mmtbx.monomer_library.correct_hydrogen_geometries)": [[308, "mmtbx.monomer_library.correct_hydrogen_geometries.correct_hydrogen_geometries", false]], "correct_sequence() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.correct_sequence", false]], "correct_special_position() (in module cctbx.crystal)": [[23, "cctbx.crystal.correct_special_position", false]], "correction_vectors (class in xfel.metrology.mark0)": [[347, "xfel.metrology.mark0.correction_vectors", false]], "correlation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.correlation", false]], "correlation() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.correlation", false]], "correlation_analyses (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.correlation_analyses", false]], "cos_alpha (class in cctbx.examples.structure_factor_calculus.site_derivatives)": [[115, "cctbx.examples.structure_factor_calculus.site_derivatives.cos_alpha", false]], "cos_alpha (class in cctbx.examples.structure_factor_calculus.sites_derivatives)": [[116, "cctbx.examples.structure_factor_calculus.sites_derivatives.cos_alpha", false]], "cos_angle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.cos_angle", false]], "cos_angle() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.cos_angle", false]], "cos_sin_table() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.cos_sin_table", false]], "coset_lookup() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.coset_lookup", false]], "cosets() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.cosets", false]], "cosets_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.cosets_form", false]], "count() (cctbx.sgtbx.harker.planes_cartesian method)": [[177, "cctbx.sgtbx.harker.planes_cartesian.count", false]], "count() (mmtbx.geometry.clash.clashpoint method)": [[289, "mmtbx.geometry.clash.ClashPoint.count", false]], "count() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.count", false]], "count() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.count", false]], "count() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.count", false]], "count() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.count", false]], "count() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.count", false]], "count() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.count", false]], "count() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.count", false]], "count() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.count", false]], "count() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.count", false]], "count() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.count", false]], "count_and_fraction_in_bins() (cctbx.miller.array method)": [[148, "cctbx.miller.array.count_and_fraction_in_bins", false]], "count_atoms_per_chain() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.count_atoms_per_chain", false]], "count_coordinating_residues() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.count_coordinating_residues", false]], "count_dict_values() (mmtbx.validation.test_utils method)": [[326, "mmtbx.validation.test_utils.count_dict_values", false]], "count_non_hydrogen_atoms() (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer method)": [[328, "mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer.count_non_hydrogen_atoms", false]], "count_occupancies() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.count_occupancies", false]], "count_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.count_rotatable", false]], "counter (class in mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.counter", false]], "counterexamples() (in module cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.counterexamples", false]], "counters (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.counters", false]], "counts() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.counts", false]], "counts() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.counts", false]], "counts() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.counts", false]], "counts() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.counts", false]], "create() (mmtbx.geometry.clash.case class method)": [[289, "mmtbx.geometry.clash.Case.create", false]], "create() (mmtbx.geometry.topology.compound class method)": [[289, "mmtbx.geometry.topology.Compound.create", false]], "create_all_new_restraints() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.create_all_new_restraints", false]], "create_all_subgroups() (in module cctbx.examples.maximum_subgroups)": [[100, "cctbx.examples.maximum_subgroups.create_all_subgroups", false]], "create_and_populate_indexer() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.create_and_populate_indexer", false]], "create_den_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.create_den_manager", false]], "create_description() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.create_description", false]], "create_disulfides() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.create_disulfides", false]], "create_fine_spacing_array() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.create_fine_spacing_array", false]], "create_fmodel() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.create_fmodel", false]], "create_helix_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.create_helix_hydrogen_bond_proxies", false]], "create_link() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.create_link", false]], "create_manager() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.create_manager", false]], "create_map_from_pdb_and_mtz() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.create_map_from_pdb_and_mtz", false]], "create_map_manager_with_value_list() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.create_map_manager_with_value_list", false]], "create_mask_around_atoms() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_atoms", false]], "create_mask_around_atoms() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_atoms", false]], "create_mask_around_density() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_density", false]], "create_mask_around_density() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_density", false]], "create_mask_around_edges() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_around_edges", false]], "create_mask_around_edges() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_mask_around_edges", false]], "create_mask_with_map_data() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.create_mask_with_map_data", false]], "create_masked_copies_of_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_masked_copies_of_maps", false]], "create_model_manager() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.create_model_manager", false]], "create_omit_regions() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.create_omit_regions", false]], "create_plot_panel() (xfel.cxi.gfx.status_plot.statusframe method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.create_plot_panel", false]], "create_plot_panel() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.create_plot_panel", false]], "create_plot_panel() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.create_plot_panel", false]], "create_protein_hbond_proxies() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.create_protein_hbond_proxies", false]], "create_sheet_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.create_sheet_hydrogen_bond_proxies", false]], "create_spherical_mask() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.create_spherical_mask", false]], "create_target_functors() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.create_target_functors", false]], "createfromtext() (mmtbx.rotamer.n_dim_table.ndimtable static method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.createFromText", false]], "cross() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.cross", false]], "cross() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.cross", false]], "cross_check() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.cross_check", false]], "cross_correlation_cutoff_for_centring (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.cross_correlation_cutoff_for_centring", false]], "cross_correlation_peaks() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.cross_correlation_peaks", false]], "cross_product_as_unit_axis() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method)": [[325, "mmtbx.utils.fab_elbow_angle.fab_elbow_angle.cross_product_as_unit_axis", false]], "cross_product_matrix() (in module scitbx.matrix)": [[334, "scitbx.matrix.cross_product_matrix", false]], "crystal() (in module dxtbx.serialize.load)": [[258, "dxtbx.serialize.load.crystal", false]], "crystal_density() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.crystal_density", false]], "crystal_family_symbols (cctbx.sgtbx.bravais_types.bravais_lattice attribute)": [[166, "cctbx.sgtbx.bravais_types.bravais_lattice.crystal_family_symbols", false]], "crystal_gridding (class in cctbx.maptbx)": [[139, "cctbx.maptbx.crystal_gridding", false]], "crystal_gridding() (cctbx.miller.set method)": [[148, "cctbx.miller.set.crystal_gridding", false]], "crystal_gridding() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.crystal_gridding", false]], "crystal_gridding_tags (class in cctbx.maptbx)": [[139, "cctbx.maptbx.crystal_gridding_tags", false]], "crystal_symmetry (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.crystal_symmetry", false]], "crystal_symmetry (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.crystal_symmetry", false]], "crystal_symmetry() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.crystal_symmetry", false]], "crystal_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.crystal_symmetry", false]], "crystal_symmetry() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.crystal_symmetry", false]], "crystal_symmetry() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.crystal_symmetry", false]], "crystal_symmetry() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.crystal_symmetry", false]], "crystal_symmetry() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.crystal_symmetry", false]], "crystal_symmetry() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.crystal_symmetry", false]], "crystal_symmetry() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.crystal_symmetry", false]], "crystal_symmetry() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.crystal_symmetry", false]], "crystal_symmetry() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.crystal_symmetry", false]], "crystal_symmetry() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.crystal_symmetry", false]], "crystal_symmetry_from_cryst1() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.crystal_symmetry_from_cryst1", false]], "crystal_symmetry_from_cryst1() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.crystal_symmetry_from_cryst1", false]], "crystal_symmetry_is_compatible_with_symmetry_from_file (class in cctbx.miller)": [[148, "cctbx.miller.crystal_symmetry_is_compatible_with_symmetry_from_file", false]], "crystal_symmetry_is_compatible_with_symmetry_from_file() (cctbx.miller.array method)": [[148, "cctbx.miller.array.crystal_symmetry_is_compatible_with_symmetry_from_file", false]], "crystal_symmetry_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.crystal_symmetry_parser", false]], "crystal_symmetry_to_ncs() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.crystal_symmetry_to_ncs", false]], "crystal_system_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.crystal_system_table", false]], "crystalfactory (class in dxtbx.model.crystal)": [[257, "dxtbx.model.crystal.CrystalFactory", false]], "crystallographic_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.crystallographic_section", false]], "crystallographic_section() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.crystallographic_section", false]], "crystfel_to_cctbx_coord_system() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.crystfel_to_cctbx_coord_system", false]], "cspad2x2_bad_pixel_mask_cxi_run7() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.cspad2x2_bad_pixel_mask_cxi_run7", false]], "cspad2x2image() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPad2x2Image", false]], "cspad_unbound_pixel_mask() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.cspad_unbound_pixel_mask", false]], "cspaddetector() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPadDetector", false]], "cspadelement() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.CsPadElement", false]], "cubic_unit_cell_around_centered_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.cubic_unit_cell_around_centered_scatterers", false]], "cull_braggs() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.cull_braggs", false]], "cull_braggs() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, 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"detached_copy() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.detached_copy", false]], "detached_copy() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.detached_copy", false]], "detached_copy() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.detached_copy", false]], "detached_copy() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.detached_copy", false]], "detached_copy() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.detached_copy", false]], "detect_hydrogen_nomenclature_problem (class in mmtbx.utils)": [[325, "mmtbx.utils.detect_hydrogen_nomenclature_problem", false]], "detect_outliers() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers", false]], "detect_outliers_rms() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_rms", false]], "detect_outliers_sigma() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_sigma", false]], "detect_outliers_solve() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.detect_outliers_solve", false]], "detect_problem() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.detect_problem", false]], "detect_pseudo_translations (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations", false]], "detect_sequence_disorder() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.detect_sequence_disorder", false]], "detector_normal (xfel.metrology.mark0.correction_vectors attribute)": [[347, "xfel.metrology.mark0.correction_vectors.DETECTOR_NORMAL", false]], "detector_origin_analysis() (xfel.metrology.mark10.fit_translation4 method)": [[347, "xfel.metrology.mark10.fit_translation4.detector_origin_analysis", false]], "detectorfactory (class in dxtbx.model.detector)": [[257, "dxtbx.model.detector.DetectorFactory", false]], "detectorplot (class in xfel.cxi.gfx.wx_detectors)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot", false]], "detectorplotframe (class in xfel.cxi.gfx.wx_detectors)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame", false]], "determinant() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.determinant", false]], "determine_chemical_element_simple() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.determine_chemical_element_simple", false]], "determine_mean_i_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.determine_mean_I_mproc", false]], "determine_n_bins() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, 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"mmtbx.validation.cbetadev.cbeta.deviation", false]], "df_d_params() (cctbx.examples.structure_factor_derivatives_3.structure_factor method)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factor.df_d_params", false]], "df_d_params() (cctbx.examples.structure_factor_derivatives_4.structure_factor method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factor.df_d_params", false]], "dfc (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.DFC", false]], "diag (class in scitbx.matrix)": [[334, "scitbx.matrix.diag", false]], "dict_with_default_0 (class in libtbx)": [[273, "libtbx.dict_with_default_0", false]], "diff_map (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.diff_map", false]], "difference_vectors_cart() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.difference_vectors_cart", false]], "different_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.different_occ", false]], "dihedral (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.dihedral", false]], "dihedral (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation.dihedral", false]], "dihedral_angle() (in module scitbx.matrix)": [[334, "scitbx.matrix.dihedral_angle", false]], "dihedral_angle_def (class in cctbx.crystal)": [[23, "cctbx.crystal.dihedral_angle_def", false]], "dihedral_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.dihedral_counters", false]], "dihedral_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.dihedral_deviations", false]], "dihedral_nabb (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.dihedral_NABB", false]], "dihedral_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry", false]], "dihedrals (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.dihedrals", false]], "dihedrals (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.dihedrals", false]], "direct (cctbx.crystal_orientation.basis_type attribute)": [[31, "cctbx.crystal_orientation.basis_type.direct", false]], "direct() (in module mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.direct", false]], "direct_space_asu (class in cctbx.crystal.direct_space_asu)": [[27, "cctbx.crystal.direct_space_asu.direct_space_asu", false]], "direct_space_asu (class in cctbx.sgtbx.direct_space_asu)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu", false]], "direct_space_asu() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.direct_space_asu", false]], "direct_space_asu() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.direct_space_asu", false]], "direct_summation_at_point() (cctbx.miller.array method)": [[148, "cctbx.miller.array.direct_summation_at_point", false]], "direct_summation_cuda_platform (class in cctbx.xray.structure_factors.from_scatterers_direct_parallel)": [[242, "cctbx.xray.structure_factors.from_scatterers_direct_parallel.direct_summation_cuda_platform", false]], "direct_summation_simple (class in cctbx.xray.structure_factors.from_scatterers_direct_parallel)": [[242, "cctbx.xray.structure_factors.from_scatterers_direct_parallel.direct_summation_simple", false]], "directory_input (class in iotbx.file_reader)": [[265, "iotbx.file_reader.directory_input", false]], "disagreeable_reflections() (cctbx.miller.array method)": [[148, "cctbx.miller.array.disagreeable_reflections", false]], "discard_conflicting_pdb_element_column() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.discard_conflicting_pdb_element_column", false]], "discard_last() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.discard_last", false]], "discard_scattering_type_registry() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.discard_scattering_type_registry", false]], "discard_sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.discard_sigmas", false]], "discard_symmetry() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.discard_symmetry", false]], "discard_table() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.discard_table", false]], "discard_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.discard_tables", false]], "discard_tables() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.discard_tables", false]], "disordered_segment (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.disordered_segment", false]], "display() (xfel.cxi.display_spots.wrapper_of_callback method)": [[342, "xfel.cxi.display_spots.wrapper_of_callback.display", false]], "display_all() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.display_all", false]], "display_calib() (in module xfel.cxi.cspad_ana.display_calib)": [[343, "xfel.cxi.cspad_ana.display_calib.display_calib", false]], "display_r() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.display_r", false]], "display_rt() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.display_rt", false]], 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"mmtbx.refinement.ensemble_refinement.ensemble_utils.dist2", false]], "distance() (cctbx.sgtbx.harker.plane_cartesian method)": [[177, "cctbx.sgtbx.harker.plane_cartesian.distance", false]], "distance() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.distance", false]], "distance() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.distance", false]], "distance() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.distance", false]], "distance_based_clustering (class in cctbx.crystal)": [[23, "cctbx.crystal.distance_based_clustering", false]], "distance_based_simple_two_way_bond_sets() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.distance_based_simple_two_way_bond_sets", false]], "distance_from() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.distance_from", false]], "distance_from() (xfel.clustering.singleframe.singleframe 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"mmtbx.geometry.topology.Compound.distances_from", false]], "distances_info (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.distances_info", false]], "distances_to_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.distances_to_peaks", false]], "distl_filter() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.distl_filter", false]], "distl_hitfinder (class in xfel.cxi.cspad_ana.hitfinder_tbx)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder", false]], "distribution_as_array() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.distribution_as_array", false]], "distribution_as_xplor_file() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.distribution_as_xplor_file", false]], "divisor() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.divisor", false]], "dm_stats (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.dm_stats", false]], "do() (scitbx.lstbx.normal_eqns_solving.iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations.do", false]], "do() (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations.do", false]], "do() (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns method)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns.do", false]], "do() (scitbx.lstbx.normal_eqns_solving.naive_iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations.do", false]], "do() (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping method)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping.do", false]], "do() (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit method)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit.do", false]], "do_damping() (scitbx.lstbx.normal_eqns_solving.iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations.do_damping", false]], "do_dirty_work() (in module cctbx.development.cns_density_modification)": [[33, "cctbx.development.cns_density_modification.do_dirty_work", false]], "do_photon_counting() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.do_photon_counting", false]], "do_scale_shifts() (scitbx.lstbx.normal_eqns_solving.iterations method)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations.do_scale_shifts", false]], "do_sigma_scaling() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.do_sigma_scaling", false]], "dot() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.dot", false]], "dot() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.dot", false]], "dot() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.dot", false]], "dot() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.dot", false]], "dot3() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.dot3", false]], "dot6fdot() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6fdot", false]], "dot6fdot_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6fdot_list", false]], "dot6g_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6g_list", false]], "dot6gdot() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6gdot", false]], "dot6gdot_list() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.dot6gdot_list", false]], "double (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.double", false]], "double_cosets (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.double_cosets", false]], "double_step_filtration() (cctbx.miller.array method)": [[148, "cctbx.miller.array.double_step_filtration", false]], "double_unique() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.double_unique", false]], "dpack() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dpack", false]], "draw() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw", false]], "draw_box() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_box", false]], "draw_dashed_line() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_dashed_line", false]], "draw_filled_circle() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_filled_circle", false]], "draw_filled_circle() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_filled_circle", false]], "draw_filled_circle() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_filled_circle", false]], "draw_labels() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_labels", false]], "draw_line() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_line", false]], "draw_line() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_line", false]], "draw_line() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_line", false]], "draw_open_circle() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_open_circle", false]], "draw_open_circle() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_open_circle", false]], "draw_open_circle() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_open_circle", false]], "draw_plot() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.draw_plot", false]], "draw_plot() (mmtbx.rotamer.graphics.rotarama_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.rotarama_plot_mixin.draw_plot", false]], "draw_plot() (mmtbx.validation.graphics.rotarama_plot_mixin method)": [[326, "mmtbx.validation.graphics.rotarama_plot_mixin.draw_plot", false]], "draw_plot_to_file() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.draw_plot_to_file", false]], "draw_ramachandran_plot() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.draw_ramachandran_plot", false]], "draw_ramachandran_plot() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.draw_ramachandran_plot", false]], "draw_rotamer_plot() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.draw_rotamer_plot", false]], "draw_rotamer_plot() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.draw_rotamer_plot", false]], "draw_solid_line() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.draw_solid_line", false]], "draw_text() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.draw_text", false]], "draw_text() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.draw_text", false]], "draw_text() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.draw_text", false]], "dummy_map_manager() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.dummy_map_manager", false]], "dummy_miller_set() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.dummy_miller_set", false]], "dummy_structure() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.dummy_structure", false]], "dummy_validation (class in mmtbx.validation)": [[326, "mmtbx.validation.dummy_validation", false]], "dump_as_mtz() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.dump_as_mtz", false]], "dump_den_network() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.dump_den_network", false]], "dump_file_list() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.dump_file_list", false]], "dump_sites() (in module mmtbx.ions.svm.dump_sites)": [[300, "mmtbx.ions.svm.dump_sites.dump_sites", false]], "dump_statistics() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.dump_statistics", false]], "duplicate_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.duplicate_atoms", false]], "duplicate_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.duplicate_atoms", false]], "duplicate_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.duplicate_id", false]], "duplicate_map_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.duplicate_map_manager", false]], "dwritef() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dwritef", false]], "dwritef2() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.dwritef2", false]], "dxtbx.model.beam": [[257, "module-dxtbx.model.beam", false]], "dxtbx.model.crystal": [[257, "module-dxtbx.model.crystal", false]], "dxtbx.model.detector": [[257, "module-dxtbx.model.detector", false]], "dxtbx.model.goniometer": [[257, "module-dxtbx.model.goniometer", false]], "dxtbx.model.scan": [[257, "module-dxtbx.model.scan", false]], "dxtbx.serialize.load": [[258, "module-dxtbx.serialize.load", false]], "dxtbx.serialize.xds": [[258, "module-dxtbx.serialize.xds", false]], "dynamic_shift_limit_site (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.dynamic_shift_limit_site", false]], "dynamic_shift_limit_u_iso (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.dynamic_shift_limit_u_iso", false]], "e_pot() (cctbx.omz.tardy_adaptor.potential_object method)": [[161, "cctbx.omz.tardy_adaptor.potential_object.e_pot", false]], "e_pot() (mmtbx.refinement.tardy.potential_object method)": [[313, "mmtbx.refinement.tardy.potential_object.e_pot", false]], "each_abs() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.each_abs", false]], "each_mod_short() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.each_mod_short", false]], "each_normalize() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.each_normalize", false]], "each_normalize() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.each_normalize", false]], "easy (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.easy", false]], "edge_geometry() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.edge_geometry", false]], "edge_inclusive_flag (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment.edge_inclusive_flag", false]], "edge_list (cctbx.omz.cif_refine.extract_from_cif_files attribute)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.edge_list", false]], "edge_list (cctbx.omz.cod_select_and_pickle.cod_data attribute)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.edge_list", false]], "edge_object (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.edge_object", false]], "edge_position() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_position", false]], "edge_segment (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment", false]], "edge_with_cut_points (class in cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points", false]], "edit_blank_altloc() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.edit_blank_altloc", false]], "effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.effective_resolution", false]], "effective_resolution() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.effective_resolution", false]], "eight_point_interpolation() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.eight_point_interpolation", false]], "eight_point_interpolation_with_gradients() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.eight_point_interpolation_with_gradients", false]], "electron_density_map() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.electron_density_map", false]], "element (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.element", false]], "element (iotbx.shelx.tokens.element_token attribute)": [[271, "iotbx.shelx.tokens.element_token.element", false]], "element (mmtbx.ions.environment.atom_contact attribute)": [[295, "id17", false], [295, "mmtbx.ions.environment.atom_contact.element", false]], "element (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.element", false]], "element (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.element", false]], "element (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.element", false]], "element (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.element", false]], "element (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.element", false]], "element (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.element", false]], "element_is_hydrogen() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.element_is_hydrogen", false]], "element_is_ion() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.element_is_ion", false]], "element_is_negative_ion() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.element_is_negative_ion", false]], "element_is_positive_ion() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.element_is_positive_ion", false]], "element_of() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.element_of", false]], "element_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.element_selection", false]], "element_size() (scitbx.array_family.flex.bool static method)": [[331, "scitbx.array_family.flex.bool.element_size", false]], "element_size() (scitbx.array_family.flex.complex_double static method)": [[331, "scitbx.array_family.flex.complex_double.element_size", false]], "element_size() (scitbx.array_family.flex.double static method)": [[331, "scitbx.array_family.flex.double.element_size", false]], "element_size() (scitbx.array_family.flex.float static method)": [[331, "scitbx.array_family.flex.float.element_size", false]], "element_size() (scitbx.array_family.flex.int static method)": [[331, "scitbx.array_family.flex.int.element_size", false]], "element_size() (scitbx.array_family.flex.long static method)": [[331, "scitbx.array_family.flex.long.element_size", false]], "element_size() (scitbx.array_family.flex.size_t static method)": [[331, "scitbx.array_family.flex.size_t.element_size", false]], "element_size() (scitbx.array_family.flex.std_string static method)": [[331, "scitbx.array_family.flex.std_string.element_size", false]], "element_size() (scitbx.array_family.flex.sym_mat3_double static method)": [[331, "scitbx.array_family.flex.sym_mat3_double.element_size", false]], "element_size() (scitbx.array_family.flex.vec2_double static method)": [[331, "scitbx.array_family.flex.vec2_double.element_size", false]], "element_size() (scitbx.array_family.flex.vec3_double static method)": [[331, "scitbx.array_family.flex.vec3_double.element_size", false]], "element_size() (scitbx.array_family.flex.vec3_int static method)": [[331, "scitbx.array_family.flex.vec3_int.element_size", false]], "element_token (class in iotbx.shelx.tokens)": [[271, "iotbx.shelx.tokens.element_token", false]], "elementaccumulator (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ElementAccumulator", false]], "elements() (mmtbx.geometry.clash.model method)": [[289, "mmtbx.geometry.clash.Model.elements", false]], "eliminate_outside_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.eliminate_outside_vertices", false]], "eliminate_sys_absent() (cctbx.miller.array method)": [[148, "cctbx.miller.array.eliminate_sys_absent", false]], "eliminate_weak_pairs() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.eliminate_weak_pairs", false]], "ellipsoidal_resolutions_and_indices_by_sigma() (cctbx.miller.array method)": [[148, "cctbx.miller.array.ellipsoidal_resolutions_and_indices_by_sigma", false]], "ellipsoidal_truncation_by_sigma() (cctbx.miller.array method)": [[148, "cctbx.miller.array.ellipsoidal_truncation_by_sigma", false]], "empirical_proof() (in module cctbx.examples.g_exp_i_partial_derivatives)": [[92, "cctbx.examples.g_exp_i_partial_derivatives.empirical_proof", false]], "empty (class in cctbx.geometry_restraints.lbfgs)": [[134, "cctbx.geometry_restraints.lbfgs.empty", false]], "empty (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.empty", false]], "empty (class in cctbx.statistics)": [[195, "cctbx.statistics.empty", false]], "empty (class in cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.empty", false]], "empty (class in cctbx.web.replay)": [[227, "cctbx.web.replay.empty", false]], "empty (class in mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.empty", false]], "empty (class in mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.empty", false]], "empty (class in xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.empty", false]], "empty() (in module mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Empty", false]], "enable_multiprocessing_if_possible() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.enable_multiprocessing_if_possible", false]], "end_points (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.end_points", false]], "endjob() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.endjob", false]], "endjob() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.endjob", false]], "endjob() (xfel.cxi.cspad_ana.mod_xes.mod_xes method)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes.endjob", false]], "endjob() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.endjob", false]], "ener_lib (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.ener_lib", false]], "ener_lib_as_nonbonded_params() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.ener_lib_as_nonbonded_params", false]], "energies (class in cctbx.adp_restraints.energies)": [[3, "cctbx.adp_restraints.energies.energies", false]], "energies (class in cctbx.geometry_restraints.energies)": [[132, "cctbx.geometry_restraints.energies.energies", false]], "energies_iso (class in cctbx.adp_restraints)": [[2, "cctbx.adp_restraints.energies_iso", false]], "energies_sites() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.energies_sites", false]], "energy_lib_atom (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_atom", false]], "energy_lib_synonym (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_synonym", false]], "energy_lib_vdw (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.energy_lib_vdw", false]], "enforce_positive_amplitudes() (cctbx.miller.array method)": [[148, "cctbx.miller.array.enforce_positive_amplitudes", false]], "enforce_positive_sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.enforce_positive_sigmas", false]], "ensemble_generator (class in mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.ensemble_generator", false]], "ensemble_mean_geometry_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_mean_geometry_stats", false]], "ensemble_mean_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.ensemble_mean_hierarchy", false]], "ensemble_reduction() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_reduction", false]], "ensemble_rmsf_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.ensemble_rmsf_stats", false]], "ensembler (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.ensembler", false]], "enter_block() (cctbx.eltbx.development.itvc_section61_io.table6111 method)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111.enter_block", false]], "enter_entry() (cctbx.eltbx.development.itvc_section61_io.table6111 method)": [[60, "cctbx.eltbx.development.itvc_section61_io.table6111.enter_entry", false]], "entier() (in module cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.entier", false]], "entities (mmtbx.geometry.altloc.aggregator property)": [[289, "mmtbx.geometry.altloc.Aggregator.entities", false]], "entity (class in mmtbx.validation)": [[326, "mmtbx.validation.entity", false]], "enumerate_reduced_cell_two_folds() (in module cctbx.examples.le_page_1982_vs_lebedev_2005)": [[95, "cctbx.examples.le_page_1982_vs_lebedev_2005.enumerate_reduced_cell_two_folds", false]], "env_distance() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_distance", false]], "env_dxtbx_from_slac_metrology() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.env_dxtbx_from_slac_metrology", false]], "env_injector_xyz() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_injector_xyz", false]], "env_laser_status() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_laser_status", false]], "env_sifoil() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_sifoil", false]], "env_wavelength_sxr() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.env_wavelength_sxr", false]], "eobs_and_ecalc_miller_array_normalizers() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.eobs_and_ecalc_miller_array_normalizers", false]], "eps_eq() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_eq", false]], "eps_eq() (cctbx.uctbx.reduction_base.minimum_reduction_mixin method)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin.eps_eq", false]], "eps_gt() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_gt", false]], "eps_lt() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.eps_lt", false]], "epsilon (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.epsilon", false]], "epsilon_angle (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.epsilon_angle", false]], "epsilons() (cctbx.miller.set method)": [[148, "cctbx.miller.set.epsilons", false]], "equal() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.equal", false]], "equal_penalty() (cctbx.crystal.burzlaff_zimmermann_dewolff.metriccriteria method)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria.equal_penalty", false]], "equivalent_sigma_from_cumulative_histogram_match() (in module mmtbx.utils)": [[325, "mmtbx.utils.equivalent_sigma_from_cumulative_histogram_match", false]], "erase_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.erase_scatterers", false]], "error() (mmtbx.map_names method)": [[276, "mmtbx.map_names.error", false]], "error_count() (iotbx.cif.reader method)": [[264, "iotbx.cif.reader.error_count", false]], "error_strs (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.error_strs", false]], "errors() (iotbx.pdb.hierarchy.overall_counts method)": [[268, "iotbx.pdb.hierarchy.overall_counts.errors", false]], "errors_and_warnings() (iotbx.pdb.hierarchy.overall_counts method)": [[268, "iotbx.pdb.hierarchy.overall_counts.errors_and_warnings", false]], "escape() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.escape", false]], "esd_as_weight() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.esd_as_weight", false]], "estimate_d_min() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.estimate_d_min", false]], "estimate_scale_k1() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.estimate_scale_k1", false]], "estimate_signal_to_noise() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.estimate_signal_to_noise", false]], "estimate_signal_to_noise() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.estimate_signal_to_noise", false]], "euclidean_match_symmetry (class in cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.euclidean_match_symmetry", false]], "euler_frac_to_rot_trans() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.euler_frac_to_rot_trans", false]], "eval_logs() (in module cctbx.omz.eval_iso_vs_refined)": [[159, "cctbx.omz.eval_iso_vs_refined.eval_logs", false]], "eval_residue_completeness() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.eval_residue_completeness", false]], "eval_sidechain_completeness() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.eval_sidechain_completeness", false]], "evalscore() (mmtbx.validation.ramalyze.ramalyze static method)": [[326, "mmtbx.validation.ramalyze.ramalyze.evalScore", false]], "evaluate (class in mmtbx.monomer_library.rna_sugar_pucker_analysis)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate", false]], "evaluate() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.evaluate", false]], "evaluate() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.evaluate", false]], "evaluate() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate", false]], "evaluate_after_end() (mmtbx.refinement.rigid_body.manager method)": [[313, "mmtbx.refinement.rigid_body.manager.evaluate_after_end", false]], "evaluate_backrub_pair_impl() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.evaluate_backrub_pair_impl", false]], "evaluate_model (class in mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.evaluate_model", false]], "evaluate_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.evaluate_model", false]], "evaluate_registry_process_result() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.evaluate_registry_process_result", false]], "evaluate_residue() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.evaluate_residue", false]], "evaluate_residue() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate_residue", false]], "evaluate_residue() (mmtbx.validation.rotalyze.residue_evaluator method)": [[326, "mmtbx.validation.rotalyze.residue_evaluator.evaluate_residue", false]], "evaluate_residue_2() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.evaluate_residue_2", false]], "evaluate_rotamer() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.evaluate_rotamer", false]], "evaluate_sites() (mmtbx.rotamer.ramachandran_eval.ramachandraneval method)": [[316, "mmtbx.rotamer.ramachandran_eval.RamachandranEval.evaluate_sites", false]], "evaluatescore() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.evaluateScore", false]], "evaluatescore() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.evaluateScore", false]], "evaluation (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.evaluation", false]], "evaluation (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.evaluation", false]], "event() (xfel.cxi.cspad_ana.average_tbx.average_mixin method)": [[343, "xfel.cxi.cspad_ana.average_tbx.average_mixin.event", false]], "event() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method)": [[343, "xfel.cxi.cspad_ana.common_mode.common_mode_correction.event", false]], "event() (xfel.cxi.cspad_ana.mod_average.mod_average method)": [[343, "xfel.cxi.cspad_ana.mod_average.mod_average.event", false]], "event() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.event", false]], "event() (xfel.cxi.cspad_ana.mod_dump.mod_dump method)": [[343, "xfel.cxi.cspad_ana.mod_dump.mod_dump.event", false]], "event() (xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap method)": [[343, "xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap.event", false]], "event() (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.mod_event_info.event", false]], "event() (xfel.cxi.cspad_ana.mod_filter.mod_filter method)": [[343, "xfel.cxi.cspad_ana.mod_filter.mod_filter.event", false]], "event() (xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5 method)": [[343, "xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5.event", false]], "event() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method)": [[343, "xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind.event", false]], "event() (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method)": [[343, "xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter.event", false]], "event() (xfel.cxi.cspad_ana.mod_mar.mod_mar method)": [[343, "xfel.cxi.cspad_ana.mod_mar.mod_mar.event", false]], "event() (xfel.cxi.cspad_ana.mod_param.mod_param method)": [[343, "xfel.cxi.cspad_ana.mod_param.mod_param.event", false]], "event() (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method)": [[343, "xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump.event", false]], "event() (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method)": [[343, "xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average.event", false]], "event() (xfel.cxi.cspad_ana.mod_xes.mod_xes method)": [[343, "xfel.cxi.cspad_ana.mod_xes.mod_xes.event", false]], "event() (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms.event", false]], "everything (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.everything", false]], "evt_beam_charge() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_beam_charge", false]], "evt_get_quads() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_get_quads", false]], "evt_pulse_energy() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_pulse_energy", false]], "evt_pulse_length() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_pulse_length", false]], "evt_repetition_rate() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_repetition_rate", false]], "evt_seqno() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_seqno", false]], "evt_time() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_time", false]], "evt_timestamp() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_timestamp", false]], "evt_wavelength() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.evt_wavelength", false]], "exact_density() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_density", false]], "exact_density_at_r() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_density_at_r", false]], "exact_gradient_at_r() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.exact_gradient_at_r", false]], "examine_model() (mmtbx.building.make_library.extract_related_models method)": [[277, "mmtbx.building.make_library.extract_related_models.examine_model", false]], "examples() (in module cctbx.examples.steve_collins)": [[113, "cctbx.examples.steve_collins.examples", false]], "exception_handling_parameters (class in scitbx.lbfgs)": [[332, "scitbx.lbfgs.exception_handling_parameters", false]], "exchangeable_hd_selections() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.exchangeable_hd_selections", false]], "exclude() (mmtbx.geometry.indexing.containment_predicate static method)": [[289, "mmtbx.geometry.indexing.containment_predicate.exclude", false]], "exclude_outliers_from_reference_restraints_selection() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.exclude_outliers_from_reference_restraints_selection", false]], "exclude_pairs() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.exclude_pairs", false]], "exclude_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.exclude_predicate", false]], "exclusion() (mmtbx.geometry.indexing.containment_predicate class method)": [[289, "mmtbx.geometry.indexing.containment_predicate.exclusion", false]], "exclusive_or() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.exclusive_or", false]], "exercise() (in module cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.exercise", false]], "exercise() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.exercise", false]], "exercise() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.exercise", false]], "exercise() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.exercise", false]], "exercise() (in module cctbx.examples.g_exp_i_partial_derivatives)": [[92, "cctbx.examples.g_exp_i_partial_derivatives.exercise", false]], "exercise() (in module cctbx.examples.miller_transform)": [[102, "cctbx.examples.miller_transform.exercise", false]], "exercise() (in module cctbx.examples.structure_factor_calculus.site_derivatives)": [[115, "cctbx.examples.structure_factor_calculus.site_derivatives.exercise", false]], "exercise() (in module cctbx.examples.structure_factor_calculus.sites_derivatives)": [[116, "cctbx.examples.structure_factor_calculus.sites_derivatives.exercise", false]], "exercise() (in module cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives)": [[117, "cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives.exercise", false]], "exercise() (in module cctbx.examples.structure_factor_calculus.u_star_derivatives)": [[118, "cctbx.examples.structure_factor_calculus.u_star_derivatives.exercise", false]], "exercise() (in module cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.exercise", false]], "exercise() (in module cctbx.sgtbx.reticular_twin_laws)": [[184, "cctbx.sgtbx.reticular_twin_laws.exercise", false]], "exercise() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.exercise", false]], "exercise() (in module mmtbx.den.plot_weights)": [[284, "mmtbx.den.plot_weights.exercise", false]], "exercise() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.exercise", false]], "exercise() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.exercise", false]], "exercise() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.exercise", false]], "exercise() (in module mmtbx.scaling.thorough_outlier_test)": [[318, "mmtbx.scaling.thorough_outlier_test.exercise", false]], "exercise() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.exercise", false]], "exercise_alternative() (in module cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.exercise_alternative", false]], "exercise_triple() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.exercise_triple", false]], "exp_i_alpha_sum (class in cctbx.examples.exp_i_alpha_derivatives)": [[86, "cctbx.examples.exp_i_alpha_derivatives.exp_i_alpha_sum", false]], "exp_i_hx (class in cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives)": [[117, "cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives.exp_i_hx", false]], "exp_table_one_over_step_size() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.exp_table_one_over_step_size", false]], "expand (class in mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand", false]], "expand() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.expand", false]], "expand() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.expand", false]], "expand_angle_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_angle_proxies", false]], "expand_bond_params_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_bond_params_table", false]], "expand_dihedral_or_chirality_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_dihedral_or_chirality_proxies", false]], "expand_mask() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.expand_mask", false]], "expand_model_or_conformer_indices() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_model_or_conformer_indices", false]], "expand_nonbonded_types() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_nonbonded_types", false]], "expand_pair_sym_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_pair_sym_table", false]], "expand_planarity_proxies() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_planarity_proxies", false]], "expand_shelx_latt() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.expand_shelx_latt", false]], "expand_site_symmetry_table() (in module mmtbx.refinement.orca)": [[313, "mmtbx.refinement.orca.expand_site_symmetry_table", false]], "expand_to_p1() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.expand_to_p1", false]], "expand_to_p1() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.expand_to_p1", false]], "expand_to_p1() (cctbx.miller.array method)": [[148, "cctbx.miller.array.expand_to_p1", false]], "expand_to_p1() (cctbx.miller.set method)": [[148, "cctbx.miller.set.expand_to_p1", false]], "expand_to_p1() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.expand_to_p1", false]], "expand_to_p1() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.expand_to_p1", false]], "expand_to_p1_iselection() (cctbx.miller.set method)": [[148, "cctbx.miller.set.expand_to_p1_iselection", false]], "expected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.expected_atoms", false]], "expected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.expected_atoms", false]], "expected_intensity (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.expected_intensity", false]], "expected_labels() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.expected_labels", false]], "experiment_list() (in module dxtbx.serialize.load)": [[258, "dxtbx.serialize.load.experiment_list", false]], "experiment_type() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.experiment_type", false]], "experiment_type() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.experiment_type", false]], "experimental_data_target_and_gradients 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"mmtbx.twinning.twin_f_model.twin_model_manager.f_model_w", false]], "f_obs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.f_obs", false]], "f_obs() (cctbx.xray.target_functors.intensity_correlation method)": [[252, "cctbx.xray.target_functors.intensity_correlation.f_obs", false]], "f_obs() (cctbx.xray.target_functors.unified_least_squares_residual method)": [[252, "cctbx.xray.target_functors.unified_least_squares_residual.f_obs", false]], "f_obs() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.f_obs", false]], "f_obs_active (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.f_obs_active", false]], "f_obs_and_f_calc_agree_well() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.f_obs_and_f_calc_agree_well", false]], "f_obs_f_calc_fan_outlier_selection() 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cctbx.french_wilson)": [[129, "cctbx.french_wilson.f_w_binning", false]], "fab_elbow_angle (class in mmtbx.utils.fab_elbow_angle)": [[325, "mmtbx.utils.fab_elbow_angle.fab_elbow_angle", false]], "face (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.face", false]], "face_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.face_polygons", false]], "face_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.face_vertices", false]], "faceset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.faceSet", false]], "fake_config (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_config", false]], "fake_cspad_elementv2 (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_cspad_ElementV2", false]], "fake_env (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_env", false]], "fake_evt (class in xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_evt", false]], "fake_get_config() (in module xfel.command_line.convert_gain_map)": [[341, "xfel.command_line.convert_gain_map.fake_get_config", false]], "fast (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.fast", false]], "fast_maps_from_hkl_file (class in mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file", false]], "fast_minimum_reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction", false]], "fatal_problems_message() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.fatal_problems_message", false]], "fatal_problems_report() 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false]], "fcalc_from_distribution() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.fcalc_from_distribution", false]], "fdp (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.fdp", false]], "fetch_labels() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.fetch_labels", false]], "fetch_labels() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.fetch_labels", false]], "fetch_pdb_data() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.fetch_pdb_data", false]], "fetch_similar_pdb_ids() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.fetch_similar_pdb_ids", false]], "fft_map (class in cctbx.miller)": [[148, "cctbx.miller.fft_map", false]], "fft_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.fft_map", false]], "fft_vs_direct() 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method)": [[331, "scitbx.array_family.flex.int.fill", false]], "fill() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.fill", false]], "fill() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.fill", false]], "fill() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.fill", false]], "fill() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.fill", false]], "fill() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.fill", false]], "fill() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.fill", false]], "fill() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.fill", false]], "filled (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FILLED", false]], "filter() (in module mmtbx.geometry.indexing)": [[289, 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"iotbx.pdb.hierarchy.atom_group.find_atom_index", false]], "find_atom_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.find_atom_pairs", false]], "find_automatically() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_automatically", false]], "find_backrubs() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.find_backrubs", false]], "find_base_pairs() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_base_pairs", false]], "find_best() (mmtbx.utils.guess_observation_type method)": [[325, "mmtbx.utils.guess_observation_type.find_best", false]], "find_best_cell (class in cctbx.crystal.find_best_cell)": [[29, "cctbx.crystal.find_best_cell.find_best_cell", false]], "find_centring_translations() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.find_centring_translations", false]], "find_chain_index() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.find_chain_index", false]], "find_closest_base_name() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.find_closest_base_name", false]], "find_compatible_space_groups (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups", false]], "find_coordination_geometry() (in module mmtbx.ions.geometry)": [[296, "mmtbx.ions.geometry.find_coordination_geometry", false]], "find_data_arrays() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.find_data_arrays", false]], "find_data_dir() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.find_data_dir", false]], "find_distances() (in module cctbx.examples.find_distances_using_cpp_objects)": [[89, "cctbx.examples.find_distances_using_cpp_objects.find_distances", false]], "find_ensemble_backrubs() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.find_ensemble_backrubs", false]], "find_helices_simple (class in mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.find_helices_simple", false]], "find_hydrogen_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.find_hydrogen_peaks", false]], "find_it() (cctbx.crystal.find_best_cell.alternative_find_best_cell method)": [[29, "cctbx.crystal.find_best_cell.alternative_find_best_cell.find_it", false]], "find_k_sol_b_sol() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.find_k_sol_b_sol", false]], "find_left_over_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.find_left_over_symops", false]], "find_logs() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.find_logs", false]], "find_map_symmetry() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.find_map_symmetry", false]], "find_maximum() (mmtbx.scaling.twin_analyses.correlation_analyses method)": [[318, "mmtbx.scaling.twin_analyses.correlation_analyses.find_maximum", false]], "find_missing_atoms() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.find_missing_atoms", false]], "find_model_index() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.find_model_index", false]], "find_mon_lib_file() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.find_mon_lib_file", false]], "find_n_highest_grid_points_as_sites_cart() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.find_n_highest_grid_points_as_sites_cart", false]], "find_ncs_in_hierarchy() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.find_ncs_in_hierarchy", false]], "find_nearby_atoms() (in module mmtbx.ions.environment)": [[295, "mmtbx.ions.environment.find_nearby_atoms", false]], "find_nearby_atoms() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.find_nearby_atoms", false]], "find_node() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.find_node", false]], "find_overlapping_selections() (in module mmtbx.utils)": [[325, "mmtbx.utils.find_overlapping_selections", false]], "find_peak() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.find_peak", false]], "find_peak() (mmtbx.ias.find_peak_at_bond method)": [[292, "mmtbx.ias.find_peak_at_bond.find_peak", false]], "find_peak_at_bond (class in mmtbx.ias)": [[292, "mmtbx.ias.find_peak_at_bond", false]], "find_peaks() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.find_peaks", false]], "find_peptide_flips() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.find_peptide_flips", false]], "find_pure_altloc_ranges() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.find_pure_altloc_ranges", false]], "find_region_max_value() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.find_region_max_value", false]], "find_residue() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.find_residue", false]], "find_residue_group_index() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.find_residue_group_index", false]], "find_rotarama_data_dir() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.find_rotarama_data_dir", false]], "find_row() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.find_row", false]], "find_sec_str() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.find_sec_str", false]], "find_sequence_mismatches() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.find_sequence_mismatches", false]], "find_similar_chains() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.find_similar_chains", false]], "find_source_dir() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.find_source_dir", false]], "find_source_dir() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.find_source_dir", false]], "find_space_group() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.find_space_group", false]], "find_triples() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.find_triples", false]], "find_triples_slowly() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.find_triples_slowly", false]], "find_version() (iotbx.xds.xparm.reader static method)": [[272, "iotbx.xds.xparm.reader.find_version", false]], "finish_job() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.finish_job", false]], "finish_job() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.finish_job", false]], "finite_difference_test() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.finite_difference_test", false]], "finite_difference_test() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.finite_difference_test", false]], "finite_differences_grads_of_xray_target_wrt_tls() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.finite_differences_grads_of_xray_target_wrt_tls", false]], "first_chain_id() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.first_chain_id", false]], "first_index() (cctbx.miller.set method)": [[148, "cctbx.miller.set.first_index", false]], "first_moment_analysis (class in xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis", false]], "first_resseq_as_int() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.first_resseq_as_int", false]], "fit_backbone() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization.fit_backbone", false]], "fit_c_beta() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.fit_c_beta", false]], "fit_gaussian() (in module mmtbx.ions.utils)": [[302, "mmtbx.ions.utils.fit_gaussian", false]], "fit_input (class in cctbx.eltbx.development.hydrogen_plots)": [[55, "cctbx.eltbx.development.hydrogen_plots.fit_input", false]], "fit_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.fit_one_histogram", false]], "fit_parameters (class in cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.fit_parameters", false]], "fit_proline() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.fit_proline", false]], "fit_residue_in_box() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.fit_residue_in_box", false]], "fit_rotamers() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization.fit_rotamers", false]], "fit_rotatable() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.fit_rotatable", false]], "fit_rotatable2() (in module mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.fit_rotatable2", false]], "fit_side_chain() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.fit_side_chain", false]], "fit_translation (class in xfel.metrology.mark1)": [[347, "xfel.metrology.mark1.fit_translation", false]], "fit_translation2 (class in xfel.metrology.mark3)": [[347, "xfel.metrology.mark3.fit_translation2", false]], "fit_translation4 (class in xfel.metrology.mark10)": [[347, "xfel.metrology.mark10.fit_translation4", false]], "fit_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.fit_water", false]], "fits_in_pdb_format() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.fits_in_pdb_format", false]], "fitted_gaussian (class in cctbx.eltbx.xray_scattering)": [[76, "cctbx.eltbx.xray_scattering.fitted_gaussian", false]], "fix() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.FIX", false]], "fix_altlocs_and_filter() (in module mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.fix_altlocs_and_filter", false]], "fixed_site_indices() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.fixed_site_indices", false]], "flag_names_and_labels (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.flag_names_and_labels", false]], "flags (class in cctbx.adp_restraints.flags)": [[4, "cctbx.adp_restraints.flags.flags", false]], "flags (class in cctbx.geometry_restraints.flags)": [[133, "cctbx.geometry_restraints.flags.flags", false]], "flags (scitbx.array_family.flex.smart_selection property)": [[331, "scitbx.array_family.flex.smart_selection.flags", false]], "flatten() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.flatten", false]], "flatten() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.flatten", false]], "flip_atoms_in_ncs_groups() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.flip_atoms_in_ncs_groups", false]], "flip_symmetric_amino_acids() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.flip_symmetric_amino_acids", false]], "float (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.float", false]], "flush() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.flush", false]], "flush_log() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.flush_log", false]], "fmod_positive() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.fmod_positive", false]], "fmodel (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.fmodel", false]], "fmodel (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.fmodel", false]], "fmodel (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.fmodel", false]], "fmodel_from_xray_structure (class in mmtbx.utils)": [[325, "mmtbx.utils.fmodel_from_xray_structure", false]], "fmodel_manager() (in module mmtbx.utils)": [[325, "mmtbx.utils.fmodel_manager", false]], "fmodel_manager2() (in module mmtbx.utils)": [[325, "mmtbx.utils.fmodel_manager2", false]], "fmodel_neutron (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.fmodel_neutron", false]], "fmodel_neutron() (mmtbx.fmodels method)": [[276, "id0", false]], "fmodel_simple() (in module mmtbx.utils)": [[325, "mmtbx.utils.fmodel_simple", false]], "fmodel_statistics_by_resolution() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.fmodel_statistics_by_resolution", false]], "fmodel_statistics_graph_data() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.fmodel_statistics_graph_data", false]], "fmodel_xray (mmtbx.fmodels attribute)": [[276, "mmtbx.fmodels.fmodel_xray", false]], "fmodel_xray() (mmtbx.fmodels method)": [[276, "id1", false]], "fmodels (class in mmtbx)": [[276, "mmtbx.fmodels", false]], "fmt3vec (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.fmt3vec", false]], "fmt_nums() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.fmt_nums", false]], "fo (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.FO", false]], "fo_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id10", false], [295, "mmtbx.ions.environment.ScatteringEnvironment.fo_density", false]], "fo_fc_alpha_over_eps_beta() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.fo_fc_alpha_over_eps_beta", false]], "fo_minus_fo_master_params() (in module mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.fo_minus_fo_master_params", false]], "focus() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.focus", false]], "focus() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.focus", false]], "focus() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.focus", false]], "focus() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.focus", false]], "focus() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.focus", false]], "focus() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.focus", false]], "focus() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.focus", false]], "focus() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.focus", false]], "focus() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.focus", false]], "focus() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.focus", false]], "focus() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.focus", false]], "focus() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.focus", false]], "focus() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.focus", false]], "focus_size_1d() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.focus_size_1d", false]], "focus_size_1d() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.focus_size_1d", false]], "fofc (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.fofc", false]], "fofc (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.fofc", false]], "fofc_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.fofc_density", false]], "fofc_hole (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.FOFC_HOLE", false]], "fofc_map() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.fofc_map", false]], "fofc_max (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.fofc_max", false]], "fofc_mean (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.fofc_mean", false]], "fofc_min (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.fofc_min", false]], "fofc_peak (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.FOFC_PEAK", false]], "fofo_density (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "mmtbx.ions.environment.ScatteringEnvironment.fofo_density", false]], "fom() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.fom", false]], "fom() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.fom", false]], "fom() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.fom", false]], "force_complex() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.force_complex", false]], "form_factor() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.form_factor", false]], "form_factor() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.form_factor", false]], "form_factor() (mmtbx.max_lik.maxlik.alpha_beta_calc method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_calc.form_factor", false]], "format() (mmtbx.map_names method)": [[276, "mmtbx.map_names.format", false]], "format_all_for_biomt() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_biomt", false]], "format_all_for_group_specification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_group_specification", false]], "format_all_for_phenix_refine() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_phenix_refine", false]], "format_all_for_resolve() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_all_for_resolve", false]], "format_anisou_record() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.format_anisou_record", false]], "format_anisou_record() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.format_anisou_record", false]], "format_atom_record() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.format_atom_record", false]], "format_atom_record() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.format_atom_record", false]], "format_atom_record_group() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.format_atom_record_group", false]], "format_atom_record_group() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.format_atom_record_group", false]], "format_chi_angles() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.format_chi_angles", false]], "format_correction_for_h() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.format_correction_for_H", false]], "format_distances_for_error_message() (in module cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.format_distances_for_error_message", false]], "format_exception_message() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.format_exception_message", false]], "format_fasta() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.format_fasta", false]], "format_fasta() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.format_fasta", false]], "format_fasta() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.format_fasta", false]], "format_for_biomt() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_biomt", false]], "format_for_phenix_refine() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_phenix_refine", false]], "format_for_resolve() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_for_resolve", false]], "format_group_specification() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.format_group_specification", false]], "format_html() (cctbx.web.asu_gallery.jv_index.crystal_system_table method)": [[209, "cctbx.web.asu_gallery.jv_index.crystal_system_table.format_html", false]], "format_html() (cctbx.web.asu_gallery.jv_index.plane_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.plane_group_table.format_html", false]], "format_html() (cctbx.web.asu_gallery.jv_index.point_group_table method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table.format_html", false]], "format_html() (cctbx.web.asu_gallery.jv_index.symbol_table method)": [[209, "cctbx.web.asu_gallery.jv_index.symbol_table.format_html", false]], "format_info_string() (mmtbx.refinement.real_space.residue_monitor method)": [[315, "mmtbx.refinement.real_space.residue_monitor.format_info_string", false]], "format_it() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method)": [[318, "mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling.format_it", false]], "format_map_coeffs_for_resolve() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.format_map_coeffs_for_resolve", false]], "format_max() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.format_max", false]], "format_mean() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.format_mean", false]], "format_min() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.format_min", false]], "format_object_from_data() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.format_object_from_data", false]], "format_old() (mmtbx.validation.cbetadev.cbeta method)": [[326, "mmtbx.validation.cbetadev.cbeta.format_old", false]], "format_old() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.format_old", false]], "format_old() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.format_old", false]], "format_old() (mmtbx.validation.ramalyze.ramachandran method)": [[326, "mmtbx.validation.ramalyze.ramachandran.format_old", false]], "format_old() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.format_old", false]], "format_phil_for_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_phil_for_ncs", false]], "format_phil_for_phenix_refine() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.format_phil_for_phenix_refine", false]], "format_ramachandran_plot_title() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.format_ramachandran_plot_title", false]], "format_ramachandran_plot_title() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.format_ramachandran_plot_title", false]], "format_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.format_rms_info", false]], "format_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.format_scale_matrix", false]], "format_scale_matrix() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.format_scale_matrix", false]], "format_score() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.format_score", false]], "format_sigatm_record() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.format_sigatm_record", false]], "format_sigatm_record() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.format_sigatm_record", false]], "format_siguij_record() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.format_siguij_record", false]], "format_siguij_record() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.format_siguij_record", false]], "format_stats_for_phenix_gui() (mmtbx.refinement.print_statistics.refinement_monitor method)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor.format_stats_for_phenix_gui", false]], "format_summary() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.format_summary", false]], "format_summary() (scitbx.array_family.flex.smart_selection method)": [[331, "scitbx.array_family.flex.smart_selection.format_summary", false]], "format_time() (in module xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.format_time", false]], "format_value() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.format_value", false]], "format_values() (mmtbx.validation.restraints.planarity method)": [[326, 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(class in cctbx.eltbx.formula)": [[66, "cctbx.eltbx.formula.formula", false]], "formula_49() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.formula_49", false]], "forward_compatible_hierarchy_as_standard() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.forward_compatible_hierarchy_as_standard", false]], "fourier_coefficients_as_map_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.fourier_coefficients_as_map_manager", false]], "fourier_filter() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.fourier_filter", false]], "fp (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.fp", false]], "fp (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id11", false], [295, "mmtbx.ions.environment.ScatteringEnvironment.fp", false]], "fpp (mmtbx.ions.environment.scatteringenvironment attribute)": [[295, "id12", false], [295, 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"from_expts() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_expts", false]], "from_files() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_files", false]], "from_iterable() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_iterable", false]], "from_list() (xfel.clustering.cluster.cluster class method)": [[340, "xfel.clustering.cluster.Cluster.from_list", false]], "from_mosflm_matrix() (dxtbx.model.crystal.crystalfactory static method)": [[257, "dxtbx.model.crystal.CrystalFactory.from_mosflm_matrix", false]], "from_phil() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.from_phil", false]], "from_phil() (dxtbx.model.detector.detectorfactory static method)": [[257, "dxtbx.model.detector.DetectorFactory.from_phil", false]], "from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, 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[[331, "scitbx.array_family.flex.bool.front", false]], "front() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.front", false]], "front() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.front", false]], "front() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.front", false]], "front() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.front", false]], "front() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.front", false]], "front() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.front", false]], "front() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.front", false]], "front() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.front", false]], "front() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.front", false]], "front() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.front", false]], "front() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.front", false]], "frozenset() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.frozenset", false]], "fs() (cctbx.examples.structure_factor_derivatives_2.structure_factors method)": [[120, "cctbx.examples.structure_factor_derivatives_2.structure_factors.fs", false]], "fs() (cctbx.examples.structure_factor_derivatives_3.structure_factors method)": [[121, "cctbx.examples.structure_factor_derivatives_3.structure_factors.fs", false]], "fs() (cctbx.examples.structure_factor_derivatives_4.structure_factors method)": [[122, "cctbx.examples.structure_factor_derivatives_4.structure_factors.fs", false]], "fsc (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.fsc", false]], "fsc() (cctbx.miller.array method)": [[148, "cctbx.miller.array.fsc", false]], "full_sys_abs_mask() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.full_sys_abs_mask", false]], "full_width_half_max() (in module xfel.command_line.overlay_spectra)": [[341, "xfel.command_line.overlay_spectra.full_width_half_max", false]], "func() (mmtbx.refinement.real_space.fit_residue.find_all_conformers method)": [[315, "mmtbx.refinement.real_space.fit_residue.find_all_conformers.func", false]], "funcl (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.funcl", false]], "functional() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.functional", false]], "functional() (cctbx.xray.minimization.occupancy_penalty_exp method)": 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mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.gamma_nucleic", false]], "gamma_protein (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein", false]], "gaussian_filter() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.gaussian_filter", false]], "general_positions_only() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.general_positions_only", false]], "general_positions_only() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.general_positions_only", false]], "generate_angles_nested() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.generate_angles_nested", false]], "generate_atoms_from_atom_groups() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.generate_atoms_from_atom_groups", false]], "generate_atoms_from_atom_groups() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.generate_atoms_from_atom_groups", false]], "generate_bijvoet_mates() (cctbx.miller.array method)": [[148, "cctbx.miller.array.generate_bijvoet_mates", false]], "generate_bivoet_mates() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_bivoet_mates", false]], "generate_cb_op_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_cb_op_up_to_order", false]], "generate_chemical_components_codes() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.generate_chemical_components_codes", false]], "generate_comparison_selections() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_comparison_selections", false]], "generate_data_from_streams() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.generate_data_from_streams", false]], "generate_dna_rna_fragments() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_dna_rna_fragments", false]], "generate_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[257, "dxtbx.model.detector.DetectorFactory.generate_from_phil", false]], "generate_inverse_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_inverse_matrix_up_to_order", false]], "generate_loop_data() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.generate_loop_data", false]], "generate_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.generate_map", false]], "generate_master_phil_with_inputs() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.generate_master_phil_with_inputs", false]], "generate_matrix() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_matrix", false]], "generate_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.generate_matrix_up_to_order", false]], "generate_missing_reflections() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.generate_missing_reflections", false]], "generate_ncs_ops() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.generate_ncs_ops", false]], "generate_p1_box() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.generate_p1_box", false]], "generate_protein_fragments() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_fragments", false]], "generate_protein_threes() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_threes", false]], "generate_protein_tuples() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_protein_tuples", false]], "generate_r_free_flags() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags", false]], "generate_r_free_flags_basic() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags_basic", false]], "generate_r_free_flags_on_lattice_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.generate_r_free_flags_on_lattice_symmetry", false]], "generate_random_f_calc() (in module cctbx.examples.random_f_calc)": [[106, "cctbx.examples.random_f_calc.generate_random_f_calc", false]], "generate_reindex_sets() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_reindex_sets", false]], "generate_residue_tuples() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.generate_residue_tuples", false]], "generate_sidechain_clusters() (in module mmtbx.building)": [[277, "mmtbx.building.generate_sidechain_clusters", false]], "generate_singles() (in module cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.generate_singles", false]], "generate_streams_from_path() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.generate_streams_from_path", false]], "generate_systematic_absences() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.generate_systematic_absences", false]], "generate_systematic_absences() (in module cctbx.miller.display)": [[149, "cctbx.miller.display.generate_systematic_absences", false]], "generate_tlsos() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.generate_tlsos", false]], "generate_torsion_restraints() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.generate_torsion_restraints", false]], "generate_twin_operators() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.generate_twin_operators", false]], "generate_view_data() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.generate_view_data", false]], "generate_water_omit_map (class in mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.generate_water_omit_map", false]], "generator() (in module iotbx.shelx.writer)": [[271, "iotbx.shelx.writer.generator", false]], "generic_metal_run() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.generic_metal_run", false]], "generic_polar_normalize() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.generic_polar_normalize", false]], "generic_simple_input_phil() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.generic_simple_input_phil", false]], "geometry (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.geometry", false]], "geometry (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.geometry", false]], "geometry (mmtbx.ions.environment.chemicalenvironment attribute)": [[295, "id4", false], [295, "mmtbx.ions.environment.ChemicalEnvironment.geometry", false]], "geometry_minimization() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.geometry_minimization", false]], "geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.process method)": [[308, "mmtbx.monomer_library.pdb_interpretation.process.geometry_restraints_manager", false]], "geometry_restraints_proxy_registries (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries", false]], "geostd_list_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.geostd_list_cif", false]], "get() (cctbx.omz.bfgs.memory_element method)": [[154, "cctbx.omz.bfgs.memory_element.get", false]], "get() (cctbx.omz.dev.shift_limit_pair method)": [[158, "cctbx.omz.dev.shift_limit_pair.get", false]], "get() (cctbx.sgtbx.symmetry_equivalent_pair_interactions method)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.get", false]], "get() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.get", false]], "get_1_char_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_1_char_after_key", false]], "get_1_value_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_1_value_after_key", false]], "get_3_values_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_3_values_after_key", false]], "get_absolute_label_position() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.get_absolute_label_position", false]], "get_absolute_rt_info() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.get_absolute_rt_info", false]], "get_active_data() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.get_active_data", false]], "get_active_infos() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_active_infos", false]], "get_alignment() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_alignment", false]], "get_all_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_all_angle_proxies", false]], "get_all_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_all_bond_proxies", false]], "get_all_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_all_conformer_distances", false]], "get_all_edge_segments() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_all_edge_segments", false]], "get_all_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.get_all_segments", false]], "get_all_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_all_vertices", false]], "get_allowed_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_allowed_count_and_fraction", false]], "get_allowed_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_allowed_goal", false]], "get_alpha() (mmtbx.scaling.twin_analyses.britton_test method)": [[318, "mmtbx.scaling.twin_analyses.britton_test.get_alpha", false]], "get_alpha_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_alpha_angle", false]], "get_alpha_beta() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_alpha_beta", false]], "get_alternative_name() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_alternative_name", false]], "get_altid_controls() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_altid_controls", false]], "get_altloc() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_altloc", false]], "get_altloc() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.get_altloc", false]], "get_altloc_from_id_str() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_altloc_from_id_str", false]], "get_altloc_from_three() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_altloc_from_three", false]], "get_angle() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_angle", false]], "get_angle() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_angle", false]], "get_angle() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method)": [[325, "mmtbx.utils.fab_elbow_angle.fab_elbow_angle.get_angle", false]], "get_angle_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_angle_outliers", false]], "get_angle_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_angle_outliers", false]], "get_angle_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_angle_proxies_without_user_supplied", false]], "get_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[257, "dxtbx.model.goniometer.MultiAxisGoniometer.get_angles", false]], "get_angles_from_included_bonds() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_angles_from_included_bonds", false]], "get_anomalous_map() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_anomalous_map", false]], "get_anomeric_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_anomeric_carbon", false]], "get_anomeric_hydrogen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_anomeric_hydrogen", false]], "get_any_linking_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_any_linking_carbon", false]], "get_any_map_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_any_map_manager", false]], "get_as_atom_group() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_as_atom_group", false]], "get_as_hierarchy() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_as_hierarchy", false]], "get_asu() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table)": [[172, "cctbx.sgtbx.direct_space_asu.plane_group_reference_table.get_asu", false]], "get_asu() (in module cctbx.sgtbx.direct_space_asu.reference_table)": [[175, "cctbx.sgtbx.direct_space_asu.reference_table.get_asu", false]], "get_atom() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.get_atom", false]], "get_atom_dict() (mmtbx.rotamer.rotamer_eval.rotamereval method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerEval.get_atom_dict", false]], "get_atom_names() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_atom_names", false]], "get_atom_selection() (in module mmtbx.utils)": [[325, "mmtbx.utils.get_atom_selection", false]], "get_atom_selection_cache() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_atom_selection_cache", false]], "get_atom_selections() (in module mmtbx.utils)": [[325, "mmtbx.utils.get_atom_selections", false]], "get_atom_type() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.get_atom_type", false]], "get_atom_type_symbol() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_atom_type_symbol", false]], "get_atoms_info() (in module mmtbx.validation)": [[326, "mmtbx.validation.get_atoms_info", false]], "get_atoms_str() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_atoms_str", false]], "get_auth_asym_id() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_auth_asym_id", false]], "get_auth_asym_id_iseq() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_auth_asym_id_iseq", false]], "get_auth_seq_id() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_auth_seq_id", false]], "get_auth_seq_id_iseq() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_auth_seq_id_iseq", false]], "get_average_cell_dimensions() (xfel.command_line.cxi_merge.unit_cell_distribution method)": [[341, "xfel.command_line.cxi_merge.unit_cell_distribution.get_average_cell_dimensions", false]], "get_average_scale_factors() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_average_scale_factors", false]], "get_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[257, "dxtbx.model.goniometer.MultiAxisGoniometer.get_axes", false]], "get_axes_and_atoms_i_seqs() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.get_axes_and_atoms_i_seqs", false]], "get_b_iso() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_b_iso", false]], "get_bad_hydrogen_i_seqs() (in module mmtbx.monomer_library.correct_hydrogen_geometries)": [[308, "mmtbx.monomer_library.correct_hydrogen_geometries.get_bad_hydrogen_i_seqs", false]], "get_basepair_target_distance() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.get_basepair_target_distance", false]], "get_basic_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.get_basic_histogram_data", false]], "get_beam() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_beam", false]], "get_best_model() (mmtbx.refinement.select_best_starting_model.select_model method)": [[313, "mmtbx.refinement.select_best_starting_model.select_model.get_best_model", false]], "get_beta_ideal() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_beta_ideal", false]], "get_bin() (mmtbx.validation.graphics.residue_binner method)": [[326, "mmtbx.validation.graphics.residue_binner.get_bin", false]], "get_bin_centers() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.get_bin_centers", false]], "get_bin_color() (mmtbx.polygon.output.blue_color_model method)": [[311, "mmtbx.polygon.output.blue_color_model.get_bin_color", false]], "get_bin_color() (mmtbx.polygon.output.color_model method)": [[311, "mmtbx.polygon.output.color_model.get_bin_color", false]], "get_bin_color() (mmtbx.polygon.output.grayscale_color_model method)": [[311, "mmtbx.polygon.output.grayscale_color_model.get_bin_color", false]], "get_bin_color() (mmtbx.polygon.output.rainbow_color_model method)": [[311, "mmtbx.polygon.output.rainbow_color_model.get_bin_color", false]], "get_bin_color() (mmtbx.polygon.output.red_color_model method)": [[311, "mmtbx.polygon.output.red_color_model.get_bin_color", false]], "get_bin_color() (mmtbx.polygon.output.rmb_color_model method)": [[311, "mmtbx.polygon.output.rmb_color_model.get_bin_color", false]], "get_bond() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.get_bond", false]], "get_bond() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_bond", false]], "get_bond() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_bond", false]], "get_bond_and_angle_outliers() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_bond_and_angle_outliers", false]], "get_bond_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_bond_outliers", false]], "get_bond_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_bond_outliers", false]], "get_bond_pairs() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_bond_pairs", false]], "get_bond_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_bond_proxies_without_user_supplied", false]], "get_bonded() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_bonded", false]], "get_bonded_from_atom_groups() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_bonded_from_atom_groups", false]], "get_bonds_angles_rmsds() (mmtbx.validation.restraints.combined method)": [[326, "mmtbx.validation.restraints.combined.get_bonds_angles_rmsds", false]], "get_bool_selection_to_keep() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_bool_selection_to_keep", false]], "get_boundaries_from_sensor_id() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.get_boundaries_from_sensor_ID", false]], "get_boxes_to_tile_map() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.get_boxes_to_tile_map", false]], "get_c1_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_C1_carbon", false]], "get_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_c_beta_torsion_proxies", false]], "get_c_beta_torsion_proxies() (in module mmtbx.geometry_restraints.c_beta)": [[290, "mmtbx.geometry_restraints.c_beta.get_c_beta_torsion_proxies", false]], "get_c_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_c_symmetry", false]], "get_calib_file_path() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.get_calib_file_path", false]], "get_calphas() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.get_calphas", false]], "get_cas_from_three() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_cas_from_three", false]], "get_cb_resseq_to_skip() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_cb_resseq_to_skip", false]], "get_cb_target_angle_pair() (in module mmtbx.geometry_restraints.c_beta)": [[290, "mmtbx.geometry_restraints.c_beta.get_cb_target_angle_pair", false]], "get_cbetas() (in module mmtbx.disorder.backbone)": [[286, "mmtbx.disorder.backbone.get_cbetas", false]], "get_center() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_center", false]], "get_center_and_radius() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.get_center_and_radius", false]], "get_center_of_box_frac() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_center_of_box_frac", false]], "get_centroid_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_centroid_hierarchy", false]], "get_chain_color() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_chain_color", false]], "get_chain_xyz() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_chain_xyz", false]], "get_chains_info() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_chains_info", false]], "get_charge() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_charge", false]], "get_charges() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_charges", false]], "get_chi1_chi2() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.get_chi1_chi2", false]], "get_chi_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_chi_torsion_proxies", false]], "get_chir_bonds_and_angles() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_chir_bonds_and_angles", false]], "get_chir_bonds_and_angles() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_chir_bonds_and_angles", false]], "get_chir_volume_ideal() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.get_chir_volume_ideal", false]], "get_chir_volume_ideal() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_chir_volume_ideal", false]], "get_chir_volume_ideal() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_chir_volume_ideal", false]], "get_chiral_i_seqs() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_chiral_i_seqs", false]], "get_chiral_sign() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_chiral_sign", false]], "get_chiral_volume() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_chiral_volume", false]], "get_chirality_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_chirality_outliers", false]], "get_cif_dictionary() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_cif_dictionary", false]], "get_cif_filename() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_cif_filename", false]], "get_cif_float() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_float", false]], "get_cif_int() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_int", false]], "get_cif_link_entries() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_cif_link_entries", false]], "get_cif_number() (in module mmtbx.wwpdb.standard_geometry_cif)": [[328, "mmtbx.wwpdb.standard_geometry_cif.get_cif_number", false]], "get_cis_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_cis_pro_count_and_fraction", false]], "get_clashscore() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_clashscore", false]], "get_clashscore_b_cutoff() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_clashscore_b_cutoff", false]], "get_classes() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_classes", false]], "get_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_classification", false]], "get_code() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_code", false]], "get_color_key() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.get_color_key", false]], "get_comp_comp_id_and_atom_name_interpretation() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_and_atom_name_interpretation", false]], "get_comp_comp_id_direct() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_direct", false]], "get_comp_comp_id_mod() (mmtbx.monomer_library.server.server method)": [[308, "mmtbx.monomer_library.server.server.get_comp_comp_id_mod", false]], "get_completeness() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_completeness", false]], "get_condensed_clashes() (mmtbx.validation.clashscore.probe_clashscore_manager method)": [[326, "mmtbx.validation.clashscore.probe_clashscore_manager.get_condensed_clashes", false]], "get_condition() (mmtbx.ligands.xtal_screens.server method)": [[304, "mmtbx.ligands.xtal_screens.server.get_condition", false]], "get_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_conformer_distances", false]], "get_conformer_indices() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_conformer_indices", false]], "get_contours() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_contours", false]], "get_converter_by_docstring() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.get_converter_by_docstring", false]], "get_converters() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.get_converters", false]], "get_coordinate_shift() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.get_coordinate_shift", false]], "get_coordinates_for_alignment_range() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_coordinates_for_alignment_range", false]], "get_coordinates_for_alignment_ranges() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_coordinates_for_alignment_ranges", false]], "get_copy_master_selections_from_match_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_copy_master_selections_from_match_dict", false]], "get_counts_and_histograms() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_counts_and_histograms", false]], "get_covalent_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_covalent_angle_proxies", false]], "get_covalent_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_covalent_bond_proxies", false]], "get_cspad_cbf_handle() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.get_cspad_cbf_handle", false]], "get_current_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_current_eq_distances", false]], "get_cursor() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.get_cursor", false]], "get_cycle_stats() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.get_cycle_stats", false]], "get_d_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_d_symmetry", false]], "get_data_file() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_data_file", false]], "get_db_result() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_db_result", false]], "get_default_bondlength() (in module mmtbx.monomer_library.bondlength_defaults)": [[308, "mmtbx.monomer_library.bondlength_defaults.get_default_bondlength", false]], "get_default_header() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_default_header", false]], "get_default_map_coefficients_phil() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_default_map_coefficients_phil", false]], "get_default_ss_params() (mmtbx.secondary_structure.manager static method)": [[319, "mmtbx.secondary_structure.manager.get_default_ss_params", false]], "get_den_atom_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_den_atom_pairs", false]], "get_density_along_line() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.get_density_along_line", false]], "get_detector() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_detector", false]], "get_diagonal_extend() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_diagonal_extend", false]], "get_diff_score_towards_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_diff_score_towards_periodic", false]], "get_difference_maps() (in module mmtbx.building)": [[277, "mmtbx.building.get_difference_maps", false]], "get_diffs_for_matching_target_and_model() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_diffs_for_matching_target_and_model", false]], "get_dihedral() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_dihedral", false]], "get_dihedral_outliers() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_dihedral_outliers", false]], "get_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_dihedral_proxies", false]], "get_dihedral_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_dihedral_proxies_without_user_supplied", false]], "get_direction() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_direction", false]], "get_distance2() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_distance2", false]], "get_distance2() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_distance2", false]], "get_edge_score_towards_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_edge_score_towards_periodic", false]], "get_edge_vectors() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_edge_vectors", false]], "get_edge_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.get_edge_vertices", false]], "get_eigenvector() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method)": [[325, "mmtbx.utils.fab_elbow_angle.fab_elbow_angle.get_eigenvector", false]], "get_element() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_element", false]], "get_element_and_charge_symbols() (in module cctbx.eltbx.xray_scattering)": [[76, "cctbx.eltbx.xray_scattering.get_element_and_charge_symbols", false]], "get_errors() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.get_errors", false]], "get_expected_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_expected_count", false]], "get_experiment_type() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.get_experiment_type", false]], "get_experiment_type() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.get_experiment_type", false]], "get_f_calc() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_f_calc", false]], "get_f_cbs() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_f_cbs", false]], "get_favored_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_favored_count_and_fraction", false]], "get_favored_goal() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_favored_goal", false]], "get_favored_goal() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_favored_goal", false]], "get_favored_peaks() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_favored_peaks", false]], "get_favored_regions() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_favored_regions", false]], "get_field_simple() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_field_simple", false]], "get_filtered_n_angle_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_angle_proxies", false]], "get_filtered_n_bond_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_bond_proxies", false]], "get_filtered_n_dihedral_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_dihedral_proxies", false]], "get_filtered_n_planarity_proxies() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.get_filtered_n_planarity_proxies", false]], "get_final_maps_and_cc (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.get_final_maps_and_cc", false]], "get_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.get_fixed_rotation", false]], "get_flag_captions() (mmtbx.ions.atom_type_flags method)": [[293, "mmtbx.ions.atom_type_flags.get_flag_captions", false]], "get_fom_for_plot() (mmtbx.density_modification.dm_stats method)": [[285, "mmtbx.density_modification.dm_stats.get_fom_for_plot", false]], "get_footer() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_footer", false]], "get_forwards_reverse_helix() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_forwards_reverse_helix", false]], "get_fp() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_fp", false]], "get_fpp() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_fpp", false]], "get_frame_dictionary() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.get_frame_dictionary", false]], "get_frames_from_mysql() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.get_frames_from_mysql", false]], "get_func() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.get_func", false]], "get_general_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_general_count_and_fraction", false]], "get_gly_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_gly_count_and_fraction", false]], "get_glyco_link_atoms() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_glyco_link_atoms", false]], "get_goniometer() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_goniometer", false]], "get_grid_values() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_grid_values", false]], "get_group() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_group", false]], "get_hand() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_hand", false]], "get_hash_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_hash_indexer_for", false]], "get_hbond_proxies_iseqs() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_hbond_proxies_iseqs", false]], "get_header() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_header", false]], "get_helical_symmetry() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_helical_symmetry", false]], "get_helix_parameters() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_helix_parameters", false]], "get_helix_parameters() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_parameters", false]], "get_helix_theta() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_theta", false]], "get_helix_types() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.get_helix_types", false]], "get_helix_z_translation() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_helix_z_translation", false]], "get_high_resolution_and_residue_count_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_high_resolution_and_residue_count_for_structures", false]], "get_high_resolution_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_high_resolution_for_structures", false]], "get_highlighted_residues() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_highlighted_residues", false]], "get_histogram_colors() (mmtbx.polygon.output.color_model method)": [[311, "mmtbx.polygon.output.color_model.get_histogram_colors", false]], "get_hydrogen_names() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_hydrogen_names", false]], "get_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.get_ias_selection", false]], "get_ileval_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_ileval_count_and_fraction", false]], "get_index() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.get_index", false]], "get_indices_from_index() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.get_indices_from_index", false]], "get_info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_info", false]], "get_info_from_match_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_info_from_match_dict", false]], "get_initial_b_iso() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_initial_b_iso", false]], "get_initial_scale() (in module mmtbx.twinning.twin_f_model)": [[324, "mmtbx.twinning.twin_f_model.get_initial_scale", false]], "get_inverse_matrix() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.get_inverse_matrix", false]], "get_inverses() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_inverses", false]], "get_inverted_atoms() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_inverted_atoms", false]], "get_ions() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_ions", false]], "get_isomer() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.get_isomer", false]], "get_k_total() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.get_k_total", false]], "get_kappa_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_angle", false]], "get_kappa_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_axis", false]], "get_kin_lots() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_kin_lots", false]], "get_kriber_coseq_file() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.get_kriber_coseq_file", false]], "get_ksdssp_exe_path() (in module mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.get_ksdssp_exe_path", false]], "get_label_alt_id_atom() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_label_alt_id_atom", false]], "get_label_alt_id_iseq() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_label_alt_id_iseq", false]], "get_label_asym_id() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_label_asym_id", false]], "get_label_asym_id_iseq() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_label_asym_id_iseq", false]], "get_label_seq_id() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_label_seq_id", false]], "get_label_seq_id_iseq() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_label_seq_id_iseq", false]], "get_lib_link() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_lib_link", false]], "get_lib_link_peptide() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_lib_link_peptide", false]], "get_ligand_info_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_ligand_info_for_structures", false]], "get_line_segments() (mmtbx.polygon.output.polygon_layout method)": [[311, "mmtbx.polygon.output.polygon_layout.get_line_segments", false]], "get_linear_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_linear_indexer_for", false]], "get_link_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_carbon", false]], "get_link_carbon_on_distance() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_carbon_on_distance", false]], "get_link_oxygen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_oxygen", false]], "get_link_oxygen_on_distance() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_oxygen_on_distance", false]], "get_link_phi_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_link_phi_carbon", false]], "get_link_records() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.get_link_records", false]], "get_list_of_best_ncs_copy_map_correlation() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_list_of_best_ncs_copy_map_correlation", false]], "get_log_p_solc() (in module mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.get_log_p_solc", false]], "get_managers() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.get_managers", false]], "get_map() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.get_map", false]], "get_map() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.get_map", false]], "get_map() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map", false]], "get_map_coeff_labels() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_map_coeff_labels", false]], "get_map_coeffs_as_fp_phi() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_map_coeffs_as_fp_phi", false]], "get_map_coeffs_for_build() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_map_coeffs_for_build", false]], "get_map_counts() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_map_counts", false]], "get_map_data_by_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_map_data_by_id", false]], "get_map_gaussian_fit() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map_gaussian_fit", false]], "get_map_histograms() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_map_histograms", false]], "get_map_manager_by_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_map_manager_by_id", false]], "get_map_model_manager_with_selected() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_map_model_manager_with_selected", false]], "get_map_rmse() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_map_rmse", false]], "get_map_sphere_variance() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_map_sphere_variance", false]], "get_maps_from_fmodel() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.get_maps_from_fmodel", false]], "get_maps_from_fmodel() (mmtbx.maps.utils.fast_maps_from_hkl_file method)": [[305, "mmtbx.maps.utils.fast_maps_from_hkl_file.get_maps_from_fmodel", false]], "get_mask_as_map_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.get_mask_as_map_manager", false]], "get_master_phil() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.get_master_phil", false]], "get_master_phil() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.get_master_phil", false]], "get_master_phil() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_master_phil", false]], "get_master_phil() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.get_master_phil", false]], "get_master_phil() (in module mmtbx.validation.molprobity.mp_geo)": [[327, "mmtbx.validation.molprobity.mp_geo.get_master_phil", false]], "get_match_rmsd() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_match_rmsd", false]], "get_matching_atom_group() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_matching_atom_group", false]], "get_matching_atoms() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_matching_atoms", false]], "get_matthews_coeff() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.get_matthews_coeff", false]], "get_matthews_coeff() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.get_matthews_coeff", false]], "get_maximal_subgroup() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.get_maximal_subgroup", false]], "get_maximal_subgroup() (in module cctbx.examples.maximum_subgroups)": [[100, "cctbx.examples.maximum_subgroups.get_maximal_subgroup", false]], "get_mean_coordinate() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_mean_coordinate", false]], "get_mean_coordinate_for_alignment_range() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_mean_coordinate_for_alignment_range", false]], "get_mean_coordinate_for_alignment_ranges() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.get_mean_coordinate_for_alignment_ranges", false]], "get_mean_intensity() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.get_mean_intensity", false]], "get_mean_xyz() (in module mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.get_mean_xyz", false]], "get_merging_statistics() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_merging_statistics", false]], "get_metal_parameters() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_metal_parameters", false]], "get_min_fractional() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.get_min_fractional", false]], "get_min_max_table() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.get_min_max_table", false]], "get_missing_chains() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_missing_chains", false]], "get_mk2_sets() (in module cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.get_mk2_sets", false]], "get_mmtbx_icalc() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.get_mmtbx_icalc", false]], "get_mmtype_from_resname() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_mmtype_from_resname", false]], "get_model_by_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_model_by_id", false]], "get_model_from_other() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_model_from_other", false]], "get_model_map_stats() (in module mmtbx.building)": [[277, "mmtbx.building.get_model_map_stats", false]], "get_n_angle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_angle_proxies", false]], "get_n_bond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_bond_proxies", false]], "get_n_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_c_beta_torsion_proxies", false]], "get_n_chi_torsion_proixes() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_chi_torsion_proixes", false]], "get_n_den_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_den_proxies", false]], "get_n_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_emsley8k_proxies", false]], "get_n_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_emsley_proxies", false]], "get_n_hangle_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_hangle_proxies", false]], "get_n_hbond_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_hbond_proxies", false]], "get_n_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_oldfield_proxies", false]], "get_n_parallelity_bp_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_parallelity_bp_proxies", false]], "get_n_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_phi_psi_2_proxies", false]], "get_n_planarity_bp_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_planarity_bp_proxies", false]], "get_n_planarity_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_planarity_proxies", false]], "get_n_proxies() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_n_proxies", false]], "get_n_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_manager.get_n_proxies", false]], "get_n_ramachandran_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_ramachandran_proxies", false]], "get_n_real_for_grid_spacing() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.get_n_real_for_grid_spacing", false]], "get_n_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_reference_coordinate_proxies", false]], "get_n_reference_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_reference_dihedral_proxies", false]], "get_n_residues_of_classes() (iotbx.pdb.hierarchy.overall_counts method)": [[268, "iotbx.pdb.hierarchy.overall_counts.get_n_residues_of_classes", false]], "get_n_stacking_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_n_stacking_proxies", false]], "get_n_total_by_model() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_n_total_by_model", false]], "get_n_total_by_model() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_n_total_by_model", false]], "get_n_total_by_model() (mmtbx.validation.restraints.restraint_validation method)": [[326, "mmtbx.validation.restraints.restraint_validation.get_n_total_by_model", false]], "get_name() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_name", false]], "get_names() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[257, "dxtbx.model.goniometer.MultiAxisGoniometer.get_names", false]], "get_nconfs() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.get_nconfs", false]], "get_ncs_from_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_ncs_from_map", false]], "get_ncs_from_model() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_ncs_from_model", false]], "get_ncs_from_text() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_ncs_from_text", false]], "get_ncs_name() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_ncs_name", false]], "get_nearby_water_selection() (in module mmtbx.building)": [[277, "mmtbx.building.get_nearby_water_selection", false]], "get_new_fcalc_map() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.get_new_fcalc_map", false]], "get_new_group() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_new_group", false]], "get_next() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_next", false]], "get_non_hydrogen_atom_indices() (in module mmtbx.building)": [[277, "mmtbx.building.get_non_hydrogen_atom_indices", false]], "get_normalization_data_for_unit_binning() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_normalization_data_for_unit_binning", false]], "get_num_scan_points() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.get_num_scan_points", false]], "get_obs_from_mysql() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.get_obs_from_mysql", false]], "get_observations() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.get_observations", false]], "get_occupancy() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_occupancy", false]], "get_omega() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.get_omega", false]], "get_omega_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_omega_angle", false]], "get_omega_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.get_omega_atoms", false]], "get_omega_atoms() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_omega_atoms", false]], "get_omega_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_omega_axis", false]], "get_optimal_indexer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_optimal_indexer_for", false]], "get_optimization_grid() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_optimization_grid", false]], "get_order_dict() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_order_dict", false]], "get_original_cs() (mmtbx.utils.extract_box_around_model_and_map method)": [[325, "mmtbx.utils.extract_box_around_model_and_map.get_original_cs", false]], "get_original_cs() (mmtbx.utils.shift_origin method)": [[325, "mmtbx.utils.shift_origin.get_original_cs", false]], "get_outlier_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_outlier_count", false]], "get_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_outlier_percent", false]], "get_outlier_plot_values() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_outlier_plot_values", false]], "get_outlier_plot_values() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.get_outlier_plot_values", false]], "get_outliers() (mmtbx.validation.restraints.angles method)": [[326, "mmtbx.validation.restraints.angles.get_outliers", false]], "get_outliers() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_outliers", false]], "get_outliers() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.get_outliers", false]], "get_outliers() (mmtbx.validation.restraints.dihedrals method)": [[326, "mmtbx.validation.restraints.dihedrals.get_outliers", false]], "get_outliers() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_outliers", false]], "get_outliers() (mmtbx.validation.restraints.restraint_validation method)": [[326, "mmtbx.validation.restraints.restraint_validation.get_outliers", false]], "get_outliers_count_and_fraction() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_outliers_count_and_fraction", false]], "get_outliers_fraction_for_model() (mmtbx.validation.validation method)": 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"mmtbx.maps.composite_omit_map.run.get_p1_map_unscaled", false]], "get_parallelity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_parallelity_proxies_without_user_supplied", false]], "get_pdb_chains() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method)": [[325, "mmtbx.utils.fab_elbow_angle.fab_elbow_angle.get_pdb_chains", false]], "get_pdb_oxygen() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.get_pdb_oxygen", false]], "get_peptide_c_alpha_selection() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.get_peptide_c_alpha_selection", false]], "get_phi() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_phi", false]], "get_phi_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_phi_angle", false]], "get_phi_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[257, 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(mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.get_planes", false]], "get_planes() (mmtbx.monomer_library.cif_types.link_link_id method)": [[308, "mmtbx.monomer_library.cif_types.link_link_id.get_planes", false]], "get_planes() (mmtbx.monomer_library.cif_types.mod_mod_id method)": [[308, "mmtbx.monomer_library.cif_types.mod_mod_id.get_planes", false]], "get_plot_data() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_plot_data", false]], "get_plot_data() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_plot_data", false]], "get_plot_statistics() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.get_plot_statistics", false]], "get_plots() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_plots", false]], "get_point_in_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.get_point_in_plane", false]], "get_pointer_to_old_dv_id_dict() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_pointer_to_old_dv_id_dict", false]], "get_polygon_intersection() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.get_polygon_intersection", false]], "get_polygon_statistics() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.get_polygon_statistics", false]], "get_preliminary_ncs_groups() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.get_preliminary_ncs_groups", false]], "get_prepro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_prepro_count_and_fraction", false]], "get_previous_conformer() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.get_previous_conformer", false]], "get_processes() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.get_processes", false]], "get_program() (in module mmtbx.wwpdb.utils)": [[328, "mmtbx.wwpdb.utils.get_program", false]], "get_program_name() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.get_program_name", false]], "get_program_name() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.get_program_name", false]], "get_psi() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.get_psi", false]], "get_r_factor() (mmtbx.utils.guess_observation_type method)": [[325, "mmtbx.utils.guess_observation_type.get_r_factor", false]], "get_r_free_as_bool() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.get_r_free_as_bool", false]], "get_r_free_stats() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.get_r_free_stats", false]], "get_r_rfree_sigma() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.get_r_rfree_sigma", false]], "get_r_rfree_sigma() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.get_r_rfree_sigma", false]], "get_r_value_total() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.get_r_value_total", false]], "get_r_work_rfree_for_structures() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.get_r_work_rfree_for_structures", false]], "get_radii() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.get_radii", false]], "get_radius() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.get_radius", false]], "get_ranges() (mmtbx.validation.graphics.residue_binner method)": [[326, "mmtbx.validation.graphics.residue_binner.get_ranges", false]], "get_rdl_database() (in module mmtbx.conformation_dependent_library.rdl_database)": [[283, "mmtbx.conformation_dependent_library.rdl_database.get_rdl_database", false]], "get_real_space_plot_values() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_real_space_plot_values", false]], "get_real_space_plot_values() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.get_real_space_plot_values", false]], "get_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_reference_coordinate_proxies", false]], "get_refine_selection() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_refine_selection", false]], "get_reflection_file_server() (mmtbx.utils.process_command_line_args method)": [[325, "mmtbx.utils.process_command_line_args.get_reflection_file_server", false]], "get_reflection_info() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.get_reflection_info", false]], "get_relative_cc() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_relative_cc", false]], "get_relative_sequence_copy_number() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_relative_sequence_copy_number", false]], "get_relative_wilson() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.get_relative_wilson", false]], "get_res_range_after_key() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.get_res_range_after_key", false]], "get_residue_bonds() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.get_residue_bonds", false]], "get_residue_group_data() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.get_residue_group_data", false]], "get_residue_ids() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.get_residue_ids", false]], "get_residue_ids() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.get_residue_ids", false]], "get_residue_key() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.get_residue_key", false]], "get_residue_name_from_selection() (in module mmtbx.secondary_structure.utils)": [[319, "mmtbx.secondary_structure.utils.get_residue_name_from_selection", false]], "get_residue_names_and_classes() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.get_residue_names_and_classes", false]], "get_residue_names_and_classes() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.get_residue_names_and_classes", false]], "get_residue_names_padded() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.get_residue_names_padded", false]], "get_residue_names_padded() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.get_residue_names_padded", false]], "get_residue_ramachandran_data() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.get_residue_ramachandran_data", false]], "get_residue_range() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_residue_range", false]], "get_residue_rotamer_data() (in module mmtbx.rotamer.graphics)": [[316, "mmtbx.rotamer.graphics.get_residue_rotamer_data", false]], "get_resolution_at_point() (cctbx.miller.display.scene method)": [[149, "cctbx.miller.display.scene.get_resolution_at_point", false]], "get_resolution_where_significant_data_present() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.get_resolution_where_significant_data_present", false]], "get_restraint_values() (in module mmtbx.conformation_dependent_library)": [[283, "mmtbx.conformation_dependent_library.get_restraint_values", false]], "get_restraints_group() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_restraints_group", false]], "get_restraints_loading_flags() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.get_restraints_loading_flags", false]], "get_restraints_tg() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.get_restraints_tg", false]], "get_restraints_used() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.get_restraints_used", false]], "get_restraints_used() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.get_restraints_used", false]], "get_result_class() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_result_class", false]], "get_result_class() (mmtbx.validation.clashscore.clashscore method)": [[326, "mmtbx.validation.clashscore.clashscore.get_result_class", false]], "get_result_class() (mmtbx.validation.experimental.real_space method)": [[326, "mmtbx.validation.experimental.real_space.get_result_class", false]], "get_result_class() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_result_class", false]], "get_result_class() (mmtbx.validation.restraints.angles method)": [[326, "mmtbx.validation.restraints.angles.get_result_class", false]], "get_result_class() (mmtbx.validation.restraints.bonds method)": [[326, "mmtbx.validation.restraints.bonds.get_result_class", false]], "get_result_class() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.get_result_class", false]], "get_result_class() (mmtbx.validation.restraints.dihedrals method)": [[326, "mmtbx.validation.restraints.dihedrals.get_result_class", false]], "get_result_class() (mmtbx.validation.restraints.planarities method)": [[326, "mmtbx.validation.restraints.planarities.get_result_class", false]], "get_result_class() (mmtbx.validation.rna_validate.rna_angles method)": [[326, "mmtbx.validation.rna_validate.rna_angles.get_result_class", false]], "get_result_class() (mmtbx.validation.rna_validate.rna_bonds method)": [[326, "mmtbx.validation.rna_validate.rna_bonds.get_result_class", false]], "get_result_class() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.get_result_class", false]], "get_result_class() (mmtbx.validation.rotalyze.rotalyze method)": [[326, "mmtbx.validation.rotalyze.rotalyze.get_result_class", false]], "get_result_class() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.get_result_class", false]], "get_result_class() (mmtbx.validation.waters.waters method)": [[326, "mmtbx.validation.waters.waters.get_result_class", false]], "get_result_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_result_count", false]], "get_results() (libtbx.program_template.programtemplate method)": [[275, "libtbx.program_template.ProgramTemplate.get_results", false]], "get_results() (mmtbx.pdbtools.modify method)": [[310, "mmtbx.pdbtools.modify.get_results", false]], "get_results_as_pdb_json() (mmtbx.validation.molprobity.molprobitytemplate method)": [[327, "mmtbx.validation.molprobity.MolProbityTemplate.get_results_as_PDB_JSON", false]], "get_rhs() (in module iotbx.xds.read_ascii)": [[272, "iotbx.xds.read_ascii.get_rhs", false]], "get_ring_carbon() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_carbon", false]], "get_ring_oxygen() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_oxygen", false]], "get_ring_oxygen_substitute() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.get_ring_oxygen_substitute", false]], "get_rms_f_list() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_rms_f_list", false]], "get_rms_info() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.get_rms_info", false]], "get_rmsf_b_factor_per_residue_per_atom() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_rmsf_B_factor_per_residue_per_atom", false]], "get_rna_backbone_dihedrals() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_rna_backbone_dihedrals", false]], "get_rna_pucker_ref() (mmtbx.validation.rna_validate.rna_pucker_ref method)": [[326, "mmtbx.validation.rna_validate.rna_pucker_ref.get_rna_pucker_ref", false]], "get_rot_y() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_rot_y", false]], "get_rot_z() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.get_rot_z", false]], "get_rotamer_angles() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamer_angles", false]], "get_rotamer_expectation_frequencies() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamer_expectation_frequencies", false]], "get_rotamer_iterator() (in module mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.get_rotamer_iterator", false]], "get_rotamer_iterator() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.get_rotamer_iterator", false]], "get_rotamers() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.get_rotamers", false]], "get_rotarama_data() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_rotarama_data", false]], "get_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.get_rotation_axis", false]], "get_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.get_rotation_axis_datum", false]], "get_rows() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.get_rows", false]], "get_scale_factor() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.get_scale_factor", false]], "get_scale_factor() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.get_scale_factor", false]], "get_scale_factor() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.get_scale_factor", false]], "get_scan() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_scan", false]], "get_scan_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[257, "dxtbx.model.goniometer.KappaGoniometer.get_scan_axis", false]], "get_scan_axis() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[257, "dxtbx.model.goniometer.MultiAxisGoniometer.get_scan_axis", false]], "get_segid_as_chainid() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.get_segid_as_chainid", false]], "get_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.get_segments", false]], "get_selected() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.get_selected", false]], "get_selected_hierarchys() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_selected_hierarchys", false]], "get_selected_sites() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.get_selected_sites", false]], "get_selection_inside_box() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_selection_inside_box", false]], "get_selection_string_from_chain_dict() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.get_selection_string_from_chain_dict", false]], "get_selection_strings() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.get_selection_strings", false]], "get_selection_to_sites_map() (in module mmtbx.geometry_restraints.reference)": [[290, "mmtbx.geometry_restraints.reference.get_selection_to_sites_map", false]], "get_selections_and_boxes_to_split_model() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_selections_and_boxes_to_split_model", false]], "get_selections_for_segments() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_selections_for_segments", false]], "get_selections_from_boxes() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_selections_from_boxes", false]], "get_sequence_n_copies() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_sequence_n_copies", false]], "get_sequence_n_copies_from_files() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.get_sequence_n_copies_from_files", false]], "get_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.get_setting_rotation", false]], "get_setting_rotation_at_scan_point() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_point", false]], "get_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_points", false]], "get_shifted_cs() (mmtbx.utils.extract_box_around_model_and_map method)": [[325, "mmtbx.utils.extract_box_around_model_and_map.get_shifted_cs", false]], "get_shifts() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.get_shifts", false]], "get_simple_bonds() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.get_simple_bonds", false]], "get_single_atom_selection_string() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.get_single_atom_selection_string", false]], "get_sites_cart_from_index() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.get_sites_cart_from_index", false]], "get_sites_carts() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.get_sites_carts", false]], "get_sites_cc() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.get_sites_cc", false]], "get_skip_waters_and_hetero_lines() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_skip_waters_and_hetero_lines", false]], "get_smiles() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_smiles", false]], "get_solvent_content() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.get_solvent_content", false]], "get_solvent_content() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.get_solvent_content", false]], "get_solvent_content() (mmtbx.utils.extract_box_around_model_and_map method)": [[325, "mmtbx.utils.extract_box_around_model_and_map.get_solvent_content", false]], "get_space_group_info() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_space_group_info", false]], "get_space_groups_compatible_with_likely_point_group() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.get_space_groups_compatible_with_likely_point_group", false]], "get_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.get_spectrum", false]], "get_sphere_selection() (in module mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.get_sphere_selection", false]], "get_split_maps_and_models() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_split_maps_and_models", false]], "get_statistics_for_phenix_gui() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.get_statistics_for_phenix_gui", false]], "get_statistics_percentiles() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.get_statistics_percentiles", false]], "get_stats() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.get_stats", false]], "get_stats_and_histogram_data() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.get_stats_and_histogram_data", false]], "get_strict_valence_flag() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.get_strict_valence_flag", false]], "get_struct_conn_mmcif() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_struct_conn_mmcif", false]], "get_sugar_xyz_mean() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.get_sugar_xyz_mean", false]], "get_symops_from_supergroup_that_are_not_in_subgroup() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)": [[181, "cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations.get_symops_from_supergroup_that_are_not_in_subgroup", false]], "get_table() (in module cctbx.eltbx.attenuation_coefficient)": [[47, "cctbx.eltbx.attenuation_coefficient.get_table", false]], "get_table_data() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.get_table_data", false]], "get_target_value() (mmtbx.refinement.real_space.fit_residue.run method)": [[315, "mmtbx.refinement.real_space.fit_residue.run.get_target_value", false]], "get_template() (dxtbx.serialize.xds.to_xds method)": [[258, "dxtbx.serialize.xds.to_xds.get_template", false]], "get_test_space_group_symbols() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.get_test_space_group_symbols", false]], "get_tg() (mmtbx.refinement.group.group_minimizer method)": [[313, "mmtbx.refinement.group.group_minimizer.get_tg", false]], "get_theta_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_theta_along_z", false]], "get_tile_center() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_center", false]], "get_tile_coords() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_coords", false]], "get_tile_id() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.get_tile_id", false]], "get_times() (in module cctbx.development.direct_or_fft)": [[35, "cctbx.development.direct_or_fft.get_times", false]], "get_tlso_group_info_from_model() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_tlso_group_info_from_model", false]], "get_tlso_resid() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_tlso_resid", false]], "get_trans_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.get_trans_along_z", false]], "get_trans_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method)": [[326, "mmtbx.validation.ramalyze.ramalyze.get_trans_pro_count_and_fraction", false]], "get_transformation() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method)": [[325, "mmtbx.utils.fab_elbow_angle.fab_elbow_angle.get_transformation", false]], "get_transformed_model2() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.get_transformed_model2", false]], "get_twin_laws() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.get_twin_laws", false]], "get_type() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.get_type", false]], "get_type_conditions() (in module cctbx.uctbx.gruber_1973_table_1)": [[201, "cctbx.uctbx.gruber_1973_table_1.get_type_conditions", false]], "get_typed_field() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.get_typed_field", false]], "get_u_cart() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.get_u_cart", false]], "get_unique_altloc() (in module mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.get_unique_altloc", false]], "get_unique_altloc2() (in module mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.get_unique_altloc2", false]], "get_unit_cell() (cctbx.web.emma.web_to_models method)": [[218, "cctbx.web.emma.web_to_models.get_unit_cell", false]], "get_unknown_atoms() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.get_unknown_atoms", false]], "get_user_supplied_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.get_user_supplied_restraints", false]], "get_valence() (mmtbx.ions.environment.chemicalenvironment method)": [[295, "mmtbx.ions.environment.ChemicalEnvironment.get_valence", false]], "get_valence_params() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.get_valence_params", false]], "get_vector_flat() (mmtbx.refinement.real_space.cluster method)": [[315, "mmtbx.refinement.real_space.cluster.get_vector_flat", false]], "get_volume() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.get_volume", false]], "get_voxelizer_for() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.get_voxelizer_for", false]], "get_weight() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.get_weight", false]], "get_weighted_outlier_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_outlier_count", false]], "get_weighted_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_outlier_percent", false]], "get_weighted_result_count() (mmtbx.validation.cbetadev.cbetadev method)": [[326, "mmtbx.validation.cbetadev.cbetadev.get_weighted_result_count", false]], "get_weights_for_unit_binning() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.get_weights_for_unit_binning", false]], "get_wildcard_string() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.get_wildcard_string", false]], "get_wildcard_strings() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.get_wildcard_strings", false]], "get_window_around_residue() (in module mmtbx.building)": [[277, "mmtbx.building.get_window_around_residue", false]], "get_xray_structure() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.get_xray_structure", false]], "get_y_limits() (mmtbx.validation.molprobity.multi_criterion_view method)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.get_y_limits", false]], "get_z_scores() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.get_z_scores", false]], "getconfig() (xfel.command_line.convert_gain_map.fake_env method)": [[341, "xfel.command_line.convert_gain_map.fake_env.getConfig", false]], "getcspadquads() (xfel.command_line.convert_gain_map.fake_evt method)": [[341, "xfel.command_line.convert_gain_map.fake_evt.getCsPadQuads", false]], "getoptbool() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptBool", false]], "getoptevalorstring() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptEvalOrString", false]], "getoptfloat() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptFloat", false]], "getoptinteger() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptInteger", false]], "getoptroi() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptROI", false]], "getoptstring() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptString", false]], "getoptstrings() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.getOptStrings", false]], "getsize() (cctbx.command_line.precession_view.render_pil method)": [[15, "cctbx.command_line.precession_view.render_pil.GetSize", false]], "getsize() (cctbx.command_line.precession_view.render_postscript method)": [[15, "cctbx.command_line.precession_view.render_postscript.GetSize", false]], "getsize() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.GetSize", false]], "gettime() (xfel.command_line.convert_gain_map.fake_evt method)": [[341, "xfel.command_line.convert_gain_map.fake_evt.getTime", false]], "glyco_link_class (class in mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class", false]], "goniometer (class in dxtbx.model.goniometer)": [[257, "dxtbx.model.goniometer.Goniometer", false]], "goniometerfactory (class in dxtbx.model.goniometer)": [[257, "dxtbx.model.goniometer.GoniometerFactory", false]], "good_atoms_selection() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.good_atoms_selection", false]], "grad_occ() (mmtbx.utils.experimental_data_target_and_gradients method)": [[325, "mmtbx.utils.experimental_data_target_and_gradients.grad_occ", false]], "grad_sites_cart() (mmtbx.utils.experimental_data_target_and_gradients method)": [[325, "mmtbx.utils.experimental_data_target_and_gradients.grad_sites_cart", false]], "gradient() (cctbx.xray.minimization.occupancy_penalty_exp method)": [[234, "cctbx.xray.minimization.occupancy_penalty_exp.gradient", false]], "gradient_flags (class in cctbx.xray.structure_factors.gradient_flags)": [[245, "cctbx.xray.structure_factors.gradient_flags.gradient_flags", false]], "gradient_threshold (scitbx.lstbx.normal_eqns_solving.iterations attribute)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations.gradient_threshold", false]], "gradients (class in cctbx.examples.g_exp_i_alpha_derivatives)": [[91, "cctbx.examples.g_exp_i_alpha_derivatives.gradients", false]], "gradients (class in cctbx.examples.structure_factor_derivatives)": [[119, "cctbx.examples.structure_factor_derivatives.gradients", false]], "gradients (class in cctbx.examples.structure_factor_derivatives_2)": [[120, "cctbx.examples.structure_factor_derivatives_2.gradients", false]], "gradients (class in cctbx.examples.structure_factor_derivatives_3)": [[121, "cctbx.examples.structure_factor_derivatives_3.gradients", false]], "gradients (class in cctbx.xray.structure_factors.gradients)": [[246, "cctbx.xray.structure_factors.gradients.gradients", false]], "gradients() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.gradients", false]], "gradients() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.gradients", false]], "gradients() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.gradients", false]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints.gradients", false]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple.gradients", false]], "gradients() (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space method)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space.gradients", false]], "gradients() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.gradients", false]], "gradients_base (class in cctbx.xray.structure_factors.gradients_base)": [[247, "cctbx.xray.structure_factors.gradients_base.gradients_base", false]], "gradients_calculator() (mmtbx.dynamics.simulated_annealing.run method)": [[287, "mmtbx.dynamics.simulated_annealing.run.gradients_calculator", false]], "gradients_calculator_geometry_restraints (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints", false]], "gradients_calculator_real_space_simple (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple", false]], "gradients_calculator_reciprocal_space (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space", false]], "gradients_direct (class in cctbx.xray.structure_factors.gradients_direct)": [[248, "cctbx.xray.structure_factors.gradients_direct.gradients_direct", false]], "gradients_fft (class in cctbx.xray.structure_factors.gradients_fft)": [[249, "cctbx.xray.structure_factors.gradients_fft.gradients_fft", false]], "gradients_work() (cctbx.xray.targets.r1.target method)": [[254, "cctbx.xray.targets.r1.target.gradients_work", false]], "gradients_work() (cctbx.xray.targets.shelxl_wght_ls method)": [[253, "cctbx.xray.targets.shelxl_wght_ls.gradients_work", false]], "gradients_wrt_atomic_parameters() (mmtbx.refinement.targets.target_result_mixin method)": [[313, "mmtbx.refinement.targets.target_result_mixin.gradients_wrt_atomic_parameters", false]], "gradients_wrt_par() (mmtbx.refinement.group.target_and_grads method)": [[313, "mmtbx.refinement.group.target_and_grads.gradients_wrt_par", false]], "gradients_wrt_r() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.gradients_wrt_r", false]], "gradients_wrt_t() (mmtbx.refinement.rigid_body.target_and_grads method)": [[313, "mmtbx.refinement.rigid_body.target_and_grads.gradients_wrt_t", false]], "grads (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.grads", false]], "grads_and_curvs_target_simple() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.grads_and_curvs_target_simple", false]], "grads_asu_to_one_ncs() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.grads_asu_to_one_ncs", false]], "grads_one_ncs_to_asu() (in module mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.grads_one_ncs_to_asu", false]], "graphviz_pg_graph() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method)": [[181, "cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg.graphviz_pg_graph", false]], "grayscale_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.grayscale_color_model", false]], "greedymatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.GreedyMatch", false]], "grid (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.grid", false]], "grid (xfel.mono_simulation.mono_treatment.refinement attribute)": [[349, "xfel.mono_simulation.mono_treatment.refinement.grid", false]], "grid (xfel.mono_simulation.mono_treatment.refinement2 attribute)": [[349, "xfel.mono_simulation.mono_treatment.refinement2.grid", false]], "grid_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.grid_asu", false]], "grid_max() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.grid_max", false]], "grid_resolution_factor (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.grid_resolution_factor", false]], "grid_resolution_factor() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.grid_resolution_factor", false]], "grid_sample_around_c_n_axis() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization.grid_sample_around_c_n_axis", false]], "grid_units_to_cart() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.grid_units_to_cart", false]], "gridding() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.gridding", false]], "group() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.group", false]], "group() (mmtbx.geometry.clash.spheremodelgroup method)": [[289, "mmtbx.geometry.clash.SphereModelGroup.group", false]], "group_args (class in libtbx)": [[273, "libtbx.group_args", false]], "group_chains_and_sequences() (in module mmtbx.validation.sequence)": [[326, "mmtbx.validation.sequence.group_chains_and_sequences", false]], "group_files (class in iotbx.file_reader)": [[265, "iotbx.file_reader.group_files", false]], "group_minimizer (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.group_minimizer", false]], "group_occupancy_grads() (mmtbx.utils.experimental_data_target_and_gradients method)": [[325, "mmtbx.utils.experimental_data_target_and_gradients.group_occupancy_grads", false]], "group_operators (class in mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.group_operators", false]], "group_planes() (in module mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.group_planes", false]], "groups_parent_setting() (cctbx.sgtbx.subgroups.subgroups method)": [[187, "cctbx.sgtbx.subgroups.subgroups.groups_parent_setting", false]], "groups_primitive_setting() (cctbx.sgtbx.subgroups.subgroups method)": [[187, "cctbx.sgtbx.subgroups.subgroups.groups_primitive_setting", false]], "gruber_parameterization (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization", false]], "guess_b_iso_real() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.guess_b_iso_real", false]], "guess_chemical_elements() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.guess_chemical_elements", false]], "guess_file_type() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.guess_file_type", false]], "guess_molecular_weight() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.guess_molecular_weight", false]], "guess_observation_type (class in mmtbx.utils)": [[325, "mmtbx.utils.guess_observation_type", false]], "guess_scattering_type_is_a_mixture_of_xray_and_neutron() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.guess_scattering_type_is_a_mixture_of_xray_and_neutron", false]], "guess_scattering_type_neutron() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.guess_scattering_type_neutron", false]], "guesstimate() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.guesstimate", false]], "guesstimate_mod_hkl() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method)": [[318, "mmtbx.scaling.twin_analyses.detect_pseudo_translations.guesstimate_mod_hkl", false]], "gui_formats (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.gui_formats", false]], "gui_formats (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.gui_formats", false]], "gui_formats (mmtbx.validation.clashscore.nqh_flips attribute)": [[326, "mmtbx.validation.clashscore.nqh_flips.gui_formats", false]], "gui_formats (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.gui_formats", false]], "gui_formats (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.gui_formats", false]], "gui_formats (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.gui_formats", false]], "gui_formats (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.gui_formats", false]], "gui_formats (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.gui_formats", false]], "gui_formats (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.gui_formats", false]], "gui_formats (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.gui_formats", false]], "gui_formats (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.gui_formats", false]], "gui_formats (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.gui_formats", false]], "gui_formats (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.gui_formats", false]], "gui_formats (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.gui_formats", false]], "gui_formats (mmtbx.validation.validation attribute)": [[326, "mmtbx.validation.validation.gui_formats", false]], "gui_list_headers (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.gui_list_headers", false]], "gui_list_headers (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.gui_list_headers", false]], "gui_list_headers (mmtbx.validation.clashscore.nqh_flips attribute)": [[326, "mmtbx.validation.clashscore.nqh_flips.gui_list_headers", false]], "gui_list_headers (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.gui_list_headers", false]], "gui_list_headers (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.gui_list_headers", false]], "gui_list_headers (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.gui_list_headers", false]], "gui_list_headers 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"mmtbx.validation.rotalyze.has_heavy_atoms", false]], "has_higher_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_higher_symmetry", false]], "has_icodes() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.has_icodes", false]], "has_pseudo_translational_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_pseudo_translational_symmetry", false]], "has_siguij() (iotbx.pdb.hierarchy.atom static method)": [[268, "iotbx.pdb.hierarchy.atom.has_siguij", false]], "has_twinning() (cctbx.miller.array method)": [[148, "cctbx.miller.array.has_twinning", false]], "has_twinning() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.has_twinning", false]], "hash() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.hash", false]], "hash_indexer_for() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.hash_indexer_for", false]], "have_bad_sigmas() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_bad_sigmas", false]], "have_close_contacts() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_close_contacts", false]], "have_conformers() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.have_conformers", false]], "have_duplicates() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.have_duplicates", false]], "have_good_timing_estimates() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.have_good_timing_estimates", false]], "have_redundant_data() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_redundant_data", false]], "have_shelxl_compatible_scattering_types() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_shelxl_compatible_scattering_types", false]], "have_suitable_hetero_distance() (in module cctbx.development.random_structure)": [[40, "cctbx.development.random_structure.have_suitable_hetero_distance", false]], "have_sym (cctbx.crystal.show_distances attribute)": [[23, "cctbx.crystal.show_distances.have_sym", false]], "have_sys_absent() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_sys_absent", false]], "have_zero_occupancies() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.have_zero_occupancies", false]], "hd_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.hd_selection", false]], "hdf5pack() 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method)": [[326, "mmtbx.validation.restraints.planarity.header", false]], "header() (mmtbx.validation.restraints.restraint static method)": [[326, "mmtbx.validation.restraints.restraint.header", false]], "header() (mmtbx.validation.rna_validate.rna_angle static method)": [[326, "mmtbx.validation.rna_validate.rna_angle.header", false]], "header() (mmtbx.validation.rna_validate.rna_bond static method)": [[326, "mmtbx.validation.rna_validate.rna_bond.header", false]], "header() (mmtbx.validation.rna_validate.rna_pucker static method)": [[326, "mmtbx.validation.rna_validate.rna_pucker.header", false]], "header() (mmtbx.validation.rotalyze.rotamer static method)": [[326, "mmtbx.validation.rotalyze.rotamer.header", false]], "header() (mmtbx.validation.waters.water static method)": [[326, "mmtbx.validation.waters.water.header", false]], "header_info (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.header_info", false]], "heights() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.heights", false]], "helix_rt_forwards() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.helix_rt_forwards", false]], "helix_rt_reverse() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.helix_rt_reverse", false]], "helix_selection() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.helix_selection", false]], "helix_selections() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.helix_selections", false]], "hemisphere_acentrics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hemisphere_acentrics", false]], "hemispheres_acentrics() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hemispheres_acentrics", false]], "hendrickson_lattman() (in module cctbx)": [[1, "cctbx.hendrickson_lattman", false]], "hermann_mauguin() (cctbx.web.asu_gallery.jv_index.point_group_symbols method)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols.hermann_mauguin", false]], "hessian() (cctbx.examples.unit_cell_minimizers.refinery method)": [[126, "cctbx.examples.unit_cell_minimizers.refinery.hessian", false]], "hessian() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.hessian", false]], "hessian() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.hessian", false]], "hessian_transform() (mmtbx.scaling.relative_scaling.refinery method)": [[318, "mmtbx.scaling.relative_scaling.refinery.hessian_transform", false]], "hessians_work() (cctbx.xray.targets.r1.target method)": [[254, "cctbx.xray.targets.r1.target.hessians_work", false]], "hessians_work() (cctbx.xray.targets.shelxl_wght_ls method)": [[253, "cctbx.xray.targets.shelxl_wght_ls.hessians_work", false]], "hetero (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.hetero", false]], "heterogen_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.heterogen_section", false]], "heterogen_section() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.heterogen_section", false]], "hexagonal_sampling() (in module cctbx.crystal.close_packing)": [[25, "cctbx.crystal.close_packing.hexagonal_sampling", false]], "hg_two_loop_recursion() (in module cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.hg_two_loop_recursion", false]], "hide_points() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.hide_points", false]], "hierarchy() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.hierarchy", false]], "high_2fofc (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_2FOFC", false]], "high_anom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_anom", false]], "high_b (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_B", false]], "high_b_iso (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_b_iso", false]], "high_fdp (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_fdp", false]], "high_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_fofc", false]], "high_occ (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_occ", false]], "high_occ (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.HIGH_OCC", false]], "high_resolution_for_twin_tests() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.high_resolution_for_twin_tests", false]], "high_two_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.high_two_fofc", false]], "hist_outline() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.hist_outline", false]], "histogram() (mmtbx.density_modification.local_standard_deviation_map method)": [[285, "mmtbx.density_modification.local_standard_deviation_map.histogram", false]], "histogram_finalise (class in xfel.cxi.cspad_ana.histogram_finalise)": [[343, "xfel.cxi.cspad_ana.histogram_finalise.histogram_finalise", false]], "histogram_layout (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.histogram_layout", false]], "histogram_slot_info (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.histogram_slot_info", false]], "histograms() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.histograms", false]], "hklf() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.HKLF", false]], "hl_coeffs (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.hl_coeffs", false]], "hl_coeffs() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.hl_coeffs", false]], "hl_coeffs_in_original_setting (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.hl_coeffs_in_original_setting", false]], "hn() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Hn", false]], "hoppe_gassmann_modification() (cctbx.miller.array method)": [[148, "cctbx.miller.array.hoppe_gassmann_modification", false]], "hsv2rgb() (in module mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.hsv2rgb", false]], "html_head_title() (in module cctbx.web.asu_gallery)": [[206, "cctbx.web.asu_gallery.html_head_title", false]], "html_loader() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.html_loader", false]], "hw() (in module cctbx.maptbx.mem)": [[140, "cctbx.maptbx.mem.Hw", false]], "hydrogen_bond_from_selection_pair() (in module mmtbx.secondary_structure.utils)": [[319, "mmtbx.secondary_structure.utils.hydrogen_bond_from_selection_pair", false]], "hydrogen_deuterium_aliases() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.hydrogen_deuterium_aliases", false]], "hydrogens (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.hydrogens", false]], "i_atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.i_atom_by_id", false]], "i_conformer (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.i_conformer", false]], "i_inv_j_multiplication_table (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.i_inv_j_multiplication_table", false]], "i_j_inv_multiplication_table (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.i_j_inv_multiplication_table", false]], "i_j_multiplication_table (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.i_j_multiplication_table", false]], "i_mod (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.i_mod", false]], "i_over_sig_i() (cctbx.miller.array method)": [[148, "cctbx.miller.array.i_over_sig_i", false]], "i_over_sigma_outer_shell (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.i_over_sigma_outer_shell", false]], "i_over_sigma_outer_shell() (mmtbx.scaling.data_statistics.data_strength_and_completeness method)": [[318, "mmtbx.scaling.data_statistics.data_strength_and_completeness.i_over_sigma_outer_shell", false]], "i_seq (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.i_seq", false]], "i_seq (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.i_seq", false]], "i_seq (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id3", false], [299, "mmtbx.ions.svm.svm_prediction.i_seq", false]], "i_seq (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.i_seq", false]], "i_seqs() (cctbx.crystal.sym_pair method)": [[23, "cctbx.crystal.sym_pair.i_seqs", false]], "i_seqs_by_value() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.i_seqs_by_value", false]], "i_seqs_from_atoms() (iotbx.shelx.parsers.restraint_parser method)": [[271, "iotbx.shelx.parsers.restraint_parser.i_seqs_from_atoms", false]], "i_sigi_completeness_stats (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.i_sigi_completeness_stats", false]], "i_vars (cctbx.sgtbx.special_op_simplified_term attribute)": [[165, "cctbx.sgtbx.special_op_simplified_term.i_vars", false]], "ias (class in mmtbx.ias)": [[292, "mmtbx.ias.ias", false]], "ias_counters (class in mmtbx.ias)": [[292, "mmtbx.ias.ias_counters", false]], "ias_position_at_lone_pairs() (in module mmtbx.ias)": [[292, "mmtbx.ias.ias_position_at_lone_pairs", false]], "ias_site_position() (in module mmtbx.ias)": [[292, "mmtbx.ias.ias_site_position", false]], "iass_as_xray_structure() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.iass_as_xray_structure", false]], "ice_ring_checker (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.ice_ring_checker", false]], "icode (iotbx.pdb.hierarchy.atom_with_labels property)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.icode", false]], "icode (iotbx.pdb.hierarchy.residue property)": [[268, "iotbx.pdb.hierarchy.residue.icode", false]], "icode (iotbx.pdb.hierarchy.residue_group property)": [[268, "iotbx.pdb.hierarchy.residue_group.icode", false]], "icode (mmtbx.disorder.analyze_model.residue_group_proxy attribute)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.icode", false]], "icode (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.icode", false]], "icode (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.icode", false]], "icode (mmtbx.validation.atom_info attribute)": [[326, "mmtbx.validation.atom_info.icode", false]], "icode (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.icode", false]], "icode (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.icode", false]], "icode (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.icode", false]], "icode (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.icode", false]], "icode (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.icode", false]], "icode (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.icode", false]], "icode (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.icode", false]], "icode (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.icode", false]], "icode (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.icode", false]], "icode (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.icode", false]], "icode (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.icode", false]], "icode (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.icode", false]], "icode (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.icode", false]], "icode (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.icode", false]], "icode (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.icode", false]], "id (iotbx.pdb.hierarchy.chain property)": [[268, "iotbx.pdb.hierarchy.chain.id", false]], "id (iotbx.pdb.hierarchy.model property)": [[268, "iotbx.pdb.hierarchy.model.id", false]], "id() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.id", false]], "id() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.id", false]], "id() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.id", false]], "id() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.id", false]], "id() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.id", false]], "id() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.id", false]], "id() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.id", false]], "id() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.id", false]], "id() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.id", false]], "id() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.id", false]], "id() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.id", false]], "id() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.id", false]], "id_dict (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.id_dict", false]], "id_str (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.id_str", false]], "id_str (mmtbx.validation.ligands.ligand_validation attribute)": [[326, "mmtbx.validation.ligands.ligand_validation.id_str", false]], "id_str (mmtbx.validation.ramalyze.c_alpha attribute)": [[326, "mmtbx.validation.ramalyze.c_alpha.id_str", false]], "id_str() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.id_str", false]], "id_str() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.id_str", false]], "id_str() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.id_str", false]], "id_str() (iotbx.pdb.hierarchy.residue method)": [[268, "iotbx.pdb.hierarchy.residue.id_str", false]], "id_str() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.id_str", false]], "id_str() (mmtbx.disorder.analyze_model.residue_group_proxy method)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy.id_str", false]], "id_str() (mmtbx.ions.environment.atom_contact method)": [[295, "mmtbx.ions.environment.atom_contact.id_str", false]], "id_str() (mmtbx.validation.atom_base method)": [[326, "mmtbx.validation.atom_base.id_str", false]], "id_str() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str", false]], "id_str() (mmtbx.validation.clashscore.nqh_flip method)": [[326, "mmtbx.validation.clashscore.nqh_flip.id_str", false]], "id_str() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.id_str", false]], "id_str() (mmtbx.validation.model_properties.atom_occupancy method)": [[326, "mmtbx.validation.model_properties.atom_occupancy.id_str", false]], "id_str() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.id_str", false]], "id_str() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.id_str", false]], "id_str() (mmtbx.validation.rna_validate.rna_angle method)": [[326, "mmtbx.validation.rna_validate.rna_angle.id_str", false]], "id_str() (mmtbx.validation.rna_validate.rna_bond method)": [[326, "mmtbx.validation.rna_validate.rna_bond.id_str", false]], "id_str() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.id_str", false]], "id_str_no_atom_name() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str_no_atom_name", false]], "id_str_old() (mmtbx.validation.ramalyze.ramachandran method)": [[326, "mmtbx.validation.ramalyze.ramachandran.id_str_old", false]], "id_str_old() (mmtbx.validation.rotalyze.rotamer method)": [[326, "mmtbx.validation.rotalyze.rotamer.id_str_old", false]], "id_str_src_atom_no_atom_name() (mmtbx.validation.clashscore.clash method)": [[326, "mmtbx.validation.clashscore.clash.id_str_src_atom_no_atom_name", false]], "ideal (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute)": [[326, "mmtbx.validation.cbetadev.calculate_ideal_and_deviation.ideal", false]], "ideal_xyz (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.ideal_xyz", false]], "idealized_calpha_angles() (in module mmtbx.validation.cbetadev)": [[326, "mmtbx.validation.cbetadev.idealized_calpha_angles", false]], "identifier() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.identifier", false]], "identify() (mmtbx.rotamer.rotamer_eval.rotamerid method)": [[316, "mmtbx.rotamer.rotamer_eval.RotamerID.identify", false]], "identity (class in scitbx.matrix)": [[334, "scitbx.matrix.identity", false]], "identity (mmtbx.building.make_library.related_chain attribute)": [[277, "mmtbx.building.make_library.related_chain.identity", false]], "identity() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.identity", false]], "identity() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.identity", false]], "identity_op_id() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.identity_op_id", false]], "identity_op_id_in_first_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.identity_op_id_in_first_group", false]], "identity_predicate (class in mmtbx.geometry.indexing)": [[289, "mmtbx.geometry.indexing.identity_predicate", false]], "identity_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.identity_predicate", false]], "ignore_hd (mmtbx.validation.model_properties.model_statistics attribute)": [[326, "mmtbx.validation.model_properties.model_statistics.ignore_hd", false]], "ignored_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.ignored_atoms", false]], "ignored_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.ignored_atoms", false]], "image() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image", false]], "image() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.image", false]], "image_from_3d() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image_from_3d", false]], "image_from_miller_indices() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.image_from_miller_indices", false]], "image_template() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.image_template", false]], "image_xpp() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.image_xpp", false]], "imagefactory() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.ImageFactory", false]], "imagefactory() (in module xfel.cxi.display_spots)": [[342, "xfel.cxi.display_spots.ImageFactory", false]], "imageset() (in module dxtbx.serialize.load)": [[258, "dxtbx.serialize.load.imageset", false]], "img_add() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.img_add", false]], "imgcif() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.imgCIF", false]], "imgcif() (dxtbx.model.detector.detectorfactory static method)": [[257, "dxtbx.model.detector.DetectorFactory.imgCIF", false]], "imgcif() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.imgCIF", false]], "imgcif() (dxtbx.model.scan.scanfactory static method)": [[257, "dxtbx.model.scan.ScanFactory.imgCIF", false]], "imgcif_h() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.detector.detectorfactory static method)": [[257, "dxtbx.model.detector.DetectorFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.scan.scanfactory static method)": [[257, "dxtbx.model.scan.ScanFactory.imgCIF_H", false]], "import_eq_distances() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.import_eq_distances", false]], "import_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.import_ncs_group", false]], "improper_cnab_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.improper_cnab_from_atoms", false]], "improper_ncab_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.improper_ncab_from_atoms", false]], "in_which_cuts() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.in_which_cuts", false]], "incident_beam (xfel.metrology.mark0.correction_vectors attribute)": [[347, "xfel.metrology.mark0.correction_vectors.INCIDENT_BEAM", false]], "include() (mmtbx.geometry.indexing.containment_predicate static method)": [[289, "mmtbx.geometry.indexing.containment_predicate.include", false]], "include_predicate() (mmtbx.geometry.indexing.structure_indexer class method)": [[289, "mmtbx.geometry.indexing.structure_indexer.include_predicate", false]], "inclusion() (mmtbx.geometry.indexing.containment_predicate class method)": [[289, "mmtbx.geometry.indexing.containment_predicate.inclusion", false]], "inclusive (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.inclusive", false]], "incomplete (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.incomplete", false]], "incomplete (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.incomplete", false]], "incomplete_info (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.incomplete_info", false]], "incomplete_info (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.incomplete_info", false]], "increment_and_track_up_from_zero() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.increment_and_track_up_from_zero", false]], "increment_category_counts() (mmtbx.validation.restraints.chiralities method)": [[326, "mmtbx.validation.restraints.chiralities.increment_category_counts", false]], "incremental_clustering (class in cctbx.crystal)": [[23, "cctbx.crystal.incremental_clustering", false]], "incremental_fits() (in module cctbx.eltbx.gaussian_fit)": [[68, "cctbx.eltbx.gaussian_fit.incremental_fits", false]], "incremental_pairs() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.incremental_pairs", false]], "index() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.index", false]], "index1d() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.index1d", false]], "index_span() (cctbx.miller.set method)": [[148, "cctbx.miller.set.index_span", false]], "indexer (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Indexer", false]], "indices (scitbx.array_family.flex.smart_selection property)": [[331, "scitbx.array_family.flex.smart_selection.indices", false]], "indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.indices", false]], "inflate() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.inflate", false]], "info (iotbx.pdb.hierarchy.root property)": [[268, "iotbx.pdb.hierarchy.root.info", false]], "info (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.info", false]], "info() (cctbx.miller.array method)": [[148, "cctbx.miller.array.info", false]], "info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.info", false]], "info() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.info", false]], "init_calc_wilson() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.init_calc_wilson", false]], "init_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.init_ncs_group", false]], "init_oper() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.init_oper", false]], "init_slots_with_none() (cctbx.omz.cif_refine.extract_from_cif_files method)": [[155, "cctbx.omz.cif_refine.extract_from_cif_files.init_slots_with_none", false]], "initialize() (mmtbx.refinement.real_space.rsr_model method)": [[315, "mmtbx.refinement.real_space.rsr_model.initialize", false]], "initialize() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.initialize", false]], "initialize() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.initialize", false]], "initialize() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status.initialize", false]], "initialize_map_data() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.initialize_map_data", false]], "initialize_maps() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.initialize_maps", false]], "initialize_table() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.initialize_table", false]], "initialize_table() (cctbx.geometry_restraints.proxy_registry_base method)": [[131, "cctbx.geometry_restraints.proxy_registry_base.initialize_table", false]], "initialize_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.initialize_tables", false]], "initialize_tables_and_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.initialize_tables_and_insert_command", false]], "inner_loop() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.inner_loop", false]], "inp_as_xray_structures() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.inp_as_xray_structures", false]], "inp_from_form() (in module cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.inp_from_form", false]], "input (class in iotbx.pdb.ext)": [[268, "iotbx.pdb.ext.input", false]], "input() (in module iotbx.pdb)": [[268, "iotbx.pdb.input", false]], "insert() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.insert", false]], "insert() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.insert", false]], "insert() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.insert", false]], "insert() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.insert", false]], "insert() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.insert", false]], "insert() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.insert", false]], "insert() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.insert", false]], "insert() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.insert", false]], "insert() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.insert", false]], "insert() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.insert", false]], "insert() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.insert", false]], "insert() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.insert", false]], "insert() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.insert", false]], "insert() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.insert", false]], "insert_atom() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.insert_atom", false]], "insert_atom_group() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.insert_atom_group", false]], "insert_atom_into_model() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.insert_atom_into_model", false]], "insert_chain() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.insert_chain", false]], "insert_model() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.insert_model", false]], "insert_residue_group() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.insert_residue_group", false]], "inserter (class in mmtbx.geometry.altloc)": [[289, "mmtbx.geometry.altloc.Inserter", false]], "inside_zero_one() (in module cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.inside_zero_one", false]], "instruction_parser (class in iotbx.shelx.parsers)": [[271, "iotbx.shelx.parsers.instruction_parser", false]], "int (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.int", false]], "integrand() (cctbx.maptbx.atom_curves method)": [[139, "cctbx.maptbx.atom_curves.integrand", false]], "integrate_one_image() (in module xfel.cxi.integrate_image_api)": [[342, "xfel.cxi.integrate_image_api.integrate_one_image", false]], "integrate_one_image() (in module xfel.cxi.strong_zulu)": [[342, "xfel.cxi.strong_zulu.integrate_one_image", false]], "intensities() (cctbx.miller.array method)": [[148, "cctbx.miller.array.intensities", false]], "intensity (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.intensity", false]], "intensity_correlation (class in cctbx.xray.target_functors)": [[252, "cctbx.xray.target_functors.intensity_correlation", false]], "intensity_flag (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.intensity_flag", false]], "intensity_group (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.intensity_group", false]], "intensity_quasi_normalisations() (cctbx.miller.array method)": [[148, "cctbx.miller.array.intensity_quasi_normalisations", false]], "intensity_quasi_unit_weighting (class in cctbx.xray.weighting_schemes)": [[255, "cctbx.xray.weighting_schemes.intensity_quasi_unit_weighting", false]], "intensity_statistics() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.intensity_statistics", false]], "interaction_counts_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interaction_counts_with", false]], "interaction_ranges_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interaction_ranges_with", false]], "interactions_with() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.interactions_with", false]], "interleaved_lbfgs_minimization (class in mmtbx.dynamics.cartesian_dynamics)": [[287, "mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization", false]], "interleaved_lbfgs_minimization (class in mmtbx.dynamics.ensemble_cd)": [[287, "mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization", false]], "interleaved_minimization() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.interleaved_minimization", false]], "interpolate() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.interpolate", false]], "interpolate() (in module cctbx.french_wilson)": [[129, "cctbx.french_wilson.interpolate", false]], "interpolate() (in module xfel.command_line.smooth_spectrum)": [[341, "xfel.command_line.smooth_spectrum.interpolate", false]], "interpolate_2d() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.interpolate_2d", false]], "interpolate_at_point() (in module mmtbx.conformation_dependent_library.utils)": [[283, "mmtbx.conformation_dependent_library.utils.interpolate_at_point", false]], "interpret_coordinate_line() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.interpret_coordinate_line", false]], "interpret_form_data() (in module cctbx.web.all_axes)": [[205, "cctbx.web.all_axes.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.browse_settings)": [[212, "cctbx.web.browse_settings.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.change_basis)": [[214, "cctbx.web.change_basis.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.change_hand)": [[215, "cctbx.web.change_hand.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.change_setting)": [[216, "cctbx.web.change_setting.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.frac_cart)": [[220, "cctbx.web.frac_cart.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.iotbx_cif_validate)": [[222, "cctbx.web.iotbx_cif_validate.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.lattice_symmetry)": [[223, "cctbx.web.lattice_symmetry.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.libtbx_help)": [[224, "cctbx.web.libtbx_help.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.phase_o_phrenia)": [[226, "cctbx.web.phase_o_phrenia.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.shelx)": [[228, "cctbx.web.shelx.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.structure_factors)": [[229, "cctbx.web.structure_factors.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.structure_factors_pdb)": [[230, "cctbx.web.structure_factors_pdb.interpret_form_data", false]], "interpret_form_data() (in module cctbx.web.wyckoff)": [[231, "cctbx.web.wyckoff.interpret_form_data", false]], "interpret_generic_coordinate_line() (in module cctbx.web.emma)": [[218, "cctbx.web.emma.interpret_generic_coordinate_line", false]], "interpret_skip_columns() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.interpret_skip_columns", false]], "intersection() (in module cctbx.adptbx)": [[5, "cctbx.adptbx.intersection", false]], "intersection() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.intersection", false]], "intersection() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.intersection", false]], "intersection_i_seqs() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.intersection_i_seqs", false]], "intersection_of_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.intersection_of_scatterers", false]], "inv_perms (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.inv_perms", false]], "inverse() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.inverse", false]], "inverse() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.inverse", false]], "inverse_hand() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.inverse_hand", false]], "inverse_permutation() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.inverse_permutation", false]], "inverse_transform_hierarchy() (mmtbx.maps.superpose.common_frame_of_reference method)": [[305, "mmtbx.maps.superpose.common_frame_of_reference.inverse_transform_hierarchy", false]], "inversion (class in scitbx.matrix)": [[334, "scitbx.matrix.inversion", false]], "invert_hand() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.invert_hand", false]], "invert_matrices() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.invert_matrices", false]], "invert_matrices() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.invert_matrices", false]], "involves_broken_bonds() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.involves_broken_bonds", false]], "involves_special_positions() (mmtbx.monomer_library.pdb_interpretation.special_position_dict method)": [[308, "mmtbx.monomer_library.pdb_interpretation.special_position_dict.involves_special_positions", false]], "ion_anomalous_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_anomalous_vector", false]], "ion_class() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_class", false]], "ion_electron_density_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_electron_density_vector", false]], "ion_geometry_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_geometry_vector", false]], "ion_master_phil() (in module mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.ion_master_phil", false]], "ion_model_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_model_vector", false]], "ion_nearby_atoms_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_nearby_atoms_vector", false]], "ion_result (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.ion_result", false]], "ion_valence_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_valence_vector", false]], "ion_vector() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.ion_vector", false]], "iotbx.file_reader": [[265, "module-iotbx.file_reader", false]], "iotbx.map_manager": [[266, "module-iotbx.map_manager", false]], "iotbx.map_model_manager": [[266, "module-iotbx.map_model_manager", false]], "iotbx.reflection_file_reader": [[270, "module-iotbx.reflection_file_reader", false]], "iotbx.shelx": [[271, "module-iotbx.shelx", false]], "iotbx.shelx.crystal_symmetry_from_ins": [[271, "module-iotbx.shelx.crystal_symmetry_from_ins", false]], "iotbx.shelx.hklf": [[271, "module-iotbx.shelx.hklf", false]], "iotbx.shelx.lexer": [[271, "module-iotbx.shelx.lexer", false]], "iotbx.shelx.parsers": [[271, "module-iotbx.shelx.parsers", false]], "iotbx.shelx.tokens": [[271, "module-iotbx.shelx.tokens", false]], "iotbx.shelx.write_ins": [[271, "module-iotbx.shelx.write_ins", false]], "iotbx.shelx.writer": [[271, "module-iotbx.shelx.writer", false]], "iotbx.xds.integrate_hkl": [[272, "module-iotbx.xds.integrate_hkl", false]], "iotbx.xds.read_ascii": [[272, "module-iotbx.xds.read_ascii", false]], "iotbx.xds.spot_xds": [[272, "module-iotbx.xds.spot_xds", false]], "iotbx.xds.xds_inp": [[272, "module-iotbx.xds.xds_inp", false]], "iotbx.xds.xparm": [[272, "module-iotbx.xds.xparm", false]], "iplace() (in module xfel.cxi.cspad_ana.cspad_tbx)": [[343, "xfel.cxi.cspad_ana.cspad_tbx.iplace", false]], "iround() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.iround", false]], "iround() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.iround", false]], "iround() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.iround", false]], "is_0_based() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.is_0_based", false]], "is_0_based() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.is_0_based", false]], "is_2p (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p", false]], "is_2p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_delta", false]], "is_2p_o3p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_o3p_distance_c1p_outbound_line", false]], "is_2p_p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_2p_p_distance_c1p_outbound_line", false]], "is_3p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_3p_delta", false]], "is_allowed_origin_shift() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.is_allowed_origin_shift", false]], "is_any_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.is_any_proxy_set", false]], "is_approx_zero() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_approx_zero", false]], "is_approximately_helical() (in module mmtbx.secondary_structure.proteins)": [[319, "mmtbx.secondary_structure.proteins.is_approximately_helical", false]], "is_atom_group_pair_linked() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_group_pair_linked", false]], "is_atom_metal_coordinated() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_metal_coordinated", false]], "is_atom_pair_linked() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_pair_linked", false]], "is_atom_pair_linked_tuple() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_atom_pair_linked_tuple", false]], "is_bad_water() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.is_bad_water", false]], "is_bonded_atoms() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.is_bonded_atoms", false]], "is_bool() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.is_bool", false]], "is_bool_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_bool_array", false]], "is_bounded_by_constant() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.is_bounded_by_constant", false]], "is_buerger_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.is_buerger_cell", false]], "is_ca_only() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.is_ca_only", false]], "is_ca_only() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.is_ca_only", false]], "is_ca_only() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.is_ca_only", false]], "is_carboxy_terminus (mmtbx.ions.environment.atom_contact attribute)": [[295, "mmtbx.ions.environment.atom_contact.is_carboxy_terminus", false]], "is_cbeta_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_cbeta_outlier", false]], "is_centric() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.is_centric", false]], "is_chemical_components_file() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.is_chemical_components_file", false]], "is_cis_peptide() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.is_cis_peptide", false]], "is_cis_peptide() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.is_cis_peptide", false]], "is_cis_peptide() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.is_cis_peptide", false]], "is_clash_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_clash_outlier", false]], "is_code() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.is_code", false]], "is_col_zero() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_col_zero", false]], "is_compatible_anomalous_scattering() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_compatible_anomalous_scattering", false]], "is_compatible_model() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.is_compatible_model", false]], "is_compatible_ncs_object() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.is_compatible_ncs_object", false]], "is_compatible_site() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_compatible_site", false]], "is_compatible_unit_cell() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_compatible_unit_cell", false]], "is_complex_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_complex_array", false]], "is_consistent_with_wrapping() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.is_consistent_with_wrapping", false]], "is_converged() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.is_converged", false]], "is_converged() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.is_converged", false]], "is_correct() (mmtbx.monomer_library.glyco_utils.glyco_link_class method)": [[308, "mmtbx.monomer_library.glyco_utils.glyco_link_class.is_correct", false]], "is_correctly_identified() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.is_correctly_identified", false]], "is_delta_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_delta_outlier", false]], "is_delta_outlier (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.is_delta_outlier", false]], "is_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_dna", false]], "is_dummy_map_manager() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.is_dummy_map_manager", false]], "is_elliptically_truncated() (mmtbx.scaling.data_statistics.analyze_resolution_limits method)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits.is_elliptically_truncated", false]], "is_empty() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_empty", false]], "is_epsilon_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute)": [[308, "mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate.is_epsilon_outlier", false]], "is_epsilon_outlier (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.is_epsilon_outlier", false]], "is_equivalent() (cctbx.sgtbx.symmetry_equivalent_pair_interactions method)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.is_equivalent", false]], "is_favorable_halide_environment() (in module mmtbx.ions.halides)": [[297, "mmtbx.ions.halides.is_favorable_halide_environment", false]], "is_first_after_break (iotbx.pdb.hierarchy.atom_with_labels property)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.is_first_after_break", false]], "is_first_conformer_in_chain (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_first_conformer_in_chain", false]], "is_first_in_chain (iotbx.pdb.hierarchy.atom_with_labels property)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.is_first_in_chain", false]], "is_flags_good() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.is_flags_good", false]], "is_forward_compatible_hierarchy() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.is_forward_compatible_hierarchy", false]], "is_full_size() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.is_full_size", false]], "is_geometry_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_geometry_outlier", false]], "is_glyco_amino_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_glyco_amino_bond", false]], "is_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_glyco_bond", false]], "is_handedness_swap() (mmtbx.validation.restraints.chirality method)": [[326, "mmtbx.validation.restraints.chirality.is_handedness_swap", false]], "is_heavy_atom() (mmtbx.validation.waters.water method)": [[326, "mmtbx.validation.waters.water.is_heavy_atom", false]], "is_helical_along_z() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_helical_along_z", false]], "is_helical_along_z() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_helical_along_z", false]], "is_hendrickson_lattman_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_hendrickson_lattman_array", false]], "is_hierarchy_altloc_consistent() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.is_hierarchy_altloc_consistent", false]], "is_identical_hierarchy() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.is_identical_hierarchy", false]], "is_identical_hierarchy() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.is_identical_hierarchy", false]], "is_identical_hierarchy() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.is_identical_hierarchy", false]], "is_identical_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_identical_symmetry", false]], "is_identity() (cctbx.sgtbx.special_op_simplified_term method)": [[165, "cctbx.sgtbx.special_op_simplified_term.is_identity", false]], "is_identity() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_identity", false]], "is_in_asu() (cctbx.miller.set method)": [[148, "cctbx.miller.set.is_in_asu", false]], "is_in_chain() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.is_in_chain", false]], "is_in_coset() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.is_in_coset", false]], "is_in_group() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group.is_in_group", false]], "is_in_group() (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group.is_in_group", false]], "is_in_list_of_cosets() (cctbx.sgtbx.cosets.double_cosets method)": [[167, "cctbx.sgtbx.cosets.double_cosets.is_in_list_of_cosets", false]], "is_in_range() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_in_range", false]], "is_in_same_conformer_as() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.is_in_same_conformer_as", false]], "is_incomplete() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_incomplete", false]], "is_inside() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.is_inside", false]], "is_inside() (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.is_inside", false]], "is_inside() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.is_inside", false]], "is_inside_mask() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.is_inside_mask", false]], "is_integer_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_integer_array", false]], "is_integrate_hkl_file() (iotbx.xds.integrate_hkl.reader static method)": [[272, "iotbx.xds.integrate_hkl.reader.is_integrate_hkl_file", false]], "is_iterate (cctbx.omz.dev.xfgc_info attribute)": [[158, "cctbx.omz.dev.xfgc_info.is_iterate", false]], "is_joined_at_calpha() (in module mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.is_joined_at_calpha", false]], "is_map_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_map_outlier", false]], "is_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.is_mask", false]], "is_match() (mmtbx.monomer_library.pdb_interpretation.link_match_one method)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match_one.is_match", false]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_angle method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_angle.is_matching_mod_for", false]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_bond method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_bond.is_matching_mod_for", false]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_chir method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_chir.is_matching_mod_for", false]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_plane_atom.is_matching_mod_for", false]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_tor method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tor.is_matching_mod_for", false]], "is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_tree method)": [[308, "mmtbx.monomer_library.cif_types.chem_mod_tree.is_matching_mod_for", false]], "is_monomer_library_file() (in module mmtbx.monomer_library)": [[308, "mmtbx.monomer_library.is_monomer_library_file", false]], "is_n_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_n_glyco_bond", false]], "is_na() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.is_na", false]], "is_na() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.is_na", false]], "is_negatively_charged_oxygen() (in module mmtbx.ions.halides)": [[297, "mmtbx.ions.halides.is_negatively_charged_oxygen", false]], "is_niggli_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.is_niggli_cell", false]], "is_nonsense() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_nonsense", false]], "is_o_glyco_bond() (in module mmtbx.monomer_library.linking_utils)": [[308, "mmtbx.monomer_library.linking_utils.is_o_glyco_bond", false]], "is_odd_numbered() (in module xfel.cxi.util)": [[342, "xfel.cxi.util.is_odd_numbered", false]], "is_one_of() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.is_one_of", false]], "is_outlier() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.is_outlier", false]], "is_padded() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.is_padded", false]], "is_padded() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.is_padded", false]], "is_padded() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.is_padded", false]], "is_padded() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.is_padded", false]], "is_padded() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.is_padded", false]], "is_padded() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.is_padded", false]], "is_padded() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.is_padded", false]], "is_padded() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.is_padded", false]], "is_padded() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.is_padded", false]], "is_padded() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.is_padded", false]], "is_padded() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.is_padded", false]], "is_padded() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.is_padded", false]], "is_padded() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.is_padded", false]], "is_part_of_segment() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.is_part_of_segment", false]], "is_patterson_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_patterson_symmetry", false]], "is_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_peptide", false]], "is_periodic() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.is_periodic", false]], "is_phenix_refinement() (mmtbx.validation.molprobity.pdb_header_info method)": [[327, "mmtbx.validation.molprobity.pdb_header_info.is_phenix_refinement", false]], "is_pinwheel_region() (in module xfel.cxi.display_powder_arcs)": [[342, "xfel.cxi.display_powder_arcs.is_pinwheel_region", false]], "is_point_group_symmetry() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_point_group_symmetry", false]], "is_point_group_symmetry() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_point_group_symmetry", false]], "is_populated (mmtbx.validation.molprobity.multi_criterion_view attribute)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.is_populated", false]], "is_positive_definite_u() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.is_positive_definite_u", false]], "is_proper_match() (mmtbx.monomer_library.pdb_interpretation.link_match method)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match.is_proper_match", false]], "is_protein() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.is_protein", false]], "is_protein() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.is_protein", false]], "is_proxy_present() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.is_proxy_present", false]], "is_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method)": [[131, "cctbx.geometry_restraints.bond_simple_proxy_registry.is_proxy_set", false]], "is_pseudochiral() (mmtbx.validation.restraints.chirality method)": [[326, "mmtbx.validation.restraints.chirality.is_pseudochiral", false]], "is_pure_main_conf (iotbx.pdb.hierarchy.residue property)": [[268, "iotbx.pdb.hierarchy.residue.is_pure_main_conf", false]], "is_r3_identity_matrix() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_r3_identity_matrix", false]], "is_r3_rotation_matrix() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_r3_rotation_matrix", false]], "is_r3_rotation_matrix_rms() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_r3_rotation_matrix_rms", false]], "is_ramachandran_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_ramachandran_outlier", false]], "is_real_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_real_array", false]], "is_reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.is_reference_setting", false]], "is_residue_specified() (in module mmtbx.chemical_components)": [[281, "mmtbx.chemical_components.is_residue_specified", false]], "is_reticular_polyholohedral() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.is_reticular_polyholohedral", false]], "is_rna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_rna", false]], "is_rna2p (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_rna2p", false]], "is_rna_dna (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_rna_dna", false]], "is_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_rna_dna", false]], "is_rotamer_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.is_rotamer_outlier", false]], "is_same_model_as_before() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.is_same_model_as_before", false]], "is_same_residue() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_same_residue", false]], "is_same_residue_group() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_same_residue_group", false]], "is_same_transform() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.is_same_transform", false]], "is_schrodinger_installed() (in module mmtbx.geometry_restraints.external)": [[290, "mmtbx.geometry_restraints.external.is_schrodinger_installed", false]], "is_self_clash() (mmtbx.geometry.clash.clashingpair method)": [[289, "mmtbx.geometry.clash.ClashingPair.is_self_clash", false]], "is_similar() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.is_similar", false]], "is_similar() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.is_similar", false]], "is_similar() (iotbx.map_manager.shift_aware_rt method)": [[266, "iotbx.map_manager.shift_aware_rt.is_similar", false]], "is_similar() (mmtbx.validation.clashscore.probe_line_info method)": [[326, "mmtbx.validation.clashscore.probe_line_info.is_similar", false]], "is_similar_hierarchy() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.is_similar_hierarchy", false]], "is_similar_hierarchy() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.is_similar_hierarchy", false]], "is_similar_hierarchy() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.is_similar_hierarchy", false]], "is_similar_hierarchy() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.is_similar_hierarchy", false]], "is_similar_ncs_group() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.is_similar_ncs_group", false]], "is_similar_ncs_object() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.is_similar_ncs_object", false]], "is_similar_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.is_similar_symmetry", false]], "is_similar_to() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.is_similar_to", false]], "is_single_residue_object() (mmtbx.validation.atom method)": [[326, "mmtbx.validation.atom.is_single_residue_object", false]], "is_single_residue_object() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.is_single_residue_object", false]], "is_single_residue_object() (mmtbx.validation.entity method)": [[326, "mmtbx.validation.entity.is_single_residue_object", false]], "is_single_residue_object() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.is_single_residue_object", false]], "is_size_t() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.is_size_t", false]], "is_square() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_square", false]], "is_square_matrix() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.is_square_matrix", false]], "is_standard_glyco_link() (in module mmtbx.monomer_library.glyco_utils)": [[308, "mmtbx.monomer_library.glyco_utils.is_standard_glyco_link", false]], "is_string_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_string_array", false]], "is_stub_residue() (in module mmtbx.building)": [[277, "mmtbx.building.is_stub_residue", false]], "is_subgroup() (cctbx.sgtbx.cosets.left_decomposition method)": [[167, "cctbx.sgtbx.cosets.left_decomposition.is_subgroup", false]], "is_subgroup() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.is_subgroup", false]], "is_super_set() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.is_super_set", false]], "is_supported_donor() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.is_supported_donor", false]], "is_supported_element() (mmtbx.ions.parameter_server method)": [[293, "mmtbx.ions.parameter_server.is_supported_element", false]], "is_terminus (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_terminus", false]], "is_terminus (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.is_terminus", false]], "is_trans_peptide() (in module mmtbx.validation.analyze_peptides)": [[326, "mmtbx.validation.analyze_peptides.is_trans_peptide", false]], "is_trivial_1d() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.is_trivial_1d", false]], "is_trivial_1d() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.is_trivial_1d", false]], "is_twin_fmodel_manager() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.is_twin_fmodel_manager", false]], "is_twinned() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.is_twinned", false]], "is_unique_set_under_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.is_unique_set_under_symmetry", false]], "is_unmerged_intensity_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_unmerged_intensity_array", false]], "is_unusual (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.is_unusual", false]], "is_unusual (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.is_unusual", false]], "is_useful() (cctbx.omz.cod_select_and_pickle.cod_data method)": [[157, "cctbx.omz.cod_select_and_pickle.cod_data.is_useful", false]], "is_valid_index() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.is_valid_index", false]], "is_water() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.is_water", false]], "is_water_last() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.is_water_last", false]], "is_xds_inp_file() (iotbx.xds.xds_inp.reader static method)": [[272, "iotbx.xds.xds_inp.reader.is_xds_inp_file", false]], "is_xparm_file() (iotbx.xds.xparm.reader static method)": [[272, "iotbx.xds.xparm.reader.is_xparm_file", false]], "is_xray_amplitude_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_amplitude_array", false]], "is_xray_data_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_data_array", false]], "is_xray_intensity_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_intensity_array", false]], "is_xray_reconstructed_amplitude_array() (cctbx.miller.array method)": [[148, "cctbx.miller.array.is_xray_reconstructed_amplitude_array", false]], "is_zero() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.is_zero", false]], "iselection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.iselection", false]], "iselection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.iselection", false]], "iselection() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.iselection", false]], "iso_b_wilson (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.iso_b_wilson", false]], "isotropic_adp_deviation() (cctbx.adp_restraints.energies.energies method)": [[3, "cctbx.adp_restraints.energies.energies.isotropic_adp_deviation", false]], "isprepro() (in module mmtbx.validation.ramalyze)": [[326, "mmtbx.validation.ramalyze.isPrePro", false]], "issue_merohedral_twinning() (iotbx.shelx.parsers.instruction_parser method)": [[271, "iotbx.shelx.parsers.instruction_parser.issue_merohedral_twinning", false]], "iter_molprobity_gui_fields() (mmtbx.validation.molprobity.summary method)": [[327, "mmtbx.validation.molprobity.summary.iter_molprobity_gui_fields", false]], "iter_residue_groups() (in module mmtbx.building)": [[277, "mmtbx.building.iter_residue_groups", false]], "iter_residue_groups() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.iter_residue_groups", false]], "iter_results() (mmtbx.validation.model_properties.xray_structure_statistics method)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.iter_results", false]], "iter_results() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.iter_results", false]], "iter_until_loop() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.iter_until_loop", false]], "iterate_sites() (in module mmtbx.ions.svm.utils)": [[301, "mmtbx.ions.svm.utils.iterate_sites", false]], "iteration_limit() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.iteration_limit", false]], "iteration_limit() (cctbx.uctbx.reduction_base.reduction_base method)": [[203, "cctbx.uctbx.reduction_base.reduction_base.iteration_limit", false]], "iteration_limit_exceeded": [[203, "cctbx.uctbx.reduction_base.iteration_limit_exceeded", false]], "iterations (class in scitbx.lstbx.normal_eqns_solving)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations", false]], "iterations() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.iterations", false]], "iterator() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.iterator", false]], "iterrows() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.iterrows", false]], "ito_vol_c_2011_table_4_3_2_2_elements() (in module cctbx.eltbx.e_scattering)": [[65, "cctbx.eltbx.e_scattering.ito_vol_c_2011_table_4_3_2_2_elements", false]], "ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian() (in module cctbx.eltbx.e_scattering)": [[65, "cctbx.eltbx.e_scattering.ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian", false]], "itvc_sampling_selection() (cctbx.eltbx.development.kissel_io.table method)": [[62, "cctbx.eltbx.development.kissel_io.table.itvc_sampling_selection", false]], "j_mod (mmtbx.disorder.backbone.backrub_residue attribute)": [[286, "mmtbx.disorder.backbone.backrub_residue.j_mod", false]], "j_seq (cctbx.crystal.sym_pair attribute)": [[23, "cctbx.crystal.sym_pair.j_seq", false]], "jacobian_frame_rotx (xfel.metrology.mark10.fit_translation4 attribute)": [[347, "xfel.metrology.mark10.fit_translation4.jacobian_frame_rotx", false]], "join_edge() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.join_edge", false]], "join_hierarchies() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.join_hierarchies", false]], "join_point() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points.join_point", false]], "join_selections() (in module mmtbx.maps.composite_omit_map)": [[305, "mmtbx.maps.composite_omit_map.join_selections", false]], "join_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.join_symmetry", false]], "journaled_non_linear_ls (class in scitbx.lstbx.normal_eqns_solving)": [[333, "scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls", false]], "jvx() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.jvx", false]], "jvx() (cctbx.web.asu_gallery.jvx.geometry method)": [[210, "cctbx.web.asu_gallery.jvx.geometry.jvx", false]], "jvx() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.jvx", false]], "jvx() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.jvx", false]], "jvx_item_colors() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.jvx_item_colors", false]], "k (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.k", false]], "k_anisotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_anisotropic", false]], "k_anisotropic() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_anisotropic", false]], "k_isotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_isotropic", false]], "k_isotropic() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_isotropic", false]], "k_mask_grid_search() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_mask_grid_search", false]], "k_masks() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_masks", false]], "k_masks() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.k_masks", false]], "k_overall_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.k_overall_to_ref", false]], "k_part() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.k_part", false]], "k_part_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.k_part_to_ref", false]], "k_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.k_sol", false]], "k_sol_b_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.k_sol_b_sol", false]], "k_sol_b_sol_b_cart_minimizer() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.k_sol_b_sol_b_cart_minimizer", false]], "k_sol_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.k_sol_to_ref", false]], "k_sol_u_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.k_sol_u_sol", false]], "k_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales.k_sols", false]], "k_sols() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.k_sols", false]], "kappa() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.kappa", false]], "kappagoniometer (class in dxtbx.model.goniometer)": [[257, "dxtbx.model.goniometer.KappaGoniometer", false]], "kb_range() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.kb_range", false]], "kb_range() (in module mmtbx.twinning.twin_f_model)": [[324, "mmtbx.twinning.twin_f_model.kb_range", false]], "kernel_normalisation (class in mmtbx.scaling.absolute_scaling)": [[318, "mmtbx.scaling.absolute_scaling.kernel_normalisation", false]], "keys() (iotbx.cif.model.block method)": [[264, "iotbx.cif.model.block.keys", false]], "keys() (iotbx.cif.model.cif method)": [[264, "iotbx.cif.model.cif.keys", false]], "keys() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.keys", false]], "keywise_printout() (in module xfel.command_line.print_pickle)": [[341, "xfel.command_line.print_pickle.keywise_printout", false]], "kick_fmodel() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.kick_fmodel", false]], "kick_map_coeffs() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.kick_map_coeffs", false]], "kin_vec() (in module mmtbx.kinemage)": [[303, "mmtbx.kinemage.kin_vec", false]], "kinemage_file (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.kinemage_file", false]], "kinemage_header (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.kinemage_header", false]], "kinemage_header (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.kinemage_header", false]], "kinemage_header (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.kinemage_header", false]], "kinemage_header (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.kinemage_header", false]], "kinemage_key() (mmtbx.validation.restraints.restraint method)": [[326, "mmtbx.validation.restraints.restraint.kinemage_key", false]], "kinetic_energy_and_temperature (class in mmtbx.dynamics)": [[287, "mmtbx.dynamics.kinetic_energy_and_temperature", false]], "kinetic_energy_as_temperature() (in module mmtbx.dynamics)": [[287, "mmtbx.dynamics.kinetic_energy_as_temperature", false]], "kinetic_energy_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.kinetic_energy_stats", false]], "known_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.known_axis", false]], "ksol_bsol_result (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling)": [[278, "mmtbx.bulk_solvent.bulk_solvent_and_scaling.ksol_bsol_result", false]], "l_test (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.l_test", false]], "l_test_mean_l (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.l_test_mean_l", false]], "l_test_mean_l_squared (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.l_test_mean_l_squared", false]], "label (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.label", false]], "label (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.label", false]], "label (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.label", false]], "labeled_fit (class in cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.labeled_fit", false]], "labelit_check_pdb_symmetry_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.labelit_check_pdb_symmetry_form", false]], "labelit_check_pdb_symmetry_short() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.labelit_check_pdb_symmetry_short", false]], "labels (mmtbx.validation.graphics.residue_bin attribute)": [[326, "mmtbx.validation.graphics.residue_bin.labels", false]], "labels (mmtbx.validation.molprobity.summary attribute)": [[327, "mmtbx.validation.molprobity.summary.labels", false]], "labels() (mmtbx.monomer_library.pdb_interpretation.source_info_server method)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server.labels", false]], "labels_refine() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.labels_refine", false]], "laser_status (class in xfel.cxi.cspad_ana.mod_event_info)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status", false]], "last() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.last", false]], "last() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.last", false]], "last() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.last", false]], "last() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.last", false]], "last() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.last", false]], "last() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.last", false]], "last() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.last", false]], "last() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.last", false]], "last() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.last", false]], "last() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.last", false]], "last() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.last", false]], "last() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.last", false]], "last() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.last", false]], "last_resseq_as_int() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.last_resseq_as_int", false]], "latt_symm() (in module iotbx.shelx.write_ins)": [[271, "iotbx.shelx.write_ins.LATT_SYMM", false]], "lattice_group (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.lattice_group", false]], "lattice_group_info() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups.lattice_group_info", false]], "latticecharacter (class in cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter", false]], "launcher (class in mmtbx.maps.fobs_minus_fobs_map)": [[305, "mmtbx.maps.fobs_minus_fobs_map.launcher", false]], "launcher (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.launcher", false]], "lbfgs (class in cctbx.geometry_restraints.lbfgs)": [[134, "cctbx.geometry_restraints.lbfgs.lbfgs", false]], "lbfgs (class in cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.lbfgs", false]], "lbfgs (class in cctbx.xray.minimization)": [[234, "cctbx.xray.minimization.lbfgs", false]], "lbfgs (class in mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.lbfgs", false]], "lbfgs (class in mmtbx.refinement.minimization)": [[313, "mmtbx.refinement.minimization.lbfgs", false]], "lbfgs (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs", false]], "lbfgs_emulation() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.lbfgs_emulation", false]], "lcm_of_denominators() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.lcm_of_denominators", false]], "le_page_1982_delta_details (class in cctbx.sgtbx)": [[165, "cctbx.sgtbx.le_page_1982_delta_details", false]], "least_squares (class in cctbx.examples.exp_i_alpha_derivatives)": [[86, "cctbx.examples.exp_i_alpha_derivatives.least_squares", false]], "least_squares (class in cctbx.xray.target_functors)": [[252, "cctbx.xray.target_functors.least_squares", false]], "least_squares_residual (in module cctbx.xray.target_functors)": [[252, "cctbx.xray.target_functors.least_squares_residual", false]], "least_squares_residual_for_amplitude (class in cctbx.xray.target_functors)": [[252, "cctbx.xray.target_functors.least_squares_residual_for_amplitude", false]], "left_decomposition (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.left_decomposition", false]], "left_decomposition_point_groups_only (class in cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.left_decomposition_point_groups_only", false]], "len_peaks() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.len_peaks", false]], "length() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.length", false]], "length() (mmtbx.geometry.topology.mcgregormatch method)": [[289, "mmtbx.geometry.topology.McGregorMatch.length", false]], "length() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.length", false]], "length() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.length", false]], "length_sq() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.length_sq", false]], "level() (in module cctbx.sgtbx.symbol_confidence)": [[188, "cctbx.sgtbx.symbol_confidence.level", false]], "levenberg_marquardt_iterations (class in scitbx.lstbx.normal_eqns_solving)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations", false]], "levenberg_marquardt_iterations_encapsulated_eqns (class in scitbx.lstbx.normal_eqns_solving)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns", false]], "lex_scatterer() (iotbx.shelx.parsers.atom_parser method)": [[271, "iotbx.shelx.parsers.atom_parser.lex_scatterer", false]], "lhs (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.lhs", false]], "lib_link (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.lib_link", false]], "libtbx": [[273, "module-libtbx", false]], "ligand_validation (class in mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.ligand_validation", false]], "ligands (mmtbx.validation.model_properties.model_statistics property)": [[326, "mmtbx.validation.model_properties.model_statistics.ligands", false]], "ligands() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.ligands", false]], "ligands_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.ligands_", false]], "like_coord (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.like_coord", false]], "like_coord (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LIKE_COORD", false]], "likelihood() (in module mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.likelihood", false]], "limit_frac_min_frac_max() (in module mmtbx.utils)": [[325, "mmtbx.utils.limit_frac_min_frac_max", false]], "line (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.line", false]], "line_sample_point() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.line_sample_point", false]], "line_search() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.line_search", false]], "linear_indexer_for() (in module mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.linear_indexer_for", false]], "lines (class in xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.lines", false]], "lineset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.lineSet", false]], "link_link_id (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.link_link_id", false]], "link_match (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match", false]], "link_match_one (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.link_match_one", false]], "link_to_previous (iotbx.pdb.hierarchy.residue property)": [[268, "iotbx.pdb.hierarchy.residue.link_to_previous", false]], "link_to_previous (iotbx.pdb.hierarchy.residue_group property)": [[268, "iotbx.pdb.hierarchy.residue_group.link_to_previous", false]], "linkexploresymmetry() (in module cctbx.web.multiple_cell)": [[225, "cctbx.web.multiple_cell.LinkExploreSymmetry", false]], "linking_mixins (class in mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.linking_mixins", false]], "list (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points.list", false]], "list() (mmtbx.scaling.absences.sgi_iterator method)": [[318, "mmtbx.scaling.absences.sgi_iterator.list", false]], "list_3d_as_bool_selection() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.list_3d_as_bool_selection", false]], "list_all_axes() (in module cctbx.examples.all_axes)": [[80, "cctbx.examples.all_axes.list_all_axes", false]], "list_dict (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.list_dict", false]], "literal_description (class in cctbx.sgtbx.literal_description)": [[179, "cctbx.sgtbx.literal_description.literal_description", false]], "literals() (xfel.cxi.correction_vector_plot.lines method)": [[342, "xfel.cxi.correction_vector_plot.lines.literals", false]], "load_all_models_in_directory() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_all_models_in_directory", false]], "load_and_validate_unmerged_data() (in module mmtbx.command_line)": [[282, "mmtbx.command_line.load_and_validate_unmerged_data", false]], "load_cc_data() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.load_cc_data", false]], "load_cxi_phil() (in module xfel.phil_preferences)": [[337, "xfel.phil_preferences.load_cxi_phil", false]], "load_data() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.load_data", false]], "load_db() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.load_db", false]], "load_den_network() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.load_den_network", false]], "load_emsley8k_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_emsley8k_tables", false]], "load_model_and_data (class in mmtbx.command_line)": [[282, "mmtbx.command_line.load_model_and_data", false]], "load_mon_lib_file() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.load_mon_lib_file", false]], "load_pdb_models() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_pdb_models", false]], "load_phi_psi_2_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_phi_psi_2_tables", false]], "load_related_models_from_pdb() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_related_models_from_pdb", false]], "load_related_models_in_directory() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.load_related_models_in_directory", false]], "load_result() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.load_result", false]], "load_tables() (in module mmtbx.geometry_restraints.ramachandran)": [[290, "mmtbx.geometry_restraints.ramachandran.load_tables", false]], "loc_res() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.loc_res", false]], "local_altloc_from_atoms() (mmtbx.validation.rna_validate.rna_puckers method)": [[326, "mmtbx.validation.rna_validate.rna_puckers.local_altloc_from_atoms", false]], "local_density_quality (class in mmtbx.building)": [[277, "mmtbx.building.local_density_quality", false]], "local_fsc() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.local_fsc", false]], "local_lsq_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_lsq_scaling", false]], "local_moment_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_moment_scaling", false]], "local_nikonov_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver.local_nikonov_scaling", false]], "local_overlap_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.local_overlap_map", false]], "local_resolution_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.local_resolution_map", false]], "local_scale (class in cctbx.maptbx)": [[139, "cctbx.maptbx.local_scale", false]], "local_scaling_driver (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.local_scaling_driver", false]], "local_standard_deviation_map (class in mmtbx.density_modification)": [[285, "mmtbx.density_modification.local_standard_deviation_map", false]], "local_standard_deviation_map() (cctbx.miller.array method)": [[148, "cctbx.miller.array.local_standard_deviation_map", false]], "local_standard_deviations_gradients() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_gradients", false]], "local_standard_deviations_target() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_target", false]], "local_standard_deviations_target_per_site() (in module cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.local_standard_deviations_target_per_site", false]], "log (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.log", false]], "log_binned_completeness (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.log_binned_completeness", false]], "log_binning() (cctbx.miller.set method)": [[148, "cctbx.miller.set.log_binning", false]], "log_p() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.log_p", false]], "log_p() (mmtbx.twinning.probabalistic_detwinning.detwin method)": [[324, "mmtbx.twinning.probabalistic_detwinning.detwin.log_p", false]], "loggraph_output (class in mmtbx.scaling)": [[318, "mmtbx.scaling.loggraph_output", false]], "lone_set() (cctbx.miller.set method)": [[148, "cctbx.miller.set.lone_set", false]], "lone_sets() (cctbx.miller.set method)": [[148, "cctbx.miller.set.lone_sets", false]], "long (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.long", false]], "long_form() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.long_form", false]], "looks_like_ccp4_flags() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.looks_like_ccp4_flags", false]], "looks_like_halide_ion() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.looks_like_halide_ion", false]], "looks_like_nucleotide_phosphate_site() (mmtbx.ions.identify.atomproperties method)": [[298, "mmtbx.ions.identify.AtomProperties.looks_like_nucleotide_phosphate_site", false]], "lookup() (mmtbx.monomer_library.conformation_dependent_restraints.pgd_server method)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.pgd_server.lookup", false]], "lookup_i_proxy() (cctbx.geometry_restraints.angle_proxy_registry method)": [[131, "cctbx.geometry_restraints.angle_proxy_registry.lookup_i_proxy", false]], "lookup_i_proxy() (cctbx.geometry_restraints.dihedral_proxy_registry method)": [[131, "cctbx.geometry_restraints.dihedral_proxy_registry.lookup_i_proxy", false]], "loop (class in iotbx.cif.model)": [[264, "iotbx.cif.model.loop", false]], "loop() (cctbx.development.random_structure.wyckoff_pair_generator method)": [[40, "cctbx.development.random_structure.wyckoff_pair_generator.loop", false]], "loop_over_space_groups() (cctbx.development.space_group_option_parser.space_group_processed_options method)": [[43, "cctbx.development.space_group_option_parser.space_group_processed_options.loop_over_space_groups", false]], "loop_over_super_cells() (in module cctbx.examples.space_subgroups)": [[112, "cctbx.examples.space_subgroups.loop_over_super_cells", false]], "loop_res_fac() (in module cctbx.examples.fft_map_electron_density_around_atom)": [[88, "cctbx.examples.fft_map_electron_density_around_atom.loop_res_fac", false]], "loop_space_groups() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.loop_space_groups", false]], "looped_data (class in mmtbx.monomer_library.cif_types)": [[308, "mmtbx.monomer_library.cif_types.looped_data", false]], "looped_ids() (mmtbx.monomer_library.cif_types.looped_data method)": [[308, "mmtbx.monomer_library.cif_types.looped_data.looped_ids", false]], "low_anom (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_anom", false]], "low_b (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LOW_B", false]], "low_b_iso (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_b_iso", false]], "low_d_cut (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.low_d_cut", false]], "low_fdp (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_fdp", false]], "low_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_fofc", false]], "low_occ (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_occ", false]], "low_occ (mmtbx.ions.identify.atomproperties attribute)": [[298, "mmtbx.ions.identify.AtomProperties.LOW_OCC", false]], "low_two_fofc (mmtbx.ions.atom_type_flags attribute)": [[293, "mmtbx.ions.atom_type_flags.low_two_fofc", false]], "low_volume_density_elimination() (in module mmtbx.maps.fem)": [[305, "mmtbx.maps.fem.low_volume_density_elimination", false]], "lower() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.lower", false]], "lower_bidiagonal() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.lower_bidiagonal", false]], "ls_ff_weights() (in module mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.ls_ff_weights", false]], "ls_ff_weights() (in module mmtbx.twinning.twin_f_model)": [[324, "mmtbx.twinning.twin_f_model.ls_ff_weights", false]], "ls_rel_scale_driver (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.ls_rel_scale_driver", false]], "ls_sigma_weights() (in module mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.ls_sigma_weights", false]], "ls_sigma_weights() (in module mmtbx.twinning.twin_f_model)": [[324, "mmtbx.twinning.twin_f_model.ls_sigma_weights", false]], "macro_cycle_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.macro_cycle_header", false]], "macromolecule_fraction() (mmtbx.scaling.matthews.density_calculator method)": [[318, "mmtbx.scaling.matthews.density_calculator.macromolecule_fraction", false]], "macromolecules (mmtbx.validation.model_properties.model_statistics property)": [[326, "mmtbx.validation.model_properties.model_statistics.macromolecules", false]], "magnification() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.magnification", false]], "magnification_anisotropic_minimization (class in cctbx.maptbx.real_space_refinement_simple)": [[142, "cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization", false]], "main() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.main", false]], "main() (in module cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.main", false]], "main() (in module cctbx.eltbx.development.itvc_approx)": [[56, "cctbx.eltbx.development.itvc_approx.main", false]], "main() (in module cctbx.eltbx.development.itvc_cross_validation)": [[57, "cctbx.eltbx.development.itvc_cross_validation.main", false]], "main() (in module cctbx.eltbx.development.itvc_fits)": [[58, "cctbx.eltbx.development.itvc_fits.main", false]], "main() (in module cctbx.eltbx.development.kissel_fits)": [[61, "cctbx.eltbx.development.kissel_fits.main", false]], "main() (in module cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.main", false]], "main() (in module xfel.cxi.average_spots)": [[342, "xfel.cxi.average_spots.main", false]], "make_and_place_nodes_and_connections() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.make_and_place_nodes_and_connections", false]], "make_beam() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.make_beam", false]], "make_big_header() (in module mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.make_big_header", false]], "make_detector() (dxtbx.model.detector.detectorfactory static method)": [[257, "dxtbx.model.detector.DetectorFactory.make_detector", false]], "make_flips_if_necessary_torsion() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.make_flips_if_necessary_torsion", false]], "make_g6() (xfel.clustering.singleframe.singleframe static method)": [[340, "xfel.clustering.singleframe.SingleFrame.make_g6", false]], "make_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.make_goniometer", false]], "make_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.make_header", false]], "make_int_pickle() (in module xfel.command_line.cxi_stream_to_pickle)": [[341, "xfel.command_line.cxi_stream_to_pickle.make_int_pickle", false]], "make_kappa_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.make_kappa_goniometer", false]], "make_list_of_target_xs_up_to_order (class in cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order", false]], "make_log_beam_stop() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_beam_stop", false]], "make_log_model() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_model", false]], "make_log_wilson() (mmtbx.scaling.outlier_rejection.outlier_manager method)": [[318, "mmtbx.scaling.outlier_rejection.outlier_manager.make_log_wilson", false]], "make_md5() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.make_md5", false]], "make_multi_axis_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.make_multi_axis_goniometer", false]], "make_multikin() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.make_multikin", false]], "make_new_cell_and_symmetry() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method)": [[186, "cctbx.sgtbx.sub_lattice_tools.compare_lattice.make_new_cell_and_symmetry", false]], "make_new_xs() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs.make_new_xs", false]], "make_new_xs() (cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order method)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order.make_new_xs", false]], "make_peak_dict() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.make_peak_dict", false]], "make_permutations() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_permutations", false]], "make_pg_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.make_pg_r_table", false]], "make_point() (in module cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.make_point", false]], "make_polarized_beam() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.make_polarized_beam", false]], "make_polychromatic_beam() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.make_polychromatic_beam", false]], "make_probe_dots() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.make_probe_dots", false]], "make_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method)": [[318, "mmtbx.scaling.twin_analyses.symmetry_issues.make_r_table", false]], "make_scan() (dxtbx.model.scan.scanfactory static method)": [[257, "dxtbx.model.scan.ScanFactory.make_scan", false]], "make_scan_from_properties() (dxtbx.model.scan.scanfactory static method)": [[257, "dxtbx.model.scan.ScanFactory.make_scan_from_properties", false]], "make_scatterer_labels_shelx_compatible_in_place() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.make_scatterer_labels_shelx_compatible_in_place", false]], "make_sub_cluster() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.make_sub_cluster", false]], "make_sub_header() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.make_sub_header", false]], "make_sym_op_table() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.make_sym_op_table", false]], "make_sys_abs_list() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)": [[181, "cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups.make_sys_abs_list", false]], "make_tlso_compatible_with_u_positive_definite() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.make_tlso_compatible_with_u_positive_definite", false]], "make_triples() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.make_triples", false]], "make_up_hl_coeffs() (cctbx.miller.array method)": [[148, "cctbx.miller.array.make_up_hl_coeffs", false]], "makeatomdict() (in module mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.makeAtomDict", false]], "manage_sql (class in xfel.cxi.correction_vector_plot)": [[342, "xfel.cxi.correction_vector_plot.manage_sql", false]], "managed_calculation_base (class in cctbx.xray.structure_factors.manager)": [[250, "cctbx.xray.structure_factors.manager.managed_calculation_base", false]], "manager (class in cctbx.geometry_restraints.manager)": [[135, "cctbx.geometry_restraints.manager.manager", false]], "manager (class in cctbx.xray.structure_factors.manager)": [[250, "cctbx.xray.structure_factors.manager.manager", false]], "manager (class in mmtbx.den.refinement)": [[284, "mmtbx.den.refinement.manager", false]], "manager (class in mmtbx.ias)": [[292, "mmtbx.ias.manager", false]], "manager (class in mmtbx.ions.identify)": [[298, "mmtbx.ions.identify.manager", false]], "manager (class in mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.manager", false]], "manager (class in mmtbx.masks)": [[306, "mmtbx.masks.manager", false]], "manager (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.manager", false]], "manager (class in mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager", false]], "manager (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.manager", false]], "manager (class in mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.manager", false]], "manager (class in mmtbx.refinement.refinement_flags)": [[313, "mmtbx.refinement.refinement_flags.manager", false]], "manager (class in mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.manager", false]], "manager (class in mmtbx.secondary_structure)": [[319, "mmtbx.secondary_structure.manager", false]], "manager (class in mmtbx.solvent.ensemble_ordered_solvent)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager", false]], "manager (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.manager", false]], "manager() (cctbx.xray.structure_factors.manager.managed_calculation_base method)": [[250, "cctbx.xray.structure_factors.manager.managed_calculation_base.manager", false]], "manager() (in module mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.manager", false]], "mandatory_factors() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.mandatory_factors", false]], "mandatory_grid_factors() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.mandatory_grid_factors", false]], "map_accumulator() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_accumulator", false]], "map_and_map_coeff_master_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.map_and_map_coeff_master_params", false]], "map_as_fourier_coefficients() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.map_as_fourier_coefficients", false]], "map_as_fourier_coefficients() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_as_fourier_coefficients", false]], "map_cc() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.map_cc", false]], "map_cc_histogram_per_atom() (mmtbx.refinement.real_space.structure_monitor method)": [[315, "mmtbx.refinement.real_space.structure_monitor.map_cc_histogram_per_atom", false]], "map_coefficients() (cctbx.maptbx.mem.run method)": [[140, "cctbx.maptbx.mem.run.map_coefficients", false]], "map_coefficients() (mmtbx.maps.composite_omit_map.run method)": [[305, "mmtbx.maps.composite_omit_map.run.map_coefficients", false]], "map_coefficients() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.map_coefficients", false]], "map_coefficients() (mmtbx.utils.extract_box_around_model_and_map method)": [[325, "mmtbx.utils.extract_box_around_model_and_map.map_coefficients", false]], "map_coefficients_from_fmodel() (in module mmtbx.maps)": [[305, "mmtbx.maps.map_coefficients_from_fmodel", false]], "map_coefficients_to_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_coefficients_to_map", false]], "map_coeffs_from_map() (mmtbx.maps.kick.run method)": [[305, "mmtbx.maps.kick.run.map_coeffs_from_map", false]], "map_coeffs_from_mtz_file() (in module mmtbx.maps.utils)": [[305, "mmtbx.maps.utils.map_coeffs_from_mtz_file", false]], "map_coeffs_in_original_setting (mmtbx.density_modification.density_modification property)": [[285, "mmtbx.density_modification.density_modification.map_coeffs_in_original_setting", false]], "map_coeffs_list (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.map_coeffs_list", false]], "map_coeffs_mtz_label_manager (class in mmtbx.maps)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager", false]], "map_correlation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.map_correlation", false]], "map_data() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_data", false]], "map_data_1() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_data_1", false]], "map_data_2() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_data_2", false]], "map_data_list() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_data_list", false]], "map_detector_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.map_detector_to_basis_dict", false]], "map_dict() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_dict", false]], "map_id_list() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_id_list", false]], "map_info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_info", false]], "map_inside_unit_cell() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.map_inside_unit_cell", false]], "map_inside_unit_cell() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.map_inside_unit_cell", false]], "map_manager (class in iotbx.map_manager)": [[266, "iotbx.map_manager.map_manager", false]], "map_manager (class in mmtbx.hydrogens)": [[291, "mmtbx.hydrogens.map_manager", false]], "map_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_manager", false]], "map_manager() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.map_manager", false]], "map_manager_1() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_manager_1", false]], "map_manager_2() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_manager_2", false]], "map_manager_mask() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_manager_mask", false]], "map_managers() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_managers", false]], "map_map_cc() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.map_map_cc", false]], "map_map_cc() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_map_cc", false]], "map_map_fsc() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_map_fsc", false]], "map_model_cc() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.map_model_cc", false]], "map_model_manager (class in iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.map_model_manager", false]], "map_names (class in mmtbx)": [[276, "mmtbx.map_names", false]], "map_of_coeff_scaled() (in module mmtbx.max_lik.max_like_non_uniform)": [[307, "mmtbx.max_lik.max_like_non_uniform.map_of_coeff_scaled", false]], "map_peak_3d_as_2d() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_peak_3d_as_2d", false]], "map_peak_filter() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.map_peak_filter", false]], "map_stats (mmtbx.ions.svm.svm_prediction attribute)": [[299, "id4", false], [299, "mmtbx.ions.svm.svm_prediction.map_stats", false]], "map_stats() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.map_stats", false]], "map_to_asu() (cctbx.miller.array method)": [[148, "cctbx.miller.array.map_to_asu", false]], "map_to_asu() (cctbx.miller.set method)": [[148, "cctbx.miller.set.map_to_asu", false]], "map_to_map_coefficients() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_to_map_coefficients", false]], "map_values_along_line_connecting_two_points() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.map_values_along_line_connecting_two_points", false]], "maps (class in mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.maps", false]], "maps_including_io_master_params() (in module mmtbx.maps)": [[305, "mmtbx.maps.maps_including_IO_master_params", false]], "marks (mmtbx.validation.graphics.residue_bin attribute)": [[326, "mmtbx.validation.graphics.residue_bin.marks", false]], "markup (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.markup", false]], "markup (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.markup", false]], "mask() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.mask", false]], "mask() (mmtbx.density_modification.local_standard_deviation_map method)": [[285, "mmtbx.density_modification.local_standard_deviation_map.mask", false]], "mask_all_maps_around_atoms() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.mask_all_maps_around_atoms", false]], "mask_all_maps_around_density() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.mask_all_maps_around_density", false]], "mask_all_maps_around_edges() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.mask_all_maps_around_edges", false]], "mask_as_xplor_map() (mmtbx.masks.bulk_solvent method)": [[306, "mmtbx.masks.bulk_solvent.mask_as_xplor_map", false]], "mask_data_whole_uc() (mmtbx.masks.asu_mask method)": [[306, "mmtbx.masks.asu_mask.mask_data_whole_uc", false]], "mask_from_xray_structure (class in mmtbx.masks)": [[306, "mmtbx.masks.mask_from_xray_structure", false]], "mask_grid() (in module mmtbx.maps.superpose)": [[305, "mmtbx.maps.superpose.mask_grid", false]], "mask_info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.mask_info", false]], "massage_data (class in mmtbx.scaling.massage_twin_detwin_data)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data", false]], "master_params() (in module mmtbx.dynamics.simulated_annealing)": [[287, "mmtbx.dynamics.simulated_annealing.master_params", false]], "master_params() (in module mmtbx.pdbtools)": [[310, "mmtbx.pdbtools.master_params", false]], "master_params() (in module mmtbx.solvent.ensemble_ordered_solvent)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.master_params", false]], "master_params() (in module mmtbx.solvent.ordered_solvent)": [[321, "mmtbx.solvent.ordered_solvent.master_params", false]], "master_phil (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.master_phil", false]], "master_phil() (in module mmtbx.ions.svm.dump_sites)": [[300, "mmtbx.ions.svm.dump_sites.master_phil", false]], "match_bijvoet_mates() (cctbx.miller.set method)": [[148, "cctbx.miller.set.match_bijvoet_mates", false]], "match_cb_to_ca() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.match_cb_to_ca", false]], "match_dihedral_to_name() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.match_dihedral_to_name", false]], "match_dod() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.match_dod", false]], "match_indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.match_indices", false]], "match_map_model_ncs (class in iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.match_map_model_ncs", false]], "match_model_b_to_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.match_model_b_to_map", false]], "match_od() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.match_od", false]], "match_record (class in cctbx.command_line.euclidean_model_matching)": [[12, "cctbx.command_line.euclidean_model_matching.match_record", false]], "match_refine (class in cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.match_refine", false]], "match_refine_times() (in module cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.match_refine_times", false]], "match_rt_from_ref_eucl_rt() (in module cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.match_rt_from_ref_eucl_rt", false]], "match_runs() (in module xfel.command_line.auto_submit)": [[341, "xfel.command_line.auto_submit.match_runs", false]], "match_sort_function() (in module cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.match_sort_function", false]], "matching_set() (cctbx.miller.array method)": [[148, "cctbx.miller.array.matching_set", false]], "mathematica_form() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.mathematica_form", false]], "mathematica_form() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.mathematica_form", false]], "mathform_adp() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathForm_adp", false]], "mathformmx33() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathFormMx33", false]], "mathformvec3() (in module cctbx.development.fmt_utils)": [[37, "cctbx.development.fmt_utils.MathFormVec3", false]], "matlab_form() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.matlab_form", false]], "matrix33 (class in cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33", false]], "matrix_back_substitution() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_back_substitution", false]], "matrix_back_substitution_given_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_back_substitution_given_transpose", false]], "matrix_copy_block() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.matrix_copy_block", false]], "matrix_copy_block() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_copy_block", false]], "matrix_copy_block() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_block", false]], "matrix_copy_block() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_copy_block", false]], "matrix_copy_block() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_copy_block", false]], "matrix_copy_column() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_column", false]], "matrix_copy_lower_to_upper_triangle_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_lower_to_upper_triangle_in_place", false]], "matrix_copy_lower_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_lower_triangle", false]], "matrix_copy_upper_to_lower_triangle_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_upper_to_lower_triangle_in_place", false]], "matrix_copy_upper_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_copy_upper_triangle", false]], "matrix_determinant_via_lu() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_determinant_via_lu", false]], "matrix_diagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal", false]], "matrix_diagonal_add_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_add_in_place", false]], "matrix_diagonal_product() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_product", false]], "matrix_diagonal_set_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_set_in_place", false]], "matrix_diagonal_sum() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_diagonal_sum", false]], "matrix_forward_substitution() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_forward_substitution", false]], "matrix_forward_substitution_given_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_forward_substitution_given_transpose", false]], "matrix_inversion() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_inversion", false]], "matrix_inversion_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_inversion_in_place", false]], "matrix_is_symmetric() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_is_symmetric", false]], "matrix_is_symmetric() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_is_symmetric", false]], "matrix_is_symmetric() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_is_symmetric", false]], "matrix_lower_bidiagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lower_bidiagonal", false]], "matrix_lower_triangle_as_packed_l() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lower_triangle_as_packed_l", false]], "matrix_lu_back_substitution() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lu_back_substitution", false]], "matrix_lu_decomposition_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_lu_decomposition_in_place", false]], "matrix_multiply() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_multiply", false]], "matrix_multiply() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply", false]], "matrix_multiply_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply_packed_u", false]], "matrix_multiply_packed_u_multiply_lhs_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply_packed_u_multiply_lhs_transpose", false]], "matrix_multiply_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_multiply_transpose", false]], "matrix_norm_1() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_norm_1", false]], "matrix_norm_frobenius() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_norm_frobenius", false]], "matrix_norm_inf() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_norm_inf", false]], "matrix_outer_product() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_outer_product", false]], "matrix_packed_l_as_lower_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_l_as_lower_triangle", false]], "matrix_packed_l_as_symmetric() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_l_as_symmetric", false]], "matrix_packed_u_as_symmetric() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_packed_u_as_symmetric", false]], "matrix_packed_u_as_symmetric() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_as_symmetric", false]], "matrix_packed_u_as_upper_triangle() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_as_upper_triangle", false]], "matrix_packed_u_diagonal() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_packed_u_diagonal", false]], "matrix_packed_u_diagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_diagonal", false]], "matrix_packed_u_diagonal_add_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_diagonal_add_in_place", false]], "matrix_packed_u_swap_rows_and_columns_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_packed_u_swap_rows_and_columns_in_place", false]], "matrix_paste_block_in_place() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.matrix_paste_block_in_place", false]], "matrix_paste_block_in_place() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_paste_block_in_place", false]], "matrix_paste_block_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_paste_block_in_place", false]], "matrix_paste_block_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_paste_block_in_place", false]], "matrix_paste_block_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_paste_block_in_place", false]], "matrix_paste_column_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_paste_column_in_place", false]], "matrix_rot90() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_rot90", false]], "matrix_rot90() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_rot90", false]], "matrix_rot90() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_rot90", false]], "matrix_swap_columns_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_swap_columns_in_place", false]], "matrix_swap_columns_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_swap_columns_in_place", false]], "matrix_swap_columns_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_swap_columns_in_place", false]], "matrix_swap_rows_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_swap_rows_in_place", false]], "matrix_swap_rows_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_swap_rows_in_place", false]], "matrix_swap_rows_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_swap_rows_in_place", false]], "matrix_symmetric_as_packed_l() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_as_packed_l", false]], "matrix_symmetric_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_as_packed_u", false]], "matrix_symmetric_upper_triangle_quadratic_form() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_upper_triangle_quadratic_form", false]], "matrix_symmetric_upper_triangle_swap_rows_and_columns_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_symmetric_upper_triangle_swap_rows_and_columns_in_place", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method)": [[138, "cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method)": [[138, "cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3.matrix_to_params", false]], "matrix_to_params() (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method)": [[138, "cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus.matrix_to_params", false]], "matrix_trace() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_trace", false]], "matrix_transpose() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.matrix_transpose", false]], "matrix_transpose() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose", false]], "matrix_transpose_in_place() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_in_place", false]], "matrix_transpose_in_place() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.matrix_transpose_in_place", false]], "matrix_transpose_in_place() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.matrix_transpose_in_place", false]], "matrix_transpose_multiply() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_multiply", false]], "matrix_transpose_multiply_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_multiply_as_packed_u", false]], "matrix_transpose_multiply_diagonal_multiply_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_transpose_multiply_diagonal_multiply_as_packed_u", false]], "matrix_upper_bidiagonal() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_upper_bidiagonal", false]], "matrix_upper_triangle_as_packed_u() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.matrix_upper_triangle_as_packed_u", false]], "matthews_analysis() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.matthews_analysis", false]], "matthews_n_copies() (mmtbx.scaling.xtriage.xtriage_analyses method)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.matthews_n_copies", false]], "matthews_rupp (class in mmtbx.scaling.matthews)": [[318, "mmtbx.scaling.matthews.matthews_rupp", false]], "max (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.max", false]], "max (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.max", false]], "max (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.max", false]], "max (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.max", false]], "max (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.max", false]], "max (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.max", false]], "max() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.max", false]], "max() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.max", false]], "max() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.max", false]], "max() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.max", false]], "max_absolute() (cctbx.xray.structure.meaningful_site_cart_differences method)": [[238, "cctbx.xray.structure.meaningful_site_cart_differences.max_absolute", false]], "max_b_factor (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.max_b_factor", false]], "max_clusters() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.max_clusters", false]], "max_clusters() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.max_clusters", false]], "max_d_min_delta() (mmtbx.scaling.data_statistics.analyze_resolution_limits method)": [[318, "mmtbx.scaling.data_statistics.analyze_resolution_limits.max_d_min_delta", false]], "max_default() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.max_default", false]], "max_distance() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.max_distance", false]], "max_distance() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.max_distance", false]], "max_distance() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.max_distance", false]], "max_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.max_distance_between_any_pair_with_id", false]], "max_distance_between_conformers() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.max_distance_between_conformers", false]], "max_distance_between_conformers() (mmtbx.disorder.analyze_model.process_pdb_hierarchy method)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.max_distance_between_conformers", false]], "max_element_length() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.max_element_length", false]], "max_estimated_twin_fraction (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.max_estimated_twin_fraction", false]], "max_fofc_value() (mmtbx.building.local_density_quality method)": [[277, "mmtbx.building.local_density_quality.max_fofc_value", false]], "max_grid_height() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.max_grid_height", false]], "max_index() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.max_index", false]], "max_like (class in cctbx.xray.target_functors)": [[252, "cctbx.xray.target_functors.max_like", false]], "max_number_of_shells() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method)": [[307, "mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution.max_number_of_shells", false]], "max_operators() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.max_operators", false]], "max_peaks() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.max_peaks", false]], "max_prime() (cctbx.maptbx.crystal_gridding method)": [[139, "cctbx.maptbx.crystal_gridding.max_prime", false]], "max_prime() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.max_prime", false]], "max_rmsd_between_conformers() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, "mmtbx.disorder.analyze_model.disordered_segment.max_rmsd_between_conformers", false]], "max_rmsd_between_conformers() (mmtbx.disorder.analyze_model.process_pdb_hierarchy method)": [[286, "mmtbx.disorder.analyze_model.process_pdb_hierarchy.max_rmsd_between_conformers", false]], "max_shift_over_esd (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit attribute)": [[333, "scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit.max_shift_over_esd", false]], "max_twin_fraction() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.max_twin_fraction", false]], "mcgregormatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.McGregorMatch", false]], "md5() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.md5", false]], "mean (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.mean", false]], "mean (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.mean", false]], "mean (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.mean", false]], "mean (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.mean", false]], "mean (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.mean", false]], "mean (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.mean", false]], "mean() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean", false]], "mean() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.mean", false]], "mean() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.mean", false]], "mean_default() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.mean_default", false]], "mean_density_at_sites() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.mean_density_at_sites", false]], "mean_distance() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.mean_distance", false]], "mean_of_intensity_divided_by_epsilon() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean_of_intensity_divided_by_epsilon", false]], "mean_of_squared_sigma_divided_by_epsilon() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean_of_squared_sigma_divided_by_epsilon", false]], "mean_phase_error() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean_phase_error", false]], "mean_scattering_density() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.mean_scattering_density", false]], "mean_sq() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean_sq", false]], "mean_weighted() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.mean_weighted", false]], "mean_weighted() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.mean_weighted", false]], "mean_weighted_phase_error() (cctbx.miller.array method)": [[148, "cctbx.miller.array.mean_weighted_phase_error", false]], "meaningful_site_cart_differences (class in cctbx.xray.structure)": [[238, "cctbx.xray.structure.meaningful_site_cart_differences", false]], "measurability() (cctbx.miller.array method)": [[148, "cctbx.miller.array.measurability", false]], "measureangle() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.measureAngle", false]], "measurechiangles() (mmtbx.rotamer.sidechain_angles.sidechainangles method)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.measureChiAngles", false]], "meets_main_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.meets_main_conditions", false]], "meets_primary_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method)": [[203, "cctbx.uctbx.reduction_base.gruber_parameterization.meets_primary_conditions", false]], "memory_element (class in cctbx.omz.bfgs)": [[154, "cctbx.omz.bfgs.memory_element", false]], "memory_id() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.memory_id", false]], "memory_id() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.memory_id", false]], "memory_id() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.memory_id", false]], "memory_id() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.memory_id", false]], "memory_id() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.memory_id", false]], "memory_id() (iotbx.pdb.hierarchy.residue method)": [[268, "iotbx.pdb.hierarchy.residue.memory_id", false]], "memory_id() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.memory_id", false]], "memory_id() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.memory_id", false]], "merge() (libtbx.group_args method)": [[273, "libtbx.group_args.merge", false]], "merge_and_overwrite_cifs() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.merge_and_overwrite_cifs", false]], "merge_atom_groups() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.merge_atom_groups", false]], "merge_atoms_at_end_to_residues() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.merge_atoms_at_end_to_residues", false]], "merge_data_and_guess_space_groups() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.merge_data_and_guess_space_groups", false]], "merge_dict() (mmtbx.validation.validation method)": [[326, "mmtbx.validation.validation.merge_dict", false]], "merge_dict() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.merge_dict", false]], "merge_disconnected_residue_groups_with_pure_altloc() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.merge_disconnected_residue_groups_with_pure_altloc", false]], "merge_equivalents (class in cctbx.miller)": [[148, "cctbx.miller.merge_equivalents", false]], "merge_equivalents() (cctbx.miller.array method)": [[148, "cctbx.miller.array.merge_equivalents", false]], "merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector)": [[257, "dxtbx.model.detector.merge_panel_scope_extracts_by_id", false]], "merge_residue_groups() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.merge_residue_groups", false]], "merge_split_maps_and_models() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.merge_split_maps_and_models", false]], "merge_two_dicts() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.merge_two_dicts", false]], "merging (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.merging", false]], "merging_and_model_statistics() (in module mmtbx.validation.experimental)": [[326, "mmtbx.validation.experimental.merging_and_model_statistics", false]], "merging_statistics (class in mmtbx.scaling.xtriage)": [[318, "mmtbx.scaling.xtriage.merging_statistics", false]], "metal_parameters (class in mmtbx.ions)": [[293, "mmtbx.ions.metal_parameters", false]], "metric_r() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method)": [[184, "cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs.metric_r", false]], "metric_subgroups (class in cctbx.sgtbx.lattice_symmetry)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_subgroups", false]], "metric_supergroup() (in module cctbx.sgtbx.lattice_symmetry)": [[178, "cctbx.sgtbx.lattice_symmetry.metric_supergroup", false]], "metriccriteria (class in cctbx.crystal.burzlaff_zimmermann_dewolff)": [[24, "cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria", false]], "metro_phil_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.metro_phil_to_basis_dict", false]], "metrology2phil() (in module xfel.cftbx.detector.metrology2phil)": [[339, "xfel.cftbx.detector.metrology2phil.metrology2phil", false]], "mfo (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.MFO", false]], "midpoint() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.midpoint", false]], "miller_array_export_as_shelx_hklf() (in module iotbx.shelx.hklf)": [[271, "iotbx.shelx.hklf.miller_array_export_as_shelx_hklf", false]], "miller_array_in_original_setting() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.miller_array_in_original_setting", false]], "miller_arrays (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.miller_arrays", false]], "miller_arrays_as_cif_block (class in iotbx.cif)": [[264, "iotbx.cif.miller_arrays_as_cif_block", false]], "miller_indices (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.miller_indices", false]], "miller_indices_as_pdb_file() (cctbx.miller.set method)": [[148, "cctbx.miller.set.miller_indices_as_pdb_file", false]], "miller_set() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.miller_set", false]], "miller_set() (cctbx.xray.structure_factors.manager.managed_calculation_base method)": [[250, "cctbx.xray.structure_factors.manager.managed_calculation_base.miller_set", false]], "miller_set() (iotbx.xds.read_ascii.reader method)": [[272, "iotbx.xds.read_ascii.reader.miller_set", false]], "min (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.min", false]], "min (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.min", false]], "min (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.min", false]], "min (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.min", false]], "min (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.min", false]], "min (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.min", false]], "min() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.min", false]], "min() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.min", false]], "min() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.min", false]], "min() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.min", false]], "min_cross_distance() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.min_cross_distance", false]], "min_cross_distance() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_cross_distance", false]], "min_cubicle_edge() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_cubicle_edge", false]], "min_default() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.min_default", false]], "min_distance() (cctbx.sgtbx.harker.planes_cartesian method)": [[177, "cctbx.sgtbx.harker.planes_cartesian.min_distance", false]], "min_distance() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.min_distance", false]], "min_distance_between_any_pair() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.min_distance_between_any_pair", false]], "min_distance_between_any_pair() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.min_distance_between_any_pair", false]], "min_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.min_distance_between_any_pair_with_id", false]], "min_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.min_distance_between_any_pair_with_id", false]], "min_distance_sym_equiv() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.min_distance_sym_equiv", false]], "min_distance_sym_equiv() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.min_distance_sym_equiv", false]], "min_f_over_sigma() (cctbx.miller.array method)": [[148, "cctbx.miller.array.min_f_over_sigma", false]], "min_index() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.min_index", false]], "min_max_d_star_sq() (cctbx.miller.set method)": [[148, "cctbx.miller.set.min_max_d_star_sq", false]], "min_max_indices() (cctbx.miller.set method)": [[148, "cctbx.miller.set.min_max_indices", false]], "min_max_mean() (mmtbx.refinement.print_statistics.coordinate_shifts method)": [[313, "mmtbx.refinement.print_statistics.coordinate_shifts.min_max_mean", false]], "min_max_mean() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.min_max_mean", false]], "min_u_cart_eigenvalue() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.min_u_cart_eigenvalue", false]], "minimize (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.minimize", false]], "minimize() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.minimize", false]], "minimize() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.minimize", false]], "minimize_divide (class in cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide", false]], "minimize_wrapper_for_ramachandran() (in module mmtbx.refinement.geometry_minimization)": [[313, "mmtbx.refinement.geometry_minimization.minimize_wrapper_for_ramachandran", false]], "minimize_wrapper_with_map (class in 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false]], "molecule (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.Molecule", false]], "molecule (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.molecule", false]], "molprobity (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.molprobity", false]], "molprobity_flags() (in module mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.molprobity_flags", false]], "molprobity_score() (in module mmtbx.validation.utils)": [[326, "mmtbx.validation.utils.molprobity_score", false]], "molprobity_score() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.molprobity_score", false]], "molprobity_table_labels (mmtbx.validation.entity attribute)": [[326, "mmtbx.validation.entity.molprobity_table_labels", false]], "molprobity_version_number (mmtbx.validation.molprobity.molprobity attribute)": [[327, 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(mmtbx.validation.model_properties.model_statistics attribute)": [[326, "mmtbx.validation.model_properties.model_statistics.n_models", false]], "n_ncs_oper() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.n_ncs_oper", false]], "n_non_hd (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.n_non_hd", false]], "n_npd (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.n_npd", false]], "n_nuc (mmtbx.validation.model_properties.model_statistics attribute)": [[326, "mmtbx.validation.model_properties.model_statistics.n_nuc", false]], "n_other (mmtbx.utils.detect_hydrogen_nomenclature_problem attribute)": [[325, "mmtbx.utils.detect_hydrogen_nomenclature_problem.n_other", false]], "n_outliers (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.n_outliers", false]], "n_outliers (mmtbx.validation.clashscore.clashscore attribute)": [[326, "mmtbx.validation.clashscore.clashscore.n_outliers", false]], "n_outliers (mmtbx.validation.clashscore.nqh_flips attribute)": [[326, "mmtbx.validation.clashscore.nqh_flips.n_outliers", false]], "n_outliers (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.n_outliers", false]], "n_outliers (mmtbx.validation.model_properties.xray_structure_statistics attribute)": [[326, "mmtbx.validation.model_properties.xray_structure_statistics.n_outliers", false]], "n_outliers (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.n_outliers", false]], "n_outliers (mmtbx.validation.restraints.angles attribute)": [[326, "mmtbx.validation.restraints.angles.n_outliers", false]], "n_outliers (mmtbx.validation.restraints.bonds attribute)": [[326, "mmtbx.validation.restraints.bonds.n_outliers", false]], "n_outliers (mmtbx.validation.restraints.chiralities attribute)": [[326, "mmtbx.validation.restraints.chiralities.n_outliers", false]], "n_outliers (mmtbx.validation.restraints.dihedrals attribute)": [[326, "mmtbx.validation.restraints.dihedrals.n_outliers", false]], "n_outliers (mmtbx.validation.restraints.planarities attribute)": [[326, "mmtbx.validation.restraints.planarities.n_outliers", false]], "n_outliers (mmtbx.validation.restraints.restraint_validation attribute)": [[326, "mmtbx.validation.restraints.restraint_validation.n_outliers", false]], "n_outliers (mmtbx.validation.rna_geometry attribute)": [[326, "mmtbx.validation.rna_geometry.n_outliers", false]], "n_outliers (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.n_outliers", false]], "n_outliers (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.n_outliers", false]], "n_outliers (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.n_outliers", false]], "n_outliers (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.n_outliers", false]], "n_outliers (mmtbx.validation.validation attribute)": [[326, "mmtbx.validation.validation.n_outliers", false]], "n_outliers (mmtbx.validation.waters.waters attribute)": [[326, "mmtbx.validation.waters.waters.n_outliers", false]], "n_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.n_outliers", false]], "n_outliers() (mmtbx.scaling.relative_wilson.summary method)": [[318, "mmtbx.scaling.relative_wilson.summary.n_outliers", false]], "n_outliers_by_model (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.n_outliers_by_model", false]], "n_outliers_by_model (mmtbx.validation.clashscore.clashscore attribute)": [[326, 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(mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.n_refl", false]], "n_refl_outer (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.n_refl_outer", false]], "n_refl_refine (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.n_refl_refine", false]], "n_refl_refine_outer (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.n_refl_refine_outer", false]], "n_reflections_by_sigi() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.n_reflections_by_sigi", false]], "n_res() (mmtbx.validation.graphics.residue_bin method)": [[326, "mmtbx.validation.graphics.residue_bin.n_res", false]], "n_residues() (mmtbx.disorder.analyze_model.disordered_segment method)": [[286, 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mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.ncs", false]], "ncs_averaging() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.ncs_averaging", false]], "ncs_cc() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.ncs_cc", false]], "ncs_cc() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.ncs_cc", false]], "ncs_domain_pdb() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.ncs_domain_pdb", false]], "ncs_from_import() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_from_import", false]], "ncs_from_pdb_input_biomt() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_from_pdb_input_BIOMT", false]], "ncs_group (class in mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.ncs_group", false]], "ncs_grouping_and_group_dict() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.ncs_grouping_and_group_dict", false]], "ncs_groups() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_groups", false]], "ncs_object() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.ncs_object", false]], "ncs_object() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.ncs_object", false]], "ncs_object() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.ncs_object", false]], "ncs_oper_in_first_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_oper_in_first_group", false]], "ncs_read() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.ncs_read", false]], "nd() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.nd", false]], "nd() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.nd", false]], "nd() (scitbx.array_family.flex.double method)": [[331, 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method)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame.OnUpdate", false]], "onzoom() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.OnZoom", false]], "op (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression.op", false]], "open_rotarama_dlite() (in module mmtbx.rotamer.rotamer_eval)": [[316, "mmtbx.rotamer.rotamer_eval.open_rotarama_dlite", false]], "oper_adds_offset() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.oper_adds_offset", false]], "operation() (cctbx.sgtbx.harker.plane_fractional method)": [[177, "cctbx.sgtbx.harker.plane_fractional.operation", false]], "operator (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.operator", false]], "opposite_of_gradient() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method)": [[333, 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false]], "original_intensities_flag() (mmtbx.scaling.xtriage.xtriage_summary method)": [[318, "mmtbx.scaling.xtriage.xtriage_summary.original_intensities_flag", false]], "ortho() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.ortho", false]], "orthogonalizer (class in cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.orthogonalizer", false]], "orthorhombic_unit_cell_around_centered_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.orthorhombic_unit_cell_around_centered_scatterers", false]], "other (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.other", false]], "out (mmtbx.scaling.printed_output attribute)": [[318, "mmtbx.scaling.printed_output.out", false]], "out_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table)": [[174, "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table.out_cpp", false]], "out_percent (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.out_percent", false]], "out_percent (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.out_percent", false]], "outer_loop() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.outer_loop", false]], "outer_product() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.outer_product", false]], "outlier (mmtbx.ions.identify.ion_result attribute)": [[298, "mmtbx.ions.identify.ion_result.outlier", false]], "outlier (mmtbx.validation.atom attribute)": [[326, "mmtbx.validation.atom.outlier", false]], "outlier (mmtbx.validation.atoms attribute)": [[326, "mmtbx.validation.atoms.outlier", false]], "outlier (mmtbx.validation.cbetadev.cbeta attribute)": [[326, "mmtbx.validation.cbetadev.cbeta.outlier", false]], "outlier (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.outlier", false]], "outlier (mmtbx.validation.clashscore.nqh_flip attribute)": [[326, "mmtbx.validation.clashscore.nqh_flip.outlier", false]], "outlier (mmtbx.validation.entity attribute)": [[326, "mmtbx.validation.entity.outlier", false]], "outlier (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.outlier", false]], "outlier (mmtbx.validation.model_properties.atom_bfactor attribute)": [[326, "mmtbx.validation.model_properties.atom_bfactor.outlier", false]], "outlier (mmtbx.validation.model_properties.atom_occupancy attribute)": [[326, "mmtbx.validation.model_properties.atom_occupancy.outlier", false]], "outlier (mmtbx.validation.model_properties.residue_bfactor attribute)": [[326, "mmtbx.validation.model_properties.residue_bfactor.outlier", false]], "outlier (mmtbx.validation.model_properties.residue_occupancy attribute)": [[326, "mmtbx.validation.model_properties.residue_occupancy.outlier", false]], "outlier (mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.outlier", false]], "outlier (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.outlier", false]], "outlier (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.outlier", false]], "outlier (mmtbx.validation.residue attribute)": [[326, "mmtbx.validation.residue.outlier", false]], "outlier (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.outlier", false]], "outlier (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.outlier", false]], "outlier (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.outlier", false]], "outlier (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.outlier", false]], "outlier (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.outlier", false]], "outlier (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.outlier", false]], "outlier (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.outlier", false]], "outlier (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.outlier", false]], "outlier (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.outlier", false]], "outlier (mmtbx.validation.rotalyze.rotamer attribute)": [[326, "mmtbx.validation.rotalyze.rotamer.outlier", false]], "outlier (mmtbx.validation.rotalyze.rotamer_ensemble attribute)": [[326, "mmtbx.validation.rotalyze.rotamer_ensemble.outlier", false]], "outlier (mmtbx.validation.waters.water attribute)": [[326, 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(mmtbx.validation.molprobity.residue_multi_criterion attribute)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion.outliers", false]], "outliers_removed (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.outliers_removed", false]], "output_header (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.output_header", false]], "output_header (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.output_header", false]], "output_header (mmtbx.validation.ramalyze.ramalyze attribute)": [[326, "mmtbx.validation.ramalyze.ramalyze.output_header", false]], "output_header (mmtbx.validation.rna_validate.rna_angles attribute)": [[326, "mmtbx.validation.rna_validate.rna_angles.output_header", false]], "output_header (mmtbx.validation.rna_validate.rna_bonds attribute)": [[326, "mmtbx.validation.rna_validate.rna_bonds.output_header", false]], "output_header (mmtbx.validation.rna_validate.rna_puckers attribute)": [[326, "mmtbx.validation.rna_validate.rna_puckers.output_header", false]], "output_header (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.output_header", false]], "output_header (mmtbx.validation.validation attribute)": [[326, "mmtbx.validation.validation.output_header", false]], "output_image() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_image", false]], "output_kinemage() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.output_kinemage", false]], "output_matlab_form() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_matlab_form", false]], "output_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.output_spectrum", false]], "overall_cc() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_cc", false]], "overall_counts (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.overall_counts", false]], "overall_counts() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.overall_counts", false]], "overall_i_sig_i (mmtbx.scaling.xtriage.xtriage_analyses property)": [[318, "mmtbx.scaling.xtriage.xtriage_analyses.overall_i_sig_i", false]], "overall_isotropic_kb_estimate() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.overall_isotropic_kb_estimate", false]], "overall_note() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_note", false]], "overall_rmsd() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.overall_rmsd", false]], "overall_rsc (mmtbx.validation.experimental.real_space attribute)": [[326, "mmtbx.validation.experimental.real_space.overall_rsc", false]], "overlap (mmtbx.validation.clashscore.clash attribute)": [[326, "mmtbx.validation.clashscore.clash.overlap", false]], "overlap_predicate (class in mmtbx.geometry.indexing)": 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module cctbx.examples.random_puckers)": [[107, "cctbx.examples.random_puckers.pentagon_sites_cart", false]], "per_frame_helper_factory() (xfel.mono_simulation.mono_treatment.refinement method)": [[349, "xfel.mono_simulation.mono_treatment.refinement.per_frame_helper_factory", false]], "percent_allowed (mmtbx.validation.ramalyze.ramalyze property)": [[326, "mmtbx.validation.ramalyze.ramalyze.percent_allowed", false]], "percent_allowed (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.percent_allowed", false]], "percent_favored (mmtbx.validation.ramalyze.ramalyze property)": [[326, "mmtbx.validation.ramalyze.ramalyze.percent_favored", false]], "percent_favored (mmtbx.validation.rotalyze.rotalyze attribute)": [[326, "mmtbx.validation.rotalyze.rotalyze.percent_favored", false]], "percent_outliers (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.percent_outliers", false]], "percent_outliers (mmtbx.validation.validation property)": [[326, "mmtbx.validation.validation.percent_outliers", false]], "perform_least_squares_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_least_squares_scaling", false]], "perform_local_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_local_scaling", false]], "perform_outlier_rejection() (mmtbx.scaling.fa_estimation.combined_scaling method)": [[318, "mmtbx.scaling.fa_estimation.combined_scaling.perform_outlier_rejection", false]], "perms (cctbx.miller.reindexing.assistant attribute)": [[150, "cctbx.miller.reindexing.assistant.perms", false]], "permutation_generator() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.permutation_generator", false]], "permute_d_range() (cctbx.miller.array method)": [[148, "cctbx.miller.array.permute_d_range", false]], "pgd_server (class in mmtbx.monomer_library.conformation_dependent_restraints)": [[308, "mmtbx.monomer_library.conformation_dependent_restraints.pgd_server", false]], "ph() (mmtbx.ligands.xtal_screens.solution method)": [[304, "mmtbx.ligands.xtal_screens.solution.pH", false]], "ph_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.pH_", false]], "phase_entropy() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phase_entropy", false]], "phase_error() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.phase_error", false]], "phase_errors() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.phase_errors", false]], "phase_errors() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.phase_errors", false]], "phase_errors() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.phase_errors", false]], "phase_errors_test() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.phase_errors_test", false]], "phase_errors_work() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.phase_errors_work", false]], "phase_integrals() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phase_integrals", false]], "phase_transfer() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phase_transfer", false]], "phased_translation_function_coeff() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phased_translation_function_coeff", false]], "phaser_sad_llg (mmtbx.map_names attribute)": [[276, "mmtbx.map_names.phaser_sad_llg", false]], "phaser_sad_target_functor (class in mmtbx.refinement.targets)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor", false]], "phases() (cctbx.miller.array method)": [[148, "cctbx.miller.array.phases", false]], "phases() (mmtbx.maps.map_coeffs_mtz_label_manager method)": [[305, "mmtbx.maps.map_coeffs_mtz_label_manager.phases", false]], "phi (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.phi", false]], "phi (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.phi", false]], "phi_from_atoms() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_from_atoms", false]], "phi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_from_sites", false]], "phi_min_max_mean() (mmtbx.validation.ramalyze.ramachandran_ensemble method)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.phi_min_max_mean", false]], "phi_psi_from_sites() (in module mmtbx.rotamer)": [[316, "mmtbx.rotamer.phi_psi_from_sites", false]], "phi_range() (mmtbx.validation.ramalyze.ramachandran_ensemble method)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.phi_range", false]], "phi_sym_acceptance_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.phi_sym_acceptance_cutoff", false]], "phi_sym_rejection_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.phi_sym_rejection_cutoff", false]], "phil_atom_selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selection", false]], "phil_atom_selection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.phil_atom_selection", false]], "phil_atom_selection_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selection_multiple", false]], "phil_atom_selections_as_i_seqs() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selections_as_i_seqs", false]], "phil_atom_selections_as_i_seqs_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.phil_atom_selections_as_i_seqs_multiple", false]], "phil_lego (class in mmtbx.scaling.make_param)": [[318, "mmtbx.scaling.make_param.phil_lego", false]], "pick_nicest_fit() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.pick_nicest_fit", false]], "pixel_histograms (class in xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms", false]], "pixel_histograms (class in xfel.cxi.cspad_ana.pixel_histograms)": [[343, "xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms", false]], "pixelfiterror": [[341, "xfel.command_line.view_pixel_histograms.PixelFitError", false]], "pixels() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.pixels", false]], "planarities (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.planarities", false]], "planarities (mmtbx.validation.restraints.combined attribute)": [[326, "mmtbx.validation.restraints.combined.planarities", false]], "planarity (class in mmtbx.validation.restraints)": [[326, "mmtbx.validation.restraints.planarity", false]], "planarity_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.planarity_counters", false]], "planarity_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.planarity_deviations", false]], "planarity_proxy_registry (class in cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.planarity_proxy_registry", false]], "plane_atom_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.plane_atom_list", false]], "plane_cartesian (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.plane_cartesian", false]], "plane_fractional (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.plane_fractional", false]], "plane_group_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.plane_group_table", false]], "planes_cartesian (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.planes_cartesian", false]], "planes_fractional (class in cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.planes_fractional", false]], "plot() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot", false]], "plot_energy() (in module xfel.cxi.cspad_ana.xes_finalise)": [[343, "xfel.cxi.cspad_ana.xes_finalise.plot_energy", false]], "plot_gaussians() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot_gaussians", false]], "plot_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.plot_one_histogram", false]], "plot_overall_completeness() (in module xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.plot_overall_completeness", false]], "plot_range() (mmtbx.validation.graphics.multi_criterion_plot_mixin method)": [[326, "mmtbx.validation.graphics.multi_criterion_plot_mixin.plot_range", false]], "plot_samples() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.plot_samples", false]], "plot_samples_ix() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.plot_samples_ix", false]], "plot_statistics (class in xfel.command_line.cxi_merge)": [[341, "xfel.command_line.cxi_merge.plot_statistics", false]], "plot_statistics_histograms() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.plot_statistics_histograms", false]], "plot_unit_cell_histograms() (xfel.command_line.cxi_merge.plot_statistics method)": [[341, "xfel.command_line.cxi_merge.plot_statistics.plot_unit_cell_histograms", false]], "plot_weights_pyplot() (in module mmtbx.den.plot_weights)": [[284, "mmtbx.den.plot_weights.plot_weights_pyplot", false]], "plot_wilson() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.plot_wilson", false]], "plotit() (in module mmtbx.scaling.outlier_plots)": [[318, "mmtbx.scaling.outlier_plots.plotit", false]], "plus_minus (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.plus_minus", false]], "plus_minus (iotbx.shelx.tokens.element_token attribute)": [[271, "iotbx.shelx.tokens.element_token.plus_minus", false]], "plus_minus() (cctbx.merging.brehm_diederichs.minimize_divide method)": [[147, "cctbx.merging.brehm_diederichs.minimize_divide.plus_minus", false]], "point (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.point", false]], "point_group_filter() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.point_group_filter", false]], "point_group_graph (class in cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph", false]], "point_group_symbols (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_symbols", false]], "point_group_table (class in cctbx.web.asu_gallery.jv_index)": [[209, "cctbx.web.asu_gallery.jv_index.point_group_table", false]], "point_in_polygon() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.point_in_polygon", false]], "point_inside_circle() (in module xfel.command_line.make_mask)": [[341, "xfel.command_line.make_mask.point_inside_circle", false]], "points (mmtbx.geometry.asa.accessiblesurfaceareas property)": [[289, "mmtbx.geometry.asa.AccessibleSurfaceAreas.points", false]], "pointset (class in cctbx.web.asu_gallery.jvx)": [[210, "cctbx.web.asu_gallery.jvx.pointSet", false]], "polarization_correction() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.polarization_correction", false]], "polygon() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.polygon", false]], "polygon_layout (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.polygon_layout", false]], "polygon_stats (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.polygon_stats", false]], "polygon_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.polygon_vertices", false]], "polymeric_type_filter() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.polymeric_type_filter", false]], "pool_map() (in module libtbx.easy_mp)": [[274, "libtbx.easy_mp.pool_map", false]], "pop_back() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.pop_back", false]], "pop_back() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.pop_back", false]], "pop_back() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.pop_back", false]], "pop_back() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.pop_back", false]], "pop_back() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.pop_back", false]], "pop_back() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.pop_back", false]], "pop_back() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.pop_back", false]], "pop_back() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.pop_back", false]], "pop_back() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.pop_back", false]], "pop_back() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.pop_back", false]], "pop_back() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.pop_back", false]], "pop_back() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.pop_back", false]], "populate_bin_to_individual_k_mask_linear_interpolation() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.populate_bin_to_individual_k_mask_linear_interpolation", false]], "pos (cctbx.omz.dev.shift_limit_pair attribute)": [[158, "cctbx.omz.dev.shift_limit_pair.pos", false]], "position (class in cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.position", false]], "positions() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.positions", false]], "positivity_constrained_density_modification (class in cctbx.maptbx)": [[139, "cctbx.maptbx.positivity_constrained_density_modification", false]], "possible_cyclic_peptide() (in module mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.possible_cyclic_peptide", false]], "possible_outliers (class in mmtbx.scaling.data_statistics)": [[318, "mmtbx.scaling.data_statistics.possible_outliers", false]], "possible_point_group_generators() (cctbx.symmetry_search.structure_factor_symmetry method)": [[196, "cctbx.symmetry_search.structure_factor_symmetry.possible_point_group_generators", false]], "possible_symmetry (class in cctbx.symmetry_search)": [[196, "cctbx.symmetry_search.possible_symmetry", false]], "post_min_recalc() (xfel.metrology.mark1.fit_translation method)": [[347, "xfel.metrology.mark1.fit_translation.post_min_recalc", false]], "post_min_recalc() (xfel.metrology.mark3.fit_translation2 method)": [[347, "xfel.metrology.mark3.fit_translation2.post_min_recalc", false]], "post_outlier_rejection() (in module xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.post_outlier_rejection", false]], "post_query() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.post_query", false]], "post_report_query_with_pdb_list() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.post_report_query_with_pdb_list", false]], "postrefine_by_frame_mproc() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.postrefine_by_frame_mproc", false]], "potential_object (class in cctbx.omz.tardy_adaptor)": [[161, "cctbx.omz.tardy_adaptor.potential_object", false]], "potential_object (class in mmtbx.refinement.tardy)": [[313, "mmtbx.refinement.tardy.potential_object", false]], "pperp_distance (mmtbx.validation.rna_validate.rna_pucker attribute)": [[326, "mmtbx.validation.rna_validate.rna_pucker.Pperp_distance", false]], "pperp_outliers() (in module mmtbx.kinemage.validation)": [[303, "mmtbx.kinemage.validation.pperp_outliers", false]], "pprocess (class in cctbx.xray.structure_factors.from_scatterers_direct_parallel)": [[242, "cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess", false]], "pre_allocate_atom_groups() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.pre_allocate_atom_groups", false]], "pre_allocate_atoms() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.pre_allocate_atoms", false]], "pre_allocate_chains() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.pre_allocate_chains", false]], "pre_allocate_models() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.pre_allocate_models", false]], "pre_allocate_residue_groups() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.pre_allocate_residue_groups", false]], "pre_check() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.pre_check", false]], "pre_get_predictions() (in module xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.pre_get_predictions", false]], "pre_scaler (class in mmtbx.scaling.pre_scale)": [[318, "mmtbx.scaling.pre_scale.pre_scaler", false]], "predict_ion() (in module mmtbx.ions.svm)": [[299, "mmtbx.ions.svm.predict_ion", false]], "prefilter (class in mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.prefilter", false]], "prepare_f_obs_and_flags() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.prepare_f_obs_and_flags", false]], "prepare_for_minimization() (mmtbx.refinement.targets.phaser_sad_target_functor method)": [[313, "mmtbx.refinement.targets.phaser_sad_target_functor.prepare_for_minimization", false]], "prepare_for_minimization() (mmtbx.refinement.targets.target_functor method)": [[313, "mmtbx.refinement.targets.target_functor.prepare_for_minimization", false]], "prepare_for_minimization() (mmtbx.twinning.twin_f_model.target_functor method)": [[324, "mmtbx.twinning.twin_f_model.target_functor.prepare_for_minimization", false]], "prepare_gaussians_symmetries_cell() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method)": [[242, "cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess.prepare_gaussians_symmetries_cell", false]], "prepare_miller_arrays_for_cuda() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method)": [[242, "cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess.prepare_miller_arrays_for_cuda", false]], "prepare_scattering_sites_for_cuda() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method)": [[242, "cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess.prepare_scattering_sites_for_cuda", false]], "prepare_target_functors_for_minimization() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.prepare_target_functors_for_minimization", false]], "preprocess_angles() (in module cctbx.macro_mol.rotation_parameters)": [[138, "cctbx.macro_mol.rotation_parameters.preprocess_angles", false]], "primary_structure_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.primary_structure_section", false]], "prime_postrefine() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.prime_postrefine", false]], "primitive_setting() (cctbx.crystal.symmetry method)": [[23, 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false]], "random_modify_u_iso() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_u_iso", false]], "random_modify_u_star() (cctbx.development.random_structure.xray_structure method)": [[40, "cctbx.development.random_structure.xray_structure.random_modify_u_star", false]], "random_omit_data (class in mmtbx.scaling.random_omit)": [[318, "mmtbx.scaling.random_omit.random_omit_data", false]], "random_origin_shift() (in module cctbx.development.debug_utils)": [[34, "cctbx.development.debug_utils.random_origin_shift", false]], "random_phases_compatible_with_phase_restrictions() (cctbx.miller.set method)": [[148, "cctbx.miller.set.random_phases_compatible_with_phase_restrictions", false]], "random_remove_sites_selection() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.random_remove_sites_selection", false]], "random_rotate_ellipsoid() (in module cctbx.adptbx)": [[5, 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"cctbx.miller.array.randomize_phases", false]], "randomize_phases() (in module cctbx.examples.map_skewness)": [[99, "cctbx.examples.map_skewness.randomize_phases", false]], "randomize_struture_factors() (in module mmtbx.maps.kick)": [[305, "mmtbx.maps.kick.randomize_struture_factors", false]], "randomize_velocity() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.randomize_velocity", false]], "rascalmatch (class in mmtbx.geometry.topology)": [[289, "mmtbx.geometry.topology.RascalMatch", false]], "rat_rot_group (class in cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group", false]], "rat_rot_group (class in cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.rat_rot_group", false]], "ratio_cutoffs (mmtbx.polygon.output.renderer attribute)": [[311, "mmtbx.polygon.output.renderer.ratio_cutoffs", false]], "raw_data (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.raw_data", false]], "raw_flags (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.raw_flags", false]], "raw_probe_line_info (class in mmtbx.validation.clashscore)": [[326, "mmtbx.validation.clashscore.raw_probe_line_info", false]], "re_apply_symmetry() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.re_apply_symmetry", false]], "read_all_mysql() (xfel.command_line.cxi_xmerge.xscaling_manager method)": [[341, "xfel.command_line.cxi_xmerge.xscaling_manager.read_all_mysql", false]], "read_cif() (in module mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.read_cif", false]], "read_data() (xfel.metrology.mark0.correction_vectors method)": [[347, "xfel.metrology.mark0.correction_vectors.read_data", false]], "read_file() (iotbx.xds.integrate_hkl.reader method)": [[272, "iotbx.xds.integrate_hkl.reader.read_file", false]], "read_file() (iotbx.xds.spot_xds.reader method)": [[272, "iotbx.xds.spot_xds.reader.read_file", false]], "read_file() (iotbx.xds.xds_inp.reader method)": [[272, "iotbx.xds.xds_inp.reader.read_file", false]], "read_file() (iotbx.xds.xparm.reader method)": [[272, "iotbx.xds.xparm.reader.read_file", false]], "read_input() (in module xfel.command_line.postrefine)": [[341, "xfel.command_line.postrefine.read_input", false]], "read_map() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.read_map", false]], "read_model() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.read_model", false]], "read_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.read_ncs", false]], "read_ncs_file() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.read_ncs_file", false]], "read_optical_metrology_from_flat_file() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.read_optical_metrology_from_flat_file", false]], "read_pickled_fits (class in cctbx.eltbx.development.format_gaussian_fits)": [[54, "cctbx.eltbx.development.format_gaussian_fits.read_pickled_fits", false]], "read_scatterer() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.read_scatterer", false]], "read_structure() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.read_structure", false]], "read_table() (in module cctbx.eltbx.development.kissel_io)": [[62, "cctbx.eltbx.development.kissel_io.read_table", false]], "read_table6111() (in module cctbx.eltbx.development.itvc_section61_io)": [[60, "cctbx.eltbx.development.itvc_section61_io.read_table6111", false]], "reader (class in iotbx.cif)": [[264, "iotbx.cif.reader", false]], "reader (class in iotbx.shelx.hklf)": [[271, "iotbx.shelx.hklf.reader", false]], "reader (class in iotbx.xds.integrate_hkl)": [[272, "iotbx.xds.integrate_hkl.reader", false]], "reader (class in iotbx.xds.read_ascii)": [[272, "iotbx.xds.read_ascii.reader", false]], "reader (class in iotbx.xds.spot_xds)": [[272, "iotbx.xds.spot_xds.reader", false]], "reader (class in iotbx.xds.xds_inp)": [[272, "iotbx.xds.xds_inp.reader", false]], "reader (class in iotbx.xds.xparm)": [[272, "iotbx.xds.xparm.reader", false]], "real_space (class in mmtbx.validation.experimental)": [[326, "mmtbx.validation.experimental.real_space", false]], "real_space (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.real_space", false]], "real_space_refine() (mmtbx.building.box_build_refine_base method)": [[277, "mmtbx.building.box_build_refine_base.real_space_refine", false]], "real_space_refine() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method)": [[315, "mmtbx.refinement.real_space.fit_residue.run_with_minimization.real_space_refine", false]], "real_space_rigid_body_gradients_simple() (in module mmtbx.refinement.real_space.rigid_body)": [[315, "mmtbx.refinement.real_space.rigid_body.real_space_rigid_body_gradients_simple", false]], "realign() (mmtbx.building.make_library.ensembler method)": [[277, "mmtbx.building.make_library.ensembler.realign", false]], "reassemble() (in module cctbx.merging.brehm_diederichs)": [[147, "cctbx.merging.brehm_diederichs.reassemble", false]], "rec (class in scitbx.matrix)": [[334, "scitbx.matrix.rec", false]], "recalc_hits() (xfel.cxi.gfx.trials_plot.run method)": [[344, "xfel.cxi.gfx.trials_plot.Run.recalc_hits", false]], "reciprocal (cctbx.crystal_orientation.basis_type attribute)": [[31, "cctbx.crystal_orientation.basis_type.reciprocal", false]], "reciprocal_space_asu() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reciprocal_space_asu", false]], "recolor_grid_points() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.recolor_grid_points", false]], "reconstructed_amplitude (class in cctbx.xray.observation_types)": [[235, "cctbx.xray.observation_types.reconstructed_amplitude", false]], "record_type_counts() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.record_type_counts", false]], "records_for_pdb_file() (mmtbx.secondary_structure.manager method)": [[319, "mmtbx.secondary_structure.manager.records_for_pdb_file", false]], "recurring_operators() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.recurring_operators", false]], "red_color_model (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.red_color_model", false]], "reduce_for_tardy() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.reduce_for_tardy", false]], "reducingaccumulator (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.ReducingAccumulator", false]], "reduction (class in cctbx.uctbx.gruber_1973)": [[200, "cctbx.uctbx.gruber_1973.reduction", false]], "reduction (class in cctbx.uctbx.krivy_gruber_1976)": [[202, "cctbx.uctbx.krivy_gruber_1976.reduction", false]], "reduction_base (class in cctbx.uctbx.reduction_base)": [[203, "cctbx.uctbx.reduction_base.reduction_base", false]], "redundancies() (cctbx.miller.merge_equivalents method)": [[148, "cctbx.miller.merge_equivalents.redundancies", false]], "ref_radii_asa_probe (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.ref_radii_asa_probe", false]], "ref_to_k_overall() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.ref_to_k_overall", false]], "ref_to_k_part() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.ref_to_k_part", false]], "ref_to_k_sol() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.ref_to_k_sol", false]], "ref_to_twin_fraction() (mmtbx.twinning.twin_f_model.twin_fraction_object method)": [[324, "mmtbx.twinning.twin_f_model.twin_fraction_object.ref_to_twin_fraction", false]], "ref_to_u_part() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.ref_to_u_part", false]], "ref_to_u_sol() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.ref_to_u_sol", false]], "ref_to_u_star() (mmtbx.twinning.twin_f_model.scaling_parameters_object method)": [[324, "mmtbx.twinning.twin_f_model.scaling_parameters_object.ref_to_u_star", false]], "reference_dihedral_deviations() (cctbx.geometry_restraints.energies.energies method)": [[132, "cctbx.geometry_restraints.energies.energies.reference_dihedral_deviations", false]], "reference_setting() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reference_setting", false]], "reference_setting_choices() (in module cctbx.sgtbx.pointgroup_tools)": [[181, "cctbx.sgtbx.pointgroup_tools.reference_setting_choices", false]], "reference_space_group_infos() (in module cctbx.sgtbx)": [[165, "cctbx.sgtbx.reference_space_group_infos", false]], "refinable_params_one_ncs_to_asu() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method)": [[313, "mmtbx.refinement.minimization_ncs_constraints.lbfgs.refinable_params_one_ncs_to_asu", false]], "refine (class in mmtbx.refinement.real_space.rigid_body)": [[315, "mmtbx.refinement.real_space.rigid_body.refine", false]], "refine() (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method)": [[315, "mmtbx.refinement.real_space.individual_sites.box_refinement_manager.refine", false]], "refine() (mmtbx.refinement.real_space.individual_sites.diff_map method)": [[315, "mmtbx.refinement.real_space.individual_sites.diff_map.refine", false]], "refine() (mmtbx.refinement.real_space.individual_sites.simple method)": [[315, "mmtbx.refinement.real_space.individual_sites.simple.refine", false]], "refine_adjusted_shift() (cctbx.euclidean_model_matching.match_refine method)": [[77, "cctbx.euclidean_model_matching.match_refine.refine_adjusted_shift", false]], "refine_adp (class in mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.refine_adp", false]], "refine_all() (xfel.mono_simulation.mono_treatment.refinement2 method)": [[349, "xfel.mono_simulation.mono_treatment.refinement2.refine_all", false]], "refine_anomalous_substructure() (in module mmtbx.refinement.anomalous_scatterer_groups)": [[313, "mmtbx.refinement.anomalous_scatterer_groups.refine_anomalous_substructure", false]], "refine_anomalous_substructure() (mmtbx.ions.identify.manager method)": [[298, "mmtbx.ions.identify.manager.refine_anomalous_substructure", false]], "refine_groups (class in mmtbx.refinement.real_space.rigid_body)": [[315, "mmtbx.refinement.real_space.rigid_body.refine_groups", false]], "refine_mz (class in mmtbx.refinement.real_space.rigid_body)": [[315, "mmtbx.refinement.real_space.rigid_body.refine_mz", false]], "refine_oat() (mmtbx.solvent.ordered_solvent.manager method)": [[321, "mmtbx.solvent.ordered_solvent.manager.refine_oat", false]], "refine_rotx_roty2() (xfel.mono_simulation.mono_treatment.refinement method)": [[349, "xfel.mono_simulation.mono_treatment.refinement.refine_rotx_roty2", false]], "refinement (class in cctbx.omz.dev)": [[158, "cctbx.omz.dev.refinement", false]], "refinement (class in xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.refinement", false]], "refinement2 (class in xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.refinement2", false]], "refinement_base (class in xfel.mono_simulation.mono_treatment)": [[349, "xfel.mono_simulation.mono_treatment.refinement_base", false]], "refinement_monitor (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.refinement_monitor", false]], "refinement_program (mmtbx.validation.molprobity.pdb_header_info attribute)": [[327, "mmtbx.validation.molprobity.pdb_header_info.refinement_program", false]], "refinery (class in cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.refinery", false]], "refinery (class in cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.refinery", false]], "refinery (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.refinery", false]], "refinery (class in mmtbx.scaling.relative_scaling)": [[318, "mmtbx.scaling.relative_scaling.refinery", false]], "refit_residues() (in module mmtbx.building.extend_sidechains)": [[277, "mmtbx.building.extend_sidechains.refit_residues", false]], "reflection_intensity_equivalent_groups() (cctbx.sgtbx.space_group_info method)": [[165, "cctbx.sgtbx.space_group_info.reflection_intensity_equivalent_groups", false]], "reflection_intensity_symmetry() (cctbx.crystal.symmetry method)": [[23, "cctbx.crystal.symmetry.reflection_intensity_symmetry", false]], "reflection_intensity_symmetry() (cctbx.miller.set method)": [[148, "cctbx.miller.set.reflection_intensity_symmetry", false]], "region_density_correlation() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.region_density_correlation", false]], "registry (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.registry", false]], "registry() (in module cctbx.xray.target_functors)": [[252, "cctbx.xray.target_functors.registry", false]], "regularize() (cctbx.miller.array method)": [[148, "cctbx.miller.array.regularize", false]], "regularize_model() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.regularize_model", false]], "reindexing (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.reindexing", false]], "reindexing_operators (class in cctbx.crystal.reindex)": [[30, "cctbx.crystal.reindex.reindexing_operators", false]], "rejected (cctbx.symmetry_search.possible_symmetry attribute)": [[196, "cctbx.symmetry_search.possible_symmetry.rejected", false]], "related_chain (class in mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.related_chain", false]], "relative_sd_on_edges() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.relative_sd_on_edges", false]], "relative_wilson (class in mmtbx.scaling.relative_wilson)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson", false]], "remapped() (mmtbx.geometry.topology.greedymatch method)": [[289, "mmtbx.geometry.topology.GreedyMatch.remapped", false]], "remapped() (mmtbx.geometry.topology.mcgregormatch method)": [[289, "mmtbx.geometry.topology.McGregorMatch.remapped", false]], "remapped() (mmtbx.geometry.topology.rascalmatch method)": [[289, "mmtbx.geometry.topology.RascalMatch.remapped", false]], "remark_3_tls() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.remark_3_tls", false]], "remark_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.remark_section", false]], "remark_section() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.remark_section", false]], "remediate_mismatches() (in module cctbx.r_free_utils)": [[162, "cctbx.r_free_utils.remediate_mismatches", false]], "remove_alt_confs() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_alt_confs", false]], "remove_angles_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_angles_in_place", false]], "remove_anisotropy() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.remove_anisotropy", false]], "remove_atom() (iotbx.pdb.hierarchy.atom_group method)": [[268, "iotbx.pdb.hierarchy.atom_group.remove_atom", false]], "remove_atom_group() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.remove_atom_group", false]], "remove_atoms() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_atoms", false]], "remove_c_beta_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_c_beta_torsion_restraints_in_place", false]], "remove_chain() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.remove_chain", false]], "remove_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_chi_torsion_restraints_in_place", false]], "remove_chiralities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_chiralities_in_place", false]], "remove_clashing_atoms() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.remove_clashing_atoms", false]], "remove_common_isotropic_adp() (mmtbx.maps.fem.run method)": [[305, "mmtbx.maps.fem.run.remove_common_isotropic_adp", false]], "remove_cone() (cctbx.miller.array method)": [[148, "cctbx.miller.array.remove_cone", false]], "remove_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_dihedrals_in_place", false]], "remove_extra() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_extra", false]], "remove_far_atoms() (in module mmtbx.ncs.ncs_search)": [[309, "mmtbx.ncs.ncs_search.remove_far_atoms", false]], "remove_hd() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_hd", false]], "remove_hetero() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_hetero", false]], "remove_incomplete_main_chain_protein() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_incomplete_main_chain_protein", false]], "remove_items_from_selection() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.remove_items_from_selection", false]], "remove_labels() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.remove_labels", false]], "remove_link() (mmtbx.monomer_library.linking_mixins.residuelinkclass method)": [[308, "mmtbx.monomer_library.linking_mixins.ResidueLinkClass.remove_link", false]], "remove_map_manager_by_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.remove_map_manager_by_id", false]], "remove_model() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_model", false]], "remove_model_by_id() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.remove_model_by_id", false]], "remove_model_outside_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.remove_model_outside_map", false]], "remove_ncs_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_ncs_dihedrals_in_place", false]], "remove_ncs_not_consistent_with_space_group_number() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_ncs_not_consistent_with_space_group_number", false]], "remove_non_matching_pairs() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.remove_non_matching_pairs", false]], "remove_origin_shift_and_unit_cell_crystal_symmetry() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.remove_origin_shift_and_unit_cell_crystal_symmetry", false]], "remove_outliers() (mmtbx.scaling.data_statistics.possible_outliers method)": [[318, "mmtbx.scaling.data_statistics.possible_outliers.remove_outliers", false]], "remove_outliers() (mmtbx.scaling.pair_analyses.outlier_rejection method)": [[318, "mmtbx.scaling.pair_analyses.outlier_rejection.remove_outliers", false]], "remove_outliers() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.remove_outliers", false]], "remove_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_parallelities_in_place", false]], "remove_patterson_origin_peak() (cctbx.miller.array method)": [[148, "cctbx.miller.array.remove_patterson_origin_peak", false]], "remove_planarities_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_planarities_in_place", false]], "remove_point_group_and_its_super_groups_from_graph() (cctbx.sgtbx.pointgroup_tools.point_group_graph method)": [[181, "cctbx.sgtbx.pointgroup_tools.point_group_graph.remove_point_group_and_its_super_groups_from_graph", false]], "remove_quotes_from_chain_id() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_quotes_from_chain_id", false]], "remove_ramachandran_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_ramachandran_in_place", false]], "remove_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_coordinate_restraints_in_place", false]], "remove_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_dihedral_manager", false]], "remove_reference_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_reference_dihedrals_in_place", false]], "remove_residue_group() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.remove_residue_group", false]], "remove_residue_groups_with_atoms_on_special_positions_selective() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_residue_groups_with_atoms_on_special_positions_selective", false]], "remove_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_secondary_structure_restraints", false]], "remove_selections() (in module mmtbx.utils)": [[325, "mmtbx.utils.remove_selections", false]], "remove_sidechain_atoms() (in module mmtbx.building)": [[277, "mmtbx.building.remove_sidechain_atoms", false]], "remove_single_quotes() (in module mmtbx.ncs.ncs)": [[309, "mmtbx.ncs.ncs.remove_single_quotes", false]], "remove_site_with_most_neighbors() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.remove_site_with_most_neighbors", false]], "remove_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.remove_solvent", false]], "remove_systematic_absences() (cctbx.miller.set method)": [[148, "cctbx.miller.set.remove_systematic_absences", false]], "remove_ter_or_break() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.remove_ter_or_break", false]], "remove_tmp_files() (in module cctbx.omz.cod_refine)": [[156, "cctbx.omz.cod_refine.remove_tmp_files", false]], "remove_user_supplied_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.remove_user_supplied_restraints_in_place", false]], "remove_zero_occupancy() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.remove_zero_occupancy", false]], "rename_angle() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_angle", false]], "rename_atom() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_atom", false]], "rename_bond() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_bond", false]], "rename_chain_id() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.rename_chain_id", false]], "rename_chir() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_chir", false]], "rename_generic() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_generic", false]], "rename_link_angle() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_angle", false]], "rename_link_bond() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_bond", false]], "rename_link_tor() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_link_tor", false]], "rename_plan() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_plan", false]], "rename_tor() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_tor", false]], "rename_tree() (in module mmtbx.monomer_library.conv_v2_v3)": [[308, "mmtbx.monomer_library.conv_v2_v3.rename_tree", false]], "render() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.render", false]], "render_2d (class in cctbx.miller.display)": [[149, "cctbx.miller.display.render_2d", false]], "render_pil (class in cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.render_pil", false]], "render_postscript (class in cctbx.command_line.precession_view)": [[15, "cctbx.command_line.precession_view.render_postscript", false]], "renderer (class in mmtbx.polygon.output)": [[311, "mmtbx.polygon.output.renderer", false]], "replace_scatterers() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.replace_scatterers", false]], "replace_site_symmetry() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.replace_site_symmetry", false]], "replace_sites_cart() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.replace_sites_cart", false]], "replace_sites_frac() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.replace_sites_frac", false]], "report() (cctbx.development.structure_factor_utils.collector method)": [[44, "cctbx.development.structure_factor_utils.collector.report", false]], "report() (cctbx.merging.brehm_diederichs.algorithm2 method)": [[147, "cctbx.merging.brehm_diederichs.algorithm2.report", false]], "report() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method)": [[308, "mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries.report", false]], "report() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.report", false]], "report_fraction_of_negative_observations_if_any() (in module cctbx.omz.cif_refine)": [[155, "cctbx.omz.cif_refine.report_fraction_of_negative_observations_if_any", false]], "report_unknown_message() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method)": [[308, "mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base.report_unknown_message", false]], "reprocess_pdb() (in module mmtbx.building)": [[277, "mmtbx.building.reprocess_pdb", false]], "requires_experimental_phases() (mmtbx.refinement.targets.target_attributes method)": [[313, "mmtbx.refinement.targets.target_attributes.requires_experimental_phases", false]], "res_type (mmtbx.validation.ramalyze.ramachandran attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran.res_type", false]], "res_type (mmtbx.validation.ramalyze.ramachandran_ensemble attribute)": [[326, "mmtbx.validation.ramalyze.ramachandran_ensemble.res_type", false]], "resample_on_different_grid() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.resample_on_different_grid", false]], "resatomstochi (mmtbx.rotamer.sidechain_angles.sidechainangles attribute)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles.resAtomsToChi", false]], "reserve() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.reserve", false]], "reserve() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.reserve", false]], "reserve() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.reserve", false]], "reserve() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.reserve", false]], "reserve() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.reserve", false]], "reserve() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.reserve", false]], "reserve() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.reserve", false]], "reserve() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.reserve", false]], "reserve() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.reserve", false]], "reserve() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.reserve", false]], "reserve() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.reserve", false]], "reserve() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.reserve", false]], "reserve() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.reserve", false]], "reset() (mmtbx.building.extend_sidechains.conformation_scorer method)": [[277, "mmtbx.building.extend_sidechains.conformation_scorer.reset", false]], "reset() (mmtbx.monomer_library.rotamer_utils.rotamer_iterator method)": [[308, "mmtbx.monomer_library.rotamer_utils.rotamer_iterator.reset", false]], "reset() (mmtbx.refinement.real_space.score method)": [[315, "mmtbx.refinement.real_space.score.reset", false]], "reset() (mmtbx.refinement.real_space.score3 method)": [[315, "mmtbx.refinement.real_space.score3.reset", false]], "reset() (mmtbx.refinement.real_space.score4 method)": [[315, "mmtbx.refinement.real_space.score4.reset", false]], "reset() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.reset", false]], "reset_atom_i_seqs() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.reset_atom_i_seqs", false]], "reset_cb_op() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.reset_cb_op", false]], "reset_i_seq() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.reset_i_seq", false]], "reset_i_seq_if_necessary() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.reset_i_seq_if_necessary", false]], "reset_internals() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.reset_internals", false]], "reset_max_error() (in module cctbx.eltbx.development.combine_fits)": [[51, "cctbx.eltbx.development.combine_fits.reset_max_error", false]], "reset_scan_points() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.reset_scan_points", false]], "reset_serial() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.reset_serial", false]], "reset_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method)": [[321, "mmtbx.solvent.ensemble_ordered_solvent.manager.reset_solvent", false]], "reset_tmp() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.reset_tmp", false]], "reset_tmp_for_occupancy_groups_simple() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.reset_tmp_for_occupancy_groups_simple", false]], "reshape() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.reshape", false]], "reshape() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.reshape", false]], "reshape() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.reshape", false]], "reshape() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.reshape", false]], "reshape() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.reshape", false]], "reshape() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.reshape", false]], "reshape() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.reshape", false]], "reshape() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.reshape", false]], "reshape() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.reshape", false]], "reshape() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.reshape", false]], "reshape() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.reshape", false]], "reshape() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.reshape", false]], "resid (mmtbx.validation.atom_base property)": [[326, "mmtbx.validation.atom_base.resid", false]], "resid (mmtbx.validation.residue property)": [[326, "mmtbx.validation.residue.resid", false]], "resid() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.resid", false]], "resid() (iotbx.pdb.hierarchy.residue method)": [[268, "iotbx.pdb.hierarchy.residue.resid", false]], "resid() (iotbx.pdb.hierarchy.residue_group method)": [[268, "iotbx.pdb.hierarchy.residue_group.resid", false]], "resid_str() (in module mmtbx.ncs.ligands)": [[309, "mmtbx.ncs.ligands.resid_str", false]], "resid_to_pymol() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.resid_to_pymol", false]], "residual (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.residual", false]], "residual (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.residual", false]], "residual (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.residual", false]], "residual (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.residual", false]], "residual (mmtbx.validation.restraints.planarity attribute)": [[326, "mmtbx.validation.restraints.planarity.residual", false]], "residual (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.residual", false]], "residual() (in module cctbx.examples.unit_cell_minimizers)": [[126, "cctbx.examples.unit_cell_minimizers.residual", false]], "residual() (in module cctbx.examples.unit_cell_refinement)": [[127, "cctbx.examples.unit_cell_refinement.residual", false]], "residue (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.residue", false]], "residue (class in mmtbx.validation)": [[326, "mmtbx.validation.residue", false]], "residue_altloc() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.residue_altloc", false]], "residue_bfactor (class in mmtbx.validation.model_properties)": [[326, "mmtbx.validation.model_properties.residue_bfactor", false]], "residue_bin (class in mmtbx.validation.graphics)": [[326, "mmtbx.validation.graphics.residue_bin", false]], "residue_binner (class in mmtbx.validation.graphics)": [[326, "mmtbx.validation.graphics.residue_binner", false]], "residue_density_quality() (in module mmtbx.building)": [[277, "mmtbx.building.residue_density_quality", false]], "residue_dict() (in module mmtbx.monomer_library.idealized_aa)": [[308, "mmtbx.monomer_library.idealized_aa.residue_dict", false]], "residue_evaluator (class in mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.residue_evaluator", false]], "residue_group (class in iotbx.pdb.hierarchy)": [[268, "iotbx.pdb.hierarchy.residue_group", false]], "residue_group (mmtbx.geometry.clash.symmetryequivalent property)": [[289, "mmtbx.geometry.clash.SymmetryEquivalent.residue_group", false]], "residue_group_id_str() (mmtbx.validation.atom_base method)": [[326, "mmtbx.validation.atom_base.residue_group_id_str", false]], "residue_group_id_str() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.residue_group_id_str", false]], "residue_group_is_linked_to_previous() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.residue_group_is_linked_to_previous", false]], "residue_group_proxy (class in mmtbx.disorder.analyze_model)": [[286, "mmtbx.disorder.analyze_model.residue_group_proxy", false]], "residue_groups() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.residue_groups", false]], "residue_groups() (iotbx.pdb.hierarchy.model method)": [[268, "iotbx.pdb.hierarchy.model.residue_groups", false]], "residue_groups() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.residue_groups", false]], "residue_groups_size() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.residue_groups_size", false]], "residue_id() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.residue_id", false]], "residue_id_str() (in module mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.residue_id_str", false]], "residue_monitor (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.residue_monitor", false]], "residue_multi_criterion (class in mmtbx.validation.molprobity)": [[327, "mmtbx.validation.molprobity.residue_multi_criterion", false]], "residue_name (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping.residue_name", false]], "residue_name (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute)": [[308, "mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary.residue_name", false]], "residue_name_plus_atom_names_interpreter() (iotbx.pdb.hierarchy.residue method)": [[268, "iotbx.pdb.hierarchy.residue.residue_name_plus_atom_names_interpreter", false]], "residue_number (iotbx.shelx.tokens.atomname_token attribute)": [[271, "iotbx.shelx.tokens.atomname_token.residue_number", false]], "residue_number (iotbx.shelx.tokens.element_token attribute)": [[271, "iotbx.shelx.tokens.element_token.residue_number", false]], "residue_occupancy (class in mmtbx.validation.model_properties)": [[326, "mmtbx.validation.model_properties.residue_occupancy", false]], "residue_real_space (class in mmtbx.validation.experimental)": [[326, "mmtbx.validation.experimental.residue_real_space", false]], "residue_token (class in iotbx.shelx.tokens)": [[271, "iotbx.shelx.tokens.residue_token", false]], "residue_type() (mmtbx.validation.ramalyze.ramachandran method)": [[326, "mmtbx.validation.ramalyze.ramachandran.residue_type", false]], "residuelinkclass (class in mmtbx.monomer_library.linking_mixins)": [[308, "mmtbx.monomer_library.linking_mixins.ResidueLinkClass", false]], "residues (mmtbx.validation.graphics.residue_bin attribute)": [[326, "mmtbx.validation.graphics.residue_bin.residues", false]], "residues (mmtbx.validation.molprobity.multi_criterion_view attribute)": [[327, "mmtbx.validation.molprobity.multi_criterion_view.residues", false]], "residues() (iotbx.pdb.hierarchy.chain method)": [[268, "iotbx.pdb.hierarchy.chain.residues", false]], "residues() (iotbx.pdb.hierarchy.conformer method)": [[268, "iotbx.pdb.hierarchy.conformer.residues", false]], "residues_are_adjacent() (in module mmtbx.building)": [[277, "mmtbx.building.residues_are_adjacent", false]], "residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.residues_in_common_list", false]], "residues_size() (iotbx.pdb.hierarchy.conformer method)": [[268, 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(mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers_and_poormap", false]], "sel_outliers_or_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_outliers_or_poormap", false]], "sel_phosphate() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_phosphate", false]], "sel_phosphate() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_phosphate", false]], "sel_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator.sel_poormap", false]], "sel_residues_within() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_residues_within", false]], "sel_ribose() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_ribose", false]], "sel_ribose() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_ribose", false]], "sel_sidechain() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_sidechain", false]], "sel_sidechain() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_sidechain", false]], "sel_within() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sel_within", false]], "sel_within() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.sel_within", false]], "select() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.select", false]], "select() (cctbx.miller.array method)": [[148, "cctbx.miller.array.select", false]], "select() (cctbx.miller.set method)": [[148, "cctbx.miller.set.select", false]], "select() (cctbx.sgtbx.literal_description.literal_description method)": [[179, "cctbx.sgtbx.literal_description.literal_description.select", false]], "select() (cctbx.xray.scatterer.anomalous_scatterer_group method)": [[237, "cctbx.xray.scatterer.anomalous_scatterer_group.select", false]], "select() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.select", false]], "select() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.select", false]], "select() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.select", false]], "select() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.select", false]], "select() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.select", false]], "select() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.select", false]], "select() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.select", false]], "select() (mmtbx.tls.tools.tls_groups method)": [[322, "mmtbx.tls.tools.tls_groups.select", false]], "select() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.select", false]], "select() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.select", false]], "select() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.select", false]], "select() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.select", false]], "select() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.select", false]], "select() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.select", false]], "select() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.select", false]], "select() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.select", false]], "select() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.select", false]], "select() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.select", false]], "select() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.select", false]], "select() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.select", false]], "select() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.select", false]], "select_acentric() (cctbx.miller.set method)": [[148, "cctbx.miller.set.select_acentric", false]], "select_and_transform() (mmtbx.scaling.pair_analyses.reindexing method)": [[318, "mmtbx.scaling.pair_analyses.reindexing.select_and_transform", false]], "select_centric() (cctbx.miller.set method)": [[148, "cctbx.miller.set.select_centric", false]], "select_color() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.select_color", false]], "select_crystal_symmetry() (in module cctbx.crystal)": [[23, "cctbx.crystal.select_crystal_symmetry", false]], "select_detached() (mmtbx.refinement.refinement_flags.manager method)": [[313, "mmtbx.refinement.refinement_flags.manager.select_detached", false]], "select_dict() (in module mmtbx.polygon)": [[311, "mmtbx.polygon.select_dict", false]], "select_first_ncs_group() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.select_first_ncs_group", false]], "select_first_ncs_operator() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.select_first_ncs_operator", false]], "select_good() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data.select_good", false]], "select_indices() (cctbx.miller.array method)": [[148, "cctbx.miller.array.select_indices", false]], "select_inplace() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.select_inplace", false]], "select_matching_segments() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.select_matching_segments", false]], "select_model (class in mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.select_model", false]], "select_n_in_biggest_cluster() (in module iotbx.map_manager)": [[266, "iotbx.map_manager.select_n_in_biggest_cluster", false]], "select_one_water() (in module mmtbx.hydrogens.find)": [[291, "mmtbx.hydrogens.find.select_one_water", false]], "select_random_den_restraints() (mmtbx.den.den_restraints method)": [[284, "mmtbx.den.den_restraints.select_random_den_restraints", false]], "select_str() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method)": [[325, "mmtbx.utils.fab_elbow_angle.fab_elbow_angle.select_str", false]], "select_sys_absent() (cctbx.miller.array method)": [[148, "cctbx.miller.array.select_sys_absent", false]], "selected_positions() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.selected_positions", false]], "selected_size (scitbx.array_family.flex.smart_selection property)": [[331, "scitbx.array_family.flex.smart_selection.selected_size", false]], "selection (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.selection", false]], "selection (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.selection", false]], "selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.selection", false]], "selection() (mmtbx.monomer_library.pdb_interpretation.selection_manager method)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager.selection", false]], "selection_around_to_negate() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.selection_around_to_negate", false]], "selection_by_symmetry() (in module mmtbx.building.make_library)": [[277, "mmtbx.building.make_library.selection_by_symmetry", false]], "selection_manager (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.selection_manager", false]], "selection_within() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.selection_within", false]], "selector() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.selector", false]], "send_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method)": [[342, "xfel.cxi.correction_vector_plot.manage_sql.send_insert_command", false]], "sense_of_polygon() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.sense_of_polygon", false]], "sensor() (dxtbx.model.detector.detectorfactory static method)": [[257, "dxtbx.model.detector.DetectorFactory.sensor", false]], "separatecheckerbuilder (class in mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.SeparateCheckerBuilder", false]], "sequence (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.sequence", false]], "sequence (mmtbx.validation.molprobity.molprobity attribute)": [[327, "mmtbx.validation.molprobity.molprobity.sequence", false]], "sequence() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.sequence", false]], "sequence_as_cif_block() (mmtbx.validation.sequence.validation method)": [[326, "mmtbx.validation.sequence.validation.sequence_as_cif_block", false]], "sequence_from_seqres() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.sequence_from_SEQRES", false]], "sequence_search() (in module mmtbx.wwpdb.rcsb_web_services)": [[328, "mmtbx.wwpdb.rcsb_web_services.sequence_search", false]], "serial (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.serial", false]], "serial (mmtbx.maps.composite_omit_map.omit_box attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_box.serial", false]], "serial (mmtbx.maps.composite_omit_map.omit_region_results attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_region_results.serial", false]], "serial (mmtbx.maps.composite_omit_map.omit_regions attribute)": [[305, "mmtbx.maps.composite_omit_map.omit_regions.serial", false]], "serial_as_int() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.serial_as_int", false]], "serial_as_int() (iotbx.pdb.hierarchy.atom_with_labels method)": [[268, "iotbx.pdb.hierarchy.atom_with_labels.serial_as_int", false]], "server (class in mmtbx.ligands.xtal_screens)": [[304, "mmtbx.ligands.xtal_screens.server", false]], "server (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.server", false]], "server_info (class in cctbx.web.cgi_utils)": [[213, "cctbx.web.cgi_utils.server_info", false]], "set (class in cctbx.miller)": [[148, "cctbx.miller.set", false]], "set() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set", false]], "set_adps_from_scatterers() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_adps_from_scatterers", false]], "set_alignment() (mmtbx.validation.sequence.chain method)": [[326, "mmtbx.validation.sequence.chain.set_alignment", false]], "set_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[257, "dxtbx.model.goniometer.MultiAxisGoniometer.set_angles", false]], "set_atomic_charge() (iotbx.pdb.hierarchy.root method)": [[268, "iotbx.pdb.hierarchy.root.set_atomic_charge", false]], "set_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[257, "dxtbx.model.goniometer.MultiAxisGoniometer.set_axes", false]], "set_b() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_b", false]], "set_b() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_b", false]], "set_b_iso() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_b_iso", false]], "set_charge() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_charge", false]], "set_chemical_element_simple_if_necessary() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_chemical_element_simple_if_necessary", false]], "set_chemical_element_simple_if_necessary() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_chemical_element_simple_if_necessary", false]], "set_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.set_classification", false]], "set_color_model() (mmtbx.polygon.output.renderer method)": [[311, "mmtbx.polygon.output.renderer.set_color_model", false]], "set_colors() (mmtbx.polygon.output.histogram_layout method)": [[311, "mmtbx.polygon.output.histogram_layout.set_colors", false]], "set_components_of_global_origin() (cctbx.symmetry_search.possible_symmetry method)": [[196, "cctbx.symmetry_search.possible_symmetry.set_components_of_global_origin", false]], "set_coordinates_from_hierarchy() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.set_coordinates_from_hierarchy", false]], "set_crystal_symmetry_to_p1() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_crystal_symmetry_to_p1", false]], "set_custom_inelastic_form_factors() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_custom_inelastic_form_factors", false]], "set_element() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_element", false]], "set_element_and_charge_from_scattering_type_if_necessary() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_element_and_charge_from_scattering_type_if_necessary", false]], "set_ensemble_b_factors_to_xyz_displacement() (in module mmtbx.disorder)": [[286, "mmtbx.disorder.set_ensemble_b_factors_to_xyz_displacement", false]], "set_experiment_type() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_experiment_type", false]], "set_experiment_type() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_experiment_type", false]], "set_external_energy_function() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_external_energy_function", false]], "set_fdp() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_fdp", false]], "set_fdp() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_fdp", false]], "set_fdps() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_fdps", false]], "set_file_type() (iotbx.file_reader.any_file_input method)": [[265, "iotbx.file_reader.any_file_input.set_file_type", false]], "set_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.set_fixed_rotation", false]], "set_focus() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.set_focus", false]], "set_fp() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_fp", false]], "set_fp() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_fp", false]], "set_fps() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_fps", false]], "set_hetero() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_hetero", false]], "set_ias_name_and_predicted_position() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_ias_name_and_predicted_position", false]], "set_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.set_ias_selection", false]], "set_inelastic_form_factors() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_inelastic_form_factors", false]], "set_info() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_info", false]], "set_info() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_info", false]], "set_is_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_is_mask", false]], "set_k_isotropic_exp() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.set_k_isotropic_exp", false]], "set_labels() (mmtbx.rotamer.graphics.ramachandran_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.ramachandran_plot_mixin.set_labels", false]], "set_labels() (mmtbx.rotamer.graphics.rotamer_plot_mixin method)": [[316, "mmtbx.rotamer.graphics.rotamer_plot_mixin.set_labels", false]], "set_labels() (mmtbx.validation.ramalyze.ramachandran_plot_mixin method)": [[326, "mmtbx.validation.ramalyze.ramachandran_plot_mixin.set_labels", false]], "set_labels() (mmtbx.validation.rotalyze.rotamer_plot_mixin method)": [[326, "mmtbx.validation.rotalyze.rotamer_plot_mixin.set_labels", false]], "set_ladp() (in module mmtbx.tls.ladp)": [[322, "mmtbx.tls.ladp.set_ladp", false]], "set_log() (in module mmtbx.utils)": [[325, "mmtbx.utils.set_log", false]], "set_log() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_log", false]], "set_log() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_log", false]], "set_log() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.set_log", false]], "set_map_data() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_map_data", false]], "set_map_id_lists() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_map_id_lists", false]], "set_map_manager() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_map_manager", false]], "set_map_to_value (class in mmtbx.utils)": [[325, "mmtbx.utils.set_map_to_value", false]], "set_mean_zero_sd_one() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_mean_zero_sd_one", false]], "set_minimum_resolution() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_minimum_resolution", false]], "set_model() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_model", false]], "set_model_symmetries_and_shift_cart_to_match_map() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_model_symmetries_and_shift_cart_to_match_map", false]], "set_model_symmetries_and_shift_cart_to_match_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_model_symmetries_and_shift_cart_to_match_map", false]], "set_multiprocessing() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_multiprocessing", false]], "set_name() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_name", false]], "set_name() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_name", false]], "set_ncs_name() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_ncs_name", false]], "set_ncs_object() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_ncs_object", false]], "set_ncs_object() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_ncs_object", false]], "set_ncs_object_shift_cart_to_match_map() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_ncs_object_shift_cart_to_match_map", false]], "set_nearby_empty_values() (in module iotbx.map_model_manager)": [[266, "iotbx.map_model_manager.set_nearby_empty_values", false]], "set_non_unit_occupancy_implies_min_distance_sym_equiv_zero() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_non_unit_occupancy_implies_min_distance_sym_equiv_zero", false]], "set_observation_type() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_observation_type", false]], "set_observation_type_xray_amplitude() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_observation_type_xray_amplitude", false]], "set_observation_type_xray_intensity() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_observation_type_xray_intensity", false]], "set_occ() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_occ", false]], "set_occ() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_occ", false]], "set_occupancies() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_occupancies", false]], "set_original_origin_and_gridding() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_original_origin_and_gridding", false]], "set_original_origin_and_gridding() (iotbx.map_model_manager.match_map_model_ncs method)": [[266, "iotbx.map_model_manager.match_map_model_ncs.set_original_origin_and_gridding", false]], "set_original_origin_grid_units() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_original_origin_grid_units", false]], "set_output_external_origin() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_output_external_origin", false]], "set_params() (xfel.cxi.gfx.trials_plot.trialsplotframe method)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame.set_params", false]], "set_peaks() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_peaks", false]], "set_program_name() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_program_name", false]], "set_pseudo_ml_weights() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.set_pseudo_ml_weights", false]], "set_ramachandran_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_ramachandran_restraints", false]], "set_random_seed() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.set_random_seed", false]], "set_refinable_parameters() (in module mmtbx.refinement.occupancies)": [[313, "mmtbx.refinement.occupancies.set_refinable_parameters", false]], "set_resolution() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_resolution", false]], "set_resolution() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_resolution", false]], "set_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.set_rotation_axis", false]], "set_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.set_rotation_axis_datum", false]], "set_run_id() (xfel.cxi.gfx.wx_detectors.detectorplot method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlot.set_run_id", false]], "set_run_id() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.set_run_id", false]], "set_scatterer_flags() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_scatterer_flags", false]], "set_scattering_table() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_scattering_table", false]], "set_scattering_table() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_scattering_table", false]], "set_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.set_secondary_structure_restraints", false]], "set_segid() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_segid", false]], "set_selected() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.set_selected", false]], "set_selected() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.set_selected", false]], "set_selected() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.set_selected", false]], "set_selected() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.set_selected", false]], "set_selected() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.set_selected", false]], "set_selected() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.set_selected", false]], "set_selected() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.set_selected", false]], "set_selected() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.set_selected", false]], "set_selected() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.set_selected", false]], "set_selected() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.set_selected", false]], "set_selected() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.set_selected", false]], "set_selected() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.set_selected", false]], "set_serial() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_serial", false]], "set_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.set_setting_rotation", false]], "set_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)": [[257, "dxtbx.model.goniometer.Goniometer.set_setting_rotation_at_scan_points", false]], "set_shift_cart() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_shift_cart", false]], "set_sigb() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_sigb", false]], "set_sigb() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_sigb", false]], "set_sigma_ratio() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate.set_sigma_ratio", false]], "set_sigma_ratio() (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate.set_sigma_ratio", false]], "set_sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.set_sigmas", false]], "set_sigocc() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_sigocc", false]], "set_sigocc() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_sigocc", false]], "set_sigxyz() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_sigxyz", false]], "set_sigxyz() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_sigxyz", false]], "set_sites_cart() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_sites_cart", false]], "set_sites_frac() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_sites_frac", false]], "set_status() (in module mmtbx.ias)": [[292, "mmtbx.ias.set_status", false]], "set_status() (mmtbx.ias.find_peak_at_bond method)": [[292, "mmtbx.ias.find_peak_at_bond.set_status", false]], "set_status() (xfel.cxi.cspad_ana.mod_event_info.laser_status method)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.set_status", false]], "set_stop_file() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_stop_file", false]], "set_u_cart() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_u_cart", false]], "set_u_iso() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.set_u_iso", false]], "set_uij() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_uij", false]], "set_uij() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_uij", false]], "set_unit_cell_crystal_symmetry() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_unit_cell_crystal_symmetry", false]], "set_unit_ncs() (mmtbx.ncs.ncs.ncs method)": [[309, "mmtbx.ncs.ncs.ncs.set_unit_ncs", false]], "set_up_hitfinder() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method)": [[343, "xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder.set_up_hitfinder", false]], "set_up_map_dict() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_up_map_dict", false]], "set_up_model_dict() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_up_model_dict", false]], "set_velocities() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.set_velocities", false]], "set_velocities() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.set_velocities", false]], "set_verbose() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.set_verbose", false]], "set_watch_dir() (xfel.cxi.gfx.wx_detectors.detectorplotframe method)": [[344, "xfel.cxi.gfx.wx_detectors.DetectorPlotFrame.set_watch_dir", false]], "set_wrapping() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.set_wrapping", false]], "set_xyz() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.set_xyz", false]], "set_xyz() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.set_xyz", false]], "settings() (in module cctbx.miller.display)": [[149, "cctbx.miller.display.settings", false]], "setup_binner() (cctbx.miller.set method)": [[148, "cctbx.miller.set.setup_binner", false]], "setup_binner_counting_sorted() (cctbx.miller.set method)": [[148, "cctbx.miller.set.setup_binner_counting_sorted", false]], "setup_binner_d_star_sq_bin_size() (cctbx.miller.set method)": [[148, "cctbx.miller.set.setup_binner_d_star_sq_bin_size", false]], "setup_binner_d_star_sq_step() (cctbx.miller.set method)": [[148, "cctbx.miller.set.setup_binner_d_star_sq_step", false]], "setup_bulk_solvent_correction() (cctbx.omz.dev.refinement method)": [[158, "cctbx.omz.dev.refinement.setup_bulk_solvent_correction", false]], "setup_colors() (cctbx.miller.display.render_2d method)": [[149, "cctbx.miller.display.render_2d.setup_colors", false]], "setup_fft() (cctbx.xray.structure_factors.manager.manager method)": [[250, "cctbx.xray.structure_factors.manager.manager.setup_fft", false]], "setup_hexagonal_sampling (class in cctbx.crystal.close_packing)": [[25, "cctbx.crystal.close_packing.setup_hexagonal_sampling", false]], "setup_ias_selection() (mmtbx.ias.manager method)": [[292, "mmtbx.ias.manager.setup_ias_selection", false]], "setup_maps() (mmtbx.ncs.ligands.sample_operators method)": [[309, "mmtbx.ncs.ligands.sample_operators.setup_maps", false]], "setup_scattering_dictionaries() (in module mmtbx.utils)": [[325, "mmtbx.utils.setup_scattering_dictionaries", false]], "setup_test() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.setup_test", false]], "setvalueat() (mmtbx.rotamer.n_dim_table.ndimtable method)": [[316, "mmtbx.rotamer.n_dim_table.NDimTable.setValueAt", false]], "sfac_disp_unit() (in module cctbx.development.run_shelx)": [[41, "cctbx.development.run_shelx.SFAC_DISP_UNIT", false]], "sfac_unit() (in module cctbx.development.run_shelx76)": [[42, "cctbx.development.run_shelx76.sfac_unit", false]], "sgi_iterator (class in mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.sgi_iterator", false]], "sgtbx_rt_mx_as_matrix_rt() (in module cctbx.euclidean_model_matching)": [[77, "cctbx.euclidean_model_matching.sgtbx_rt_mx_as_matrix_rt", false]], "shake_adp() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.shake_adp", false]], "shake_adp_if_all_equal() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.shake_adp_if_all_equal", false]], "shake_fdps() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.shake_fdps", false]], "shake_fps() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.shake_fps", false]], "shake_occupancies() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.shake_occupancies", false]], "shake_sites_in_place() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.shake_sites_in_place", false]], "shake_transformations() (in module mmtbx.ncs.ncs_utils)": [[309, "mmtbx.ncs.ncs_utils.shake_transformations", false]], "shallow_copy() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.shallow_copy", false]], "shallow_copy() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.shallow_copy", false]], "shape_only() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.shape_only", false]], "shape_vertices() (cctbx.sgtbx.direct_space_asu.direct_space_asu method)": [[168, "cctbx.sgtbx.direct_space_asu.direct_space_asu.shape_vertices", false]], "shape_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis)": [[171, "cctbx.sgtbx.direct_space_asu.facet_analysis.shape_vertices", false]], "sharpen2() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.sharpen2", false]], "shell_f_masks() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.shell_f_masks", false]], "shell_f_masks_twin() (mmtbx.masks.manager method)": [[306, "mmtbx.masks.manager.shell_f_masks_twin", false]], "shelx_commands (iotbx.shelx.lexer.command_stream attribute)": [[271, "iotbx.shelx.lexer.command_stream.shelx_commands", false]], 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"mmtbx.scaling.xtriage_output.show_text", false]], "show_text_columns() (mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.show_text_columns", false]], "show_text_columns() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.show_text_columns", false]], "show_text_columns() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.show_text_columns", false]], "show_tiles() (in module xfel.command_line.radial_average)": [[341, "xfel.command_line.radial_average.show_tiles", false]], "show_times() (in module mmtbx.refinement.adp_refinement)": [[313, "mmtbx.refinement.adp_refinement.show_times", false]], "show_times() (in module mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.show_times", false]], "show_times() (in module mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.show_times", false]], "show_times() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.show_times", false]], "show_tls (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.show_tls", false]], "show_tls_one_group (class in mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.show_tls_one_group", false]], "show_u_statistics() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.show_u_statistics", false]], "show_unit_cell_histograms() (xfel.command_line.cxi_merge.scaling_manager method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.show_unit_cell_histograms", false]], "show_unknown_scatterers() (cctbx.xray.structure_factors.from_scatterers_fft.from_scatterers_fft method)": [[243, "cctbx.xray.structure_factors.from_scatterers_fft.from_scatterers_fft.show_unknown_scatterers", false]], "show_validation_results() (in module mmtbx.validation.ligands)": [[326, "mmtbx.validation.ligands.show_validation_results", false]], "show_verdict() (mmtbx.scaling.twin_analyses.twin_results_interpretation method)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation.show_verdict", false]], "show_worrisome_shells() (mmtbx.scaling.data_statistics.wilson_scaling method)": [[318, "mmtbx.scaling.data_statistics.wilson_scaling.show_worrisome_shells", false]], "shrink_edge() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.shrink_edge", false]], "shrink_polygon() (in module cctbx.web.asu_gallery.jv_asu)": [[208, "cctbx.web.asu_gallery.jv_asu.shrink_polygon", false]], "side_chain_fit_evaluator (class in mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.side_chain_fit_evaluator", false]], "sidechainangles (class in mmtbx.rotamer.sidechain_angles)": [[316, "mmtbx.rotamer.sidechain_angles.SidechainAngles", false]], "sigb (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.sigb", false]], "sigma (mmtbx.validation.restraints.angle attribute)": [[326, "mmtbx.validation.restraints.angle.sigma", false]], "sigma (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.sigma", false]], "sigma (mmtbx.validation.restraints.chirality attribute)": [[326, "mmtbx.validation.restraints.chirality.sigma", false]], "sigma (mmtbx.validation.restraints.dihedral attribute)": [[326, "mmtbx.validation.restraints.dihedral.sigma", false]], "sigma (mmtbx.validation.restraints.restraint attribute)": [[326, "mmtbx.validation.restraints.restraint.sigma", false]], "sigma (mmtbx.validation.rna_validate.rna_angle attribute)": [[326, "mmtbx.validation.rna_validate.rna_angle.sigma", false]], "sigma (mmtbx.validation.rna_validate.rna_bond attribute)": [[326, "mmtbx.validation.rna_validate.rna_bond.sigma", false]], "sigma_as_weight() (in module cctbx.geometry_restraints)": [[131, "cctbx.geometry_restraints.sigma_as_weight", false]], "sigma_at_first_index() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sigma_at_first_index", false]], "sigma_filter() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sigma_filter", false]], "sigma_gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute)": [[318, "mmtbx.scaling.absolute_scaling.gamma_protein.sigma_gamma", false]], "sigma_miss() (in module mmtbx.max_lik.maxlik)": [[307, "mmtbx.max_lik.maxlik.sigma_miss", false]], "sigmaa() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.sigmaa", false]], "sigmaa() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.sigmaa", false]], "sigmaa_estimator (class in mmtbx.scaling.sigmaa_estimation)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator", false]], "sigmaa_estimator_kernel_width_d_star_cubed() (in module mmtbx.scaling.sigmaa_estimation)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator_kernel_width_d_star_cubed", false]], "sigmaa_estimator_kernel_width_d_star_cubed() (in module mmtbx.scaling.ta_alpha_beta_calc)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.sigmaa_estimator_kernel_width_d_star_cubed", false]], "sigmaa_model_error() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_estimator.sigmaa_model_error", false]], "sigmaa_model_error() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc.sigmaa_model_error", false]], "sigmaa_object() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.sigmaa_object", false]], "sigmaa_point_estimator (class in mmtbx.scaling.sigmaa_estimation)": [[318, "mmtbx.scaling.sigmaa_estimation.sigmaa_point_estimator", false]], "sigmaa_point_estimator (class in mmtbx.scaling.ta_alpha_beta_calc)": [[318, "mmtbx.scaling.ta_alpha_beta_calc.sigmaa_point_estimator", false]], "sigmas() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sigmas", false]], "sigmas_are_sensible() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sigmas_are_sensible", false]], "sign0() (in module cctbx.omz.dev)": [[158, "cctbx.omz.dev.sign0", false]], "signal_to_noise_statistical() (in module xfel.command_line.subtract_background)": [[341, "xfel.command_line.subtract_background.signal_to_noise_statistical", false]], "significant_change_test() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method)": [[200, "cctbx.uctbx.gruber_1973.fast_minimum_reduction.significant_change_test", false]], "significant_change_test() (cctbx.uctbx.reduction_base.minimum_reduction_mixin method)": [[203, "cctbx.uctbx.reduction_base.minimum_reduction_mixin.significant_change_test", false]], "significant_height_fraction() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.significant_height_fraction", false]], "significant_height_fraction() (cctbx.maptbx.peak_search_parameters method)": [[139, "cctbx.maptbx.peak_search_parameters.significant_height_fraction", false]], "sigocc (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.sigocc", false]], "siguij_erase() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.siguij_erase", false]], "siguij_is_defined() (iotbx.pdb.hierarchy.atom method)": [[268, "iotbx.pdb.hierarchy.atom.siguij_is_defined", false]], "sigxyz (iotbx.pdb.hierarchy.atom property)": [[268, "iotbx.pdb.hierarchy.atom.sigxyz", false]], "simple (class in mmtbx.refinement.real_space.individual_sites)": [[315, "mmtbx.refinement.real_space.individual_sites.simple", false]], "simple() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.simple", false]], "simple() (dxtbx.model.detector.detectorfactory static method)": [[257, "dxtbx.model.detector.DetectorFactory.simple", false]], "simple_and_slow() (in module cctbx.crystal.coordination_sequences)": [[26, "cctbx.crystal.coordination_sequences.simple_and_slow", false]], "simple_directional() (dxtbx.model.beam.beamfactory static method)": [[257, "dxtbx.model.beam.BeamFactory.simple_directional", false]], "simple_distance_predicate() (mmtbx.geometry.indexing.structure_indexer method)": [[289, "mmtbx.geometry.indexing.structure_indexer.simple_distance_predicate", false]], "simple_edge_list() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.simple_edge_list", false]], "simple_id() (mmtbx.validation.residue method)": [[326, "mmtbx.validation.residue.simple_id", false]], "simple_shelx_weighting (class in cctbx.xray.weighting_schemes)": [[255, "cctbx.xray.weighting_schemes.simple_shelx_weighting", false]], "simple_surface_calculation() (in module mmtbx.geometry.asa)": [[289, "mmtbx.geometry.asa.simple_surface_calculation", false]], "sin_theta_over_lambda_sq() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sin_theta_over_lambda_sq", false]], "singh_ramasheshan_fa_estimate (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate", false]], "singh_ramasheshan_fa_estimate (class in mmtbx.scaling.pair_analyses)": [[318, "mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate", false]], "single_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.single_axis", false]], "single_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.single_axis_goniometer_from_phil", false]], "single_axis_reverse() (dxtbx.model.goniometer.goniometerfactory static method)": [[257, "dxtbx.model.goniometer.GoniometerFactory.single_axis_reverse", false]], "single_file() (dxtbx.model.scan.scanfactory static method)": [[257, "dxtbx.model.scan.ScanFactory.single_file", false]], "single_peak_fit() (xfel.command_line.view_pixel_histograms.pixel_histograms method)": [[341, "xfel.command_line.view_pixel_histograms.pixel_histograms.single_peak_fit", false]], "single_reflection_histograms() (xfel.command_line.cxi_merge.scaling_manager static method)": [[341, "xfel.command_line.cxi_merge.scaling_manager.single_reflection_histograms", false]], "singleframe (class in xfel.clustering.singleframe)": [[340, "xfel.clustering.singleframe.SingleFrame", false]], "site_cart (mmtbx.ions.environment.atom_contact attribute)": [[295, "id19", false], [295, "mmtbx.ions.environment.atom_contact.site_cart", false]], "site_cluster_analysis() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_cluster_analysis", false]], "site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.site_cluster_analysis", false]], "site_ideal() (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom method)": [[328, "mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom.site_ideal", false]], "site_symmetry() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_symmetry", false]], "site_symmetry_ops_j (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute)": [[165, "cctbx.sgtbx.symmetry_equivalent_pair_interactions.site_symmetry_ops_j", false]], "site_symmetry_table() (cctbx.crystal.special_position_settings method)": [[23, "cctbx.crystal.special_position_settings.site_symmetry_table", false]], "site_symmetry_table() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.site_symmetry_table", false]], "site_symmetry_table() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.site_symmetry_table", false]], "sites() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.sites", false]], "sites_cart() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.sites_cart", false]], "sites_cart() (mmtbx.refinement.real_space.individual_sites.diff_map method)": [[315, "mmtbx.refinement.real_space.individual_sites.diff_map.sites_cart", false]], "sites_cart() (mmtbx.refinement.real_space.individual_sites.simple method)": [[315, "mmtbx.refinement.real_space.individual_sites.simple.sites_cart", false]], "sites_cart() (mmtbx.validation.atoms method)": [[326, "mmtbx.validation.atoms.sites_cart", false]], "sites_cart_exact() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method)": [[308, "mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies.sites_cart_exact", false]], "sites_cart_used_for_pair_proxies() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.sites_cart_used_for_pair_proxies", false]], "sites_frac() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.sites_frac", false]], "sites_mod_positive() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.sites_mod_positive", false]], "sites_mod_short() (cctbx.xray.structure.structure method)": [[238, "cctbx.xray.structure.structure.sites_mod_short", false]], "size() (cctbx.euclidean_model_matching.model method)": [[77, "cctbx.euclidean_model_matching.model.size", false]], "size() (cctbx.miller.array method)": [[148, "cctbx.miller.array.size", false]], "size() (cctbx.miller.set method)": [[148, "cctbx.miller.set.size", false]], "size() (cctbx.web.asu_gallery.jvx.faceset method)": [[210, "cctbx.web.asu_gallery.jvx.faceSet.size", false]], "size() (cctbx.web.asu_gallery.jvx.lineset method)": [[210, "cctbx.web.asu_gallery.jvx.lineSet.size", false]], "size() (cctbx.web.asu_gallery.jvx.pointset method)": [[210, "cctbx.web.asu_gallery.jvx.pointSet.size", false]], "size() (iotbx.cif.model.loop method)": [[264, "iotbx.cif.model.loop.size", false]], "size() (iotbx.pdb.hierarchy.af_shared_atom method)": [[268, "iotbx.pdb.hierarchy.af_shared_atom.size", false]], "size() (mmtbx.geometry.topology.molecule method)": [[289, "mmtbx.geometry.topology.Molecule.size", false]], "size() (scitbx.array_family.flex.bool method)": [[331, "scitbx.array_family.flex.bool.size", false]], "size() (scitbx.array_family.flex.complex_double method)": [[331, "scitbx.array_family.flex.complex_double.size", false]], "size() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.size", false]], "size() (scitbx.array_family.flex.float method)": [[331, "scitbx.array_family.flex.float.size", false]], "size() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.size", false]], "size() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.size", false]], "size() (scitbx.array_family.flex.size_t method)": [[331, "scitbx.array_family.flex.size_t.size", false]], "size() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.size", false]], "size() (scitbx.array_family.flex.sym_mat3_double method)": [[331, "scitbx.array_family.flex.sym_mat3_double.size", false]], "size() (scitbx.array_family.flex.vec2_double method)": [[331, "scitbx.array_family.flex.vec2_double.size", false]], "size() (scitbx.array_family.flex.vec3_double method)": [[331, "scitbx.array_family.flex.vec3_double.size", false]], "size() (scitbx.array_family.flex.vec3_int method)": [[331, "scitbx.array_family.flex.vec3_int.size", false]], "size_1d() (scitbx.array_family.flex.grid method)": [[331, "scitbx.array_family.flex.grid.size_1d", false]], "size_t (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.size_t", false]], "size_t_element_size (scitbx.array_family.flex.smart_selection attribute)": [[331, "scitbx.array_family.flex.smart_selection.size_t_element_size", false]], "sizeof_data() (iotbx.pdb.hierarchy.atom static method)": [[268, "iotbx.pdb.hierarchy.atom.sizeof_data", false]], "skewness_calculation() (in module cctbx.examples.map_skewness)": [[99, "cctbx.examples.map_skewness.skewness_calculation", false]], "skip_event_flag() (in module xfel.cxi.cspad_ana)": [[343, "xfel.cxi.cspad_ana.skip_event_flag", false]], "skip_if_non_linking() (in module mmtbx.monomer_library.linking_setup)": [[308, "mmtbx.monomer_library.linking_setup.skip_if_non_linking", false]], "slack (mmtbx.validation.restraints.bond attribute)": [[326, "mmtbx.validation.restraints.bond.slack", false]], "slice() (cctbx.miller.set method)": [[148, "cctbx.miller.set.slice", false]], "slice() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.slice", false]], "slice_to_byte_str() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.slice_to_byte_str", false]], "slice_to_byte_str() (scitbx.array_family.flex.int method)": [[331, "scitbx.array_family.flex.int.slice_to_byte_str", false]], "slice_to_byte_str() (scitbx.array_family.flex.long method)": [[331, "scitbx.array_family.flex.long.slice_to_byte_str", false]], "sliding_average() (in module xfel.command_line.view_pixel_histograms)": [[341, "xfel.command_line.view_pixel_histograms.sliding_average", false]], "slots_getstate_setstate (class in libtbx)": [[273, "libtbx.slots_getstate_setstate", false]], "slots_getstate_setstate_default_initializer (class in libtbx)": [[273, "libtbx.slots_getstate_setstate_default_initializer", false]], "smart_selection (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.smart_selection", false]], "smart_split_cif_line() (in module mmtbx.chemical_components.cif_parser)": [[281, "mmtbx.chemical_components.cif_parser.smart_split_cif_line", false]], "smooth() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.smooth", false]], "smooth() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method)": [[307, "mmtbx.max_lik.maxlik.alpha_beta_est_manager.smooth", false]], "smooth_map() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.smooth_map", false]], "smooth_mask (class in mmtbx.masks)": [[306, "mmtbx.masks.smooth_mask", false]], "snd() (mmtbx.twinning.probabalistic_detwinning.detwin method)": [[324, "mmtbx.twinning.probabalistic_detwinning.detwin.snd", false]], "soft_mask() (iotbx.map_manager.map_manager method)": [[266, "iotbx.map_manager.map_manager.soft_mask", false]], "solc() (mmtbx.scaling.matthews.p_vm_calculator method)": [[318, "mmtbx.scaling.matthews.p_vm_calculator.solc", false]], "solution (class in mmtbx.ligands.xtal_screens)": [[304, "mmtbx.ligands.xtal_screens.solution", false]], "solve() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method)": [[333, "scitbx.lstbx.normal_eqns.non_linear_ls_mixin.solve", false]], "solve() (scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls method)": [[333, "scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls.solve", false]], "solve_and_step_forward() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method)": [[333, "scitbx.lstbx.normal_eqns.non_linear_ls_mixin.solve_and_step_forward", false]], "solve_and_step_forward() (scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls method)": [[333, "scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls.solve_and_step_forward", false]], "solvent_adjust() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_adjust", false]], "solvent_flattening() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_flattening", false]], "solvent_flipping() (mmtbx.density_modification.density_modification method)": [[285, "mmtbx.density_modification.density_modification.solvent_flipping", false]], "solvent_fraction() (mmtbx.scaling.matthews.density_calculator method)": 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false]], "sort_permutation() (cctbx.miller.array method)": [[148, "cctbx.miller.array.sort_permutation", false]], "sort_permutation() (cctbx.miller.set method)": [[148, "cctbx.miller.set.sort_permutation", false]], "sort_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.sort_redundancies", false]], "sort_triple() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.sort_triple", false]], "sorted() (in module scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.sorted", false]], "sorted_as_c_h_then_by_increasing_atomic_number() (cctbx.eltbx.formula.formula method)": [[66, "cctbx.eltbx.formula.formula.sorted_as_c_h_then_by_increasing_atomic_number", false]], "sorted_by_map_value() (mmtbx.refinement.real_space.fit_residue.find_all_conformers method)": [[315, "mmtbx.refinement.real_space.fit_residue.find_all_conformers.sorted_by_map_value", false]], "sorted_cut_points() 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"iotbx.pdb.ext.input.source_info", false]], "source_info() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.source_info", false]], "source_info_server (class in mmtbx.monomer_library.pdb_interpretation)": [[308, "mmtbx.monomer_library.pdb_interpretation.source_info_server", false]], "source_of_ncs_info() (mmtbx.ncs.ncs.ncs_group method)": [[309, "mmtbx.ncs.ncs.ncs_group.source_of_ncs_info", false]], "source_short (cctbx.eltbx.xray_scattering.one_gaussian_agarwal_1978 attribute)": [[76, "cctbx.eltbx.xray_scattering.one_gaussian_agarwal_1978.source_short", false]], "source_short (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_1978 attribute)": [[76, "cctbx.eltbx.xray_scattering.two_gaussian_agarwal_1978.source_short", false]], "source_short (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_isaacs attribute)": [[76, "cctbx.eltbx.xray_scattering.two_gaussian_agarwal_isaacs.source_short", false]], "space_group() (cctbx.crystal.symmetry method)": [[23, 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method)": [[23, "cctbx.crystal.symmetry.special_position_settings", false]], "special_position_settings() (cctbx.maptbx.peak_cluster_analysis method)": [[139, "cctbx.maptbx.peak_cluster_analysis.special_position_settings", false]], "special_position_settings() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.special_position_settings", false]], "special_position_settings_from_inp() (in module cctbx.web.io_utils)": [[221, "cctbx.web.io_utils.special_position_settings_from_inp", false]], "sphere_model_group_for() (mmtbx.geometry.clash.case method)": [[289, "mmtbx.geometry.clash.Case.sphere_model_group_for", false]], "sphere_similarity_restraints (class in mmtbx.refinement.group)": [[313, "mmtbx.refinement.group.sphere_similarity_restraints", false]], "spheremodel (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SphereModel", false]], "spheremodelgroup (class in mmtbx.geometry.clash)": [[289, "mmtbx.geometry.clash.SphereModelGroup", false]], "spherical_variance_around_point (class in cctbx.maptbx)": [[139, "cctbx.maptbx.spherical_variance_around_point", false]], "sphericity_by_heuristics() (in module cctbx.maptbx)": [[139, "cctbx.maptbx.sphericity_by_heuristics", false]], "split_array() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method)": [[290, "mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data.split_array", false]], "split_resolution_range() (in module mmtbx.refinement.rigid_body)": [[313, "mmtbx.refinement.rigid_body.split_resolution_range", false]], "split_rotamer_names() (in module mmtbx.validation.rotalyze)": [[326, "mmtbx.validation.rotalyze.split_rotamer_names", false]], "split_sigma_test() (in module xfel.cxi.cxi_cc)": [[342, "xfel.cxi.cxi_cc.split_sigma_test", false]], "split_u() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.split_u", false]], "split_up_map_and_model_by_boxes() (iotbx.map_model_manager.map_model_manager method)": [[266, 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false]], "start_log_file() (mmtbx.command_line.load_model_and_data method)": [[282, "mmtbx.command_line.load_model_and_data.start_log_file", false]], "states (class in mmtbx.utils)": [[325, "mmtbx.utils.states", false]], "statistical_mean() (cctbx.miller.array method)": [[148, "cctbx.miller.array.statistical_mean", false]], "statistical_weighting (cctbx.xray.target_functors.least_squares_residual_for_amplitude attribute)": [[252, "cctbx.xray.target_functors.least_squares_residual_for_amplitude.statistical_weighting", false]], "statistics (class in cctbx.maptbx)": [[139, "cctbx.maptbx.statistics", false]], "statistics_in_resolution_bins() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.statistics_in_resolution_bins", false]], "stats (mmtbx.validation.cbetadev.cbetadev attribute)": [[326, "mmtbx.validation.cbetadev.cbetadev.stats", false]], "stats_table (class in mmtbx.refinement.print_statistics)": [[313, "mmtbx.refinement.print_statistics.stats_table", false]], "status (xfel.cxi.cspad_ana.mod_event_info.laser_status property)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.status", false]], "status_change_timestamp (xfel.cxi.cspad_ana.mod_event_info.laser_status attribute)": [[343, "xfel.cxi.cspad_ana.mod_event_info.laser_status.status_change_timestamp", false]], "statusframe (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.StatusFrame", false]], "statusframe_thread (class in xfel.cxi.cspad_ana.mod_daq_status)": [[343, "xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread", false]], "statusplot (class in xfel.cxi.gfx.status_plot)": [[344, "xfel.cxi.gfx.status_plot.StatusPlot", false]], "std() (mmtbx.scaling.relative_wilson.relative_wilson method)": [[318, "mmtbx.scaling.relative_wilson.relative_wilson.std", false]], "std_string (class in scitbx.array_family.flex)": [[331, "scitbx.array_family.flex.std_string", false]], "step() 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"step_i__compute_delta_l_r_dp() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.step_i__compute_delta_L_r_dp", false]], "step_i__get_dxdydz() (in module mmtbx.tls.tls_as_xyz)": [[322, "mmtbx.tls.tls_as_xyz.step_i__get_dxdydz", false]], "step_threshold (scitbx.lstbx.normal_eqns_solving.iterations attribute)": [[333, "scitbx.lstbx.normal_eqns_solving.iterations.step_threshold", false]], "steps (mmtbx.refinement.print_statistics.stats_table attribute)": [[313, "mmtbx.refinement.print_statistics.stats_table.steps", false]], "stop_global_motion() (mmtbx.dynamics.cartesian_dynamics.run method)": [[287, "mmtbx.dynamics.cartesian_dynamics.run.stop_global_motion", false]], "stop_global_motion() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.stop_global_motion", false]], "store_temperatures() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method)": [[287, "mmtbx.dynamics.ensemble_cd.cartesian_dynamics.store_temperatures", false]], "str_ev() (in module cctbx.examples.all_axes)": [[80, "cctbx.examples.all_axes.str_ev", false]], "str_ev() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.str_ev", false]], "str_ev() (in module cctbx.sgtbx.literal_description)": [[179, "cctbx.sgtbx.literal_description.str_ev", false]], "str_ev() (in module cctbx.web.explore_symmetry)": [[219, "cctbx.web.explore_symmetry.str_ev", false]], "strain_tensor() (mmtbx.scaling.twin_analyses.twin_law_quality method)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality.strain_tensor", false]], "string_it() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method)": [[318, "mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs.string_it", false]], "strip() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)": [[170, "cctbx.sgtbx.direct_space_asu.cut_plane.cut.strip", false]], "strip() (scitbx.array_family.flex.std_string method)": [[331, "scitbx.array_family.flex.std_string.strip", false]], "strip_model() (in module mmtbx.refinement.select_best_starting_model)": [[313, "mmtbx.refinement.select_best_starting_model.strip_model", false]], "strip_shelx_format_extension() (in module iotbx.file_reader)": [[265, "iotbx.file_reader.strip_shelx_format_extension", false]], "structure (class in cctbx.neutron)": [[152, "cctbx.neutron.structure", false]], "structure (class in cctbx.xray.structure)": [[238, "cctbx.xray.structure.structure", false]], "structure_factor (class in cctbx.examples.structure_factor_derivatives)": [[119, "cctbx.examples.structure_factor_derivatives.structure_factor", false]], "structure_factor (class in cctbx.examples.structure_factor_derivatives_2)": [[120, "cctbx.examples.structure_factor_derivatives_2.structure_factor", false]], "structure_factor (class in cctbx.examples.structure_factor_derivatives_3)": [[121, 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mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space", false]], "target_function_and_grads_reciprocal_space (class in mmtbx.refinement.minimization_ncs_constraints)": [[313, "mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space", false]], "target_function_is_invariant_under_allowed_origin_shifts() (mmtbx.refinement.targets.target_functor method)": [[313, "mmtbx.refinement.targets.target_functor.target_function_is_invariant_under_allowed_origin_shifts", false]], "target_function_is_invariant_under_allowed_origin_shifts() (mmtbx.twinning.twin_f_model.target_functor method)": [[324, "mmtbx.twinning.twin_f_model.target_functor.target_function_is_invariant_under_allowed_origin_shifts", false]], "target_functions_are_invariant_under_allowed_origin_shifts() (mmtbx.fmodels method)": [[276, "mmtbx.fmodels.target_functions_are_invariant_under_allowed_origin_shifts", false]], 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(mmtbx.twinning.twin_f_model.target_result method)": [[324, "mmtbx.twinning.twin_f_model.target_result.target_work", false]], "tau (mmtbx.scaling.twin_analyses.obliquity attribute)": [[318, "mmtbx.scaling.twin_analyses.obliquity.tau", false]], "tau (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations attribute)": [[333, "scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations.tau", false]], "temperature_as_kinetic_energy() (in module mmtbx.dynamics)": [[287, "mmtbx.dynamics.temperature_as_kinetic_energy", false]], "ter_indices() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.ter_indices", false]], "ter_indices() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.ter_indices", false]], "termination_parameters (class in scitbx.lbfgs)": [[332, "scitbx.lbfgs.termination_parameters", false]], "terms (cctbx.sgtbx.special_op_simplified attribute)": [[165, "cctbx.sgtbx.special_op_simplified.terms", false]], "test() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.test", false]], "test() (in module mmtbx.scaling.absence_likelihood)": [[318, "mmtbx.scaling.absence_likelihood.test", false]], "test() (in module mmtbx.scaling.absences)": [[318, "mmtbx.scaling.absences.test", false]], "test_all() (in module cctbx.sgtbx.direct_space_asu.check_redundancies)": [[169, "cctbx.sgtbx.direct_space_asu.check_redundancies.test_all", false]], "test_average() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_average", false]], "test_call_back() (in module cctbx.sgtbx.harker)": [[177, "cctbx.sgtbx.harker.test_call_back", false]], "test_cdl_lookup() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_cdl_lookup", false]], "test_cis_trans_peptide() (in module mmtbx.conformation_dependent_library.tst_cdl)": [[283, "mmtbx.conformation_dependent_library.tst_cdl.test_cis_trans_peptide", false]], "test_detwin() (in module mmtbx.twinning.probabalistic_detwinning)": [[324, "mmtbx.twinning.probabalistic_detwinning.test_detwin", false]], "test_double_coset_decomposition() (in module cctbx.sgtbx.cosets)": [[167, "cctbx.sgtbx.cosets.test_double_coset_decomposition", false]], "test_flag_value (mmtbx.command_line.load_model_and_data attribute)": [[282, "mmtbx.command_line.load_model_and_data.test_flag_value", false]], "test_for_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_peptide", false]], "test_for_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_rna_dna", false]], "test_for_water() (mmtbx.monomer_library.cif_types.comp_comp_id method)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.test_for_water", false]], "test_lattice_translation_aware_left_decomposition() (in module cctbx.sgtbx.cosets)": [[167, 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"xfel.metrology.mark0.correction_vectors.tile_weight", false]], "timings() (in module cctbx.command_line.structure_factor_timings)": [[17, "cctbx.command_line.structure_factor_timings.timings", false]], "timings() (in module cctbx.development.electron_density_sampling)": [[36, "cctbx.development.electron_density_sampling.timings", false]], "title_section() (iotbx.pdb.ext.input method)": [[268, "iotbx.pdb.ext.input.title_section", false]], "title_section() (iotbx.pdb.mmcif.cif_input method)": [[268, "iotbx.pdb.mmcif.cif_input.title_section", false]], "tls_from_map() (iotbx.map_model_manager.map_model_manager method)": [[266, "iotbx.map_model_manager.map_model_manager.tls_from_map", false]], "tls_from_pdb_inp() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_from_pdb_inp", false]], "tls_from_u_cart() (in module mmtbx.tls.tools)": [[322, "mmtbx.tls.tools.tls_from_u_cart", false]], "tls_from_uaniso_minimizer (class in mmtbx.tls.tools)": [[322, 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false]], "topology() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.topology", false]], "tor_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute)": [[308, "mmtbx.monomer_library.cif_types.comp_comp_id.tor_list", false]], "torsion_search() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.torsion_search", false]], "torsion_search_nested() (in module mmtbx.refinement.real_space)": [[315, "mmtbx.refinement.real_space.torsion_search_nested", false]], "total_intensity_filter() (xfel.clustering.cluster.cluster method)": [[340, "xfel.clustering.cluster.Cluster.total_intensity_filter", false]], "trace() (cctbx.macro_mol.rotation_parameters.matrix33 method)": [[138, "cctbx.macro_mol.rotation_parameters.matrix33.trace", false]], "trace() (scitbx.matrix.rec method)": [[334, "scitbx.matrix.rec.trace", false]], "trace_atoms_in_map() (iotbx.map_manager.map_manager method)": [[266, 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"scitbx.matrix.rec.transpose_multiply", false]], "trialsplot (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlot", false]], "trialsplotframe (class in xfel.cxi.gfx.trials_plot)": [[344, "xfel.cxi.gfx.trials_plot.TrialsPlotFrame", false]], "tricubic_interpolation() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.tricubic_interpolation", false]], "tricubic_interpolation_with_gradients() (scitbx.array_family.flex.double method)": [[331, "scitbx.array_family.flex.double.tricubic_interpolation_with_gradients", false]], "trim_res_limit() (xfel.clustering.singleframe.singleframe method)": [[340, "xfel.clustering.singleframe.SingleFrame.trim_res_limit", false]], "triplet_generator() (in module cctbx.dmtbx)": [[45, "cctbx.dmtbx.triplet_generator", false]], "trivial_html_tag_filter (class in mmtbx.monomer_library.server)": [[308, "mmtbx.monomer_library.server.trivial_html_tag_filter", false]], "truncate() (in module cctbx.maptbx)": 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[[284, "mmtbx.den.refinement.manager.try_den_weight_cartesian", false]], "try_den_weight_torsion() (mmtbx.den.refinement.manager method)": [[284, "mmtbx.den.refinement.manager.try_den_weight_torsion", false]], "try_scale() (mmtbx.bulk_solvent.scaler.run method)": [[278, "mmtbx.bulk_solvent.scaler.run.try_scale", false]], "try_weight() (mmtbx.refinement.adp_refinement.refine_adp method)": [[313, "mmtbx.refinement.adp_refinement.refine_adp.try_weight", false]], "tst_bravais_types() (in module cctbx.sgtbx.bravais_types)": [[166, "cctbx.sgtbx.bravais_types.tst_bravais_types", false]], "tst_build_edge_list() (in module cctbx.eltbx.distance_based_connectivity)": [[64, "cctbx.eltbx.distance_based_connectivity.tst_build_edge_list", false]], "tst_build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_build_reticular_twin_laws", false]], "tst_centered_cells() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_centered_cells", false]], "tst_compare() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.tst_compare", false]], "tst_compare() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_compare", false]], "tst_compare() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_compare", false]], "tst_groups() (in module cctbx.sgtbx.rational_matrices_point_groups)": [[182, "cctbx.sgtbx.rational_matrices_point_groups.tst_groups", false]], "tst_groups() (in module cctbx.sgtbx.reticular_pg_tools)": [[183, "cctbx.sgtbx.reticular_pg_tools.tst_groups", false]], "tst_make_bigger_cell() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_make_bigger_cell", false]], "tst_run_requiring_cns() (in module cctbx.development.make_cns_input)": [[38, "cctbx.development.make_cns_input.tst_run_requiring_cns", false]], "tst_sublattice() (in module cctbx.sgtbx.sub_lattice_tools)": [[186, "cctbx.sgtbx.sub_lattice_tools.tst_sublattice", false]], "tube_number_ (mmtbx.ligands.xtal_screens.solution attribute)": [[304, "mmtbx.ligands.xtal_screens.solution.tube_number_", false]], "tune_up (class in mmtbx.refinement.real_space.fit_residue)": [[315, "mmtbx.refinement.real_space.fit_residue.tune_up", false]], "twin_analyses (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_analyses", false]], "twin_analyses_brief() (in module mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_analyses_brief", false]], "twin_data() (cctbx.miller.array method)": [[148, "cctbx.miller.array.twin_data", false]], "twin_fraction_object (class in mmtbx.twinning.twin_f_model)": [[324, "mmtbx.twinning.twin_f_model.twin_fraction_object", false]], "twin_fraction_scan() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.twin_fraction_scan", false]], "twin_fraction_to_ref() (mmtbx.twinning.twin_f_model.twin_fraction_object method)": [[324, "mmtbx.twinning.twin_f_model.twin_fraction_object.twin_fraction_to_ref", false]], "twin_law (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law", false]], "twin_law (mmtbx.validation.experimental.data_statistics attribute)": [[326, "mmtbx.validation.experimental.data_statistics.twin_law", false]], "twin_law() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.twin_law", false]], "twin_law_dependent_twin_tests (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests", false]], "twin_law_quality (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_law_quality", false]], "twin_laws (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_laws", false]], "twin_model_manager (class in mmtbx.twinning.twin_f_model)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager", false]], "twin_results_interpretation (class in mmtbx.scaling.twin_analyses)": [[318, "mmtbx.scaling.twin_analyses.twin_results_interpretation", false]], "twin_test() (mmtbx.twinning.twin_f_model.twin_model_manager method)": [[324, "mmtbx.twinning.twin_f_model.twin_model_manager.twin_test", false]], "twin_type (mmtbx.scaling.twin_analyses.twin_law attribute)": [[318, "mmtbx.scaling.twin_analyses.twin_law.twin_type", false]], "twmad_fa_driver (class in mmtbx.scaling.fa_estimation)": [[318, "mmtbx.scaling.fa_estimation.twmad_fa_driver", false]], "two_fofc (mmtbx.validation.experimental.residue_real_space attribute)": [[326, "mmtbx.validation.experimental.residue_real_space.two_fofc", false]], "two_fofc (mmtbx.validation.waters.water attribute)": [[326, "mmtbx.validation.waters.water.two_fofc", false]], "two_fofc_map() 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(mmtbx.scaling.loggraph_output method)": [[318, "mmtbx.scaling.loggraph_output.write", false]], "write() (mmtbx.scaling.printed_output method)": [[318, "mmtbx.scaling.printed_output.write", false]], "write() (mmtbx.scaling.xtriage_output method)": [[318, "mmtbx.scaling.xtriage_output.write", false]], "write() (mmtbx.utils.states method)": [[325, "mmtbx.utils.states.write", false]], "write_as_xplor_map() (mmtbx.real_space.sampled_model_density method)": [[312, "mmtbx.real_space.sampled_model_density.write_as_xplor_map", false]], "write_atoms() (in module mmtbx.hydrogens.build_hydrogens)": [[291, "mmtbx.hydrogens.build_hydrogens.write_atoms", false]], "write_centroid_hierarchy() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)": [[314, "mmtbx.refinement.ensemble_refinement.ensemble_utils.manager.write_centroid_hierarchy", false]], "write_coot_script() (mmtbx.validation.molprobity.molprobity method)": [[327, "mmtbx.validation.molprobity.molprobity.write_coot_script", false]], "write_cspad_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx)": [[339, "xfel.cftbx.detector.cspad_cbf_tbx.write_cspad_cbf", false]], "write_data() (mmtbx.scaling.massage_twin_detwin_data.massage_data method)": [[318, "mmtbx.scaling.massage_twin_detwin_data.massage_data.write_data", false]], "write_datasets() (mmtbx.scaling.random_omit.random_omit_data method)": [[318, "mmtbx.scaling.random_omit.random_omit_data.write_datasets", false]], "write_file() (iotbx.xds.spot_xds.writer method)": [[272, "iotbx.xds.spot_xds.writer.write_file", false]], "write_file() (iotbx.xds.xparm.writer method)": [[272, "iotbx.xds.xparm.writer.write_file", false]], "write_fit_group() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp)": [[52, "cctbx.eltbx.development.create_n_gaussian_raw_cpp.write_fit_group", false]], "write_geo_file() (cctbx.geometry_restraints.manager.manager method)": [[135, "cctbx.geometry_restraints.manager.manager.write_geo_file", false]], "write_header() (in 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"cctbx.crystal.close_packing module", "cctbx.crystal.coordination_sequences module", "cctbx.crystal.direct_space_asu module", "cctbx.crystal.distance_based_connectivity module", "cctbx.crystal.find_best_cell module", "cctbx.crystal.reindex module", "cctbx.crystal_orientation module", "cctbx.development package", "cctbx.development.cns_density_modification module", "cctbx.development.debug_utils module", "cctbx.development.direct_or_fft module", "cctbx.development.electron_density_sampling module", "cctbx.development.fmt_utils module", "cctbx.development.make_cns_input module", "cctbx.development.make_settings module", "cctbx.development.random_structure module", "cctbx.development.run_shelx module", "cctbx.development.run_shelx76 module", "cctbx.development.space_group_option_parser module", "cctbx.development.structure_factor_utils module", "cctbx.dmtbx module", "cctbx.eltbx package", "cctbx.eltbx.attenuation_coefficient module", "cctbx.eltbx.chemical_elements module", "cctbx.eltbx.covalent_radii module", "cctbx.eltbx.development package", "cctbx.eltbx.development.combine_fits module", "cctbx.eltbx.development.create_n_gaussian_raw_cpp module", "cctbx.eltbx.development.e_scattering_plots module", "cctbx.eltbx.development.format_gaussian_fits module", "cctbx.eltbx.development.hydrogen_plots module", "cctbx.eltbx.development.itvc_approx module", "cctbx.eltbx.development.itvc_cross_validation module", "cctbx.eltbx.development.itvc_fits module", "cctbx.eltbx.development.itvc_kissel module", "cctbx.eltbx.development.itvc_section61_io module", "cctbx.eltbx.development.kissel_fits module", "cctbx.eltbx.development.kissel_io module", "cctbx.eltbx.development.rez_rez_grant module", "cctbx.eltbx.distance_based_connectivity module", "cctbx.eltbx.e_scattering module", "cctbx.eltbx.formula module", "cctbx.eltbx.fp_fdp module", "cctbx.eltbx.gaussian_fit module", "cctbx.eltbx.henke module", "cctbx.eltbx.icsd_radii module", "cctbx.eltbx.neutron module", "cctbx.eltbx.sasaki module", "cctbx.eltbx.tiny_pse module", "cctbx.eltbx.van_der_waals_radii module", "cctbx.eltbx.wavelengths module", "cctbx.eltbx.xray_scattering package", "cctbx.euclidean_model_matching module", "cctbx.examples package", "cctbx.examples.adp_symmetry_constraints module", "cctbx.examples.all_axes module", "cctbx.examples.analyze_adp module", "cctbx.examples.change_hand_p31 module", "cctbx.examples.convert_ccp4_symop_lib module", "cctbx.examples.cr2o3_consistency_checks module", "cctbx.examples.cr2o3_primitive_cell module", "cctbx.examples.exp_i_alpha_derivatives module", "cctbx.examples.f_model_example module", "cctbx.examples.fft_map_electron_density_around_atom module", "cctbx.examples.find_distances_using_cpp_objects module", "cctbx.examples.find_sys_abs_equiv_space_groups module", "cctbx.examples.g_exp_i_alpha_derivatives module", "cctbx.examples.g_exp_i_partial_derivatives module", "cctbx.examples.getting_started module", "cctbx.examples.hirshfeld_test module", "cctbx.examples.le_page_1982_vs_lebedev_2005 module", "cctbx.examples.lebedev_2005_perturbation module", "cctbx.examples.list_non_principal_continuous_shifts module", "cctbx.examples.location_part module", "cctbx.examples.map_skewness module", "cctbx.examples.maximum_subgroups module", "cctbx.examples.miller_common_sets module", "cctbx.examples.miller_transform module", "cctbx.examples.neutron_structure_factors module", "cctbx.examples.phase_o_phrenia module", "cctbx.examples.quartz_structure module", "cctbx.examples.random_f_calc module", "cctbx.examples.random_puckers module", "cctbx.examples.reduced_cell_two_folds module", "cctbx.examples.site_symmetry_constraints module", "cctbx.examples.site_symmetry_table module", "cctbx.examples.space_group_matrices module", "cctbx.examples.space_subgroups module", "cctbx.examples.steve_collins module", "cctbx.examples.structure_factor_calculus package", "cctbx.examples.structure_factor_calculus.site_derivatives module", "cctbx.examples.structure_factor_calculus.sites_derivatives module", "cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives module", "cctbx.examples.structure_factor_calculus.u_star_derivatives module", "cctbx.examples.structure_factor_derivatives module", "cctbx.examples.structure_factor_derivatives_2 module", "cctbx.examples.structure_factor_derivatives_3 module", "cctbx.examples.structure_factor_derivatives_4 module", "cctbx.examples.sub_group_graph module", "cctbx.examples.symops_530 module", "cctbx.examples.trigonal_r_vs_tetragonal_i module", "cctbx.examples.unit_cell_minimizers module", "cctbx.examples.unit_cell_refinement module", "cctbx.examples.view_fft_map module", "cctbx.french_wilson module", "cctbx.geometry package", "cctbx.geometry_restraints package", "cctbx.geometry_restraints.energies module", "cctbx.geometry_restraints.flags module", "cctbx.geometry_restraints.lbfgs module", "cctbx.geometry_restraints.manager module", "cctbx.libtbx_refresh module", "cctbx.macro_mol package", "cctbx.macro_mol.rotation_parameters module", "cctbx.maptbx package", "cctbx.maptbx.mem module", "cctbx.maptbx.real_space_refinement module", "cctbx.maptbx.real_space_refinement_simple module", "cctbx.maptbx.real_space_target_and_gradients module", "cctbx.masks package", "cctbx.math_module module", "cctbx.merging package", "cctbx.merging.brehm_diederichs module", "cctbx.miller package", "cctbx.miller.display module", "cctbx.miller.reindexing module", "cctbx.multipolar module", "cctbx.neutron package", "cctbx.omz package", "cctbx.omz.bfgs module", "cctbx.omz.cif_refine module", "cctbx.omz.cod_refine module", "cctbx.omz.cod_select_and_pickle module", "cctbx.omz.dev module", "cctbx.omz.eval_iso_vs_refined module", "cctbx.omz.pdb_dev module", "cctbx.omz.tardy_adaptor module", "cctbx.r_free_utils module", "cctbx.run_examples module", "cctbx.run_tests module", "cctbx.sgtbx package", "cctbx.sgtbx.bravais_types module", "cctbx.sgtbx.cosets module", "cctbx.sgtbx.direct_space_asu package", "cctbx.sgtbx.direct_space_asu.check_redundancies module", "cctbx.sgtbx.direct_space_asu.cut_plane module", "cctbx.sgtbx.direct_space_asu.facet_analysis module", "cctbx.sgtbx.direct_space_asu.plane_group_reference_table module", "cctbx.sgtbx.direct_space_asu.proto package", "cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table module", "cctbx.sgtbx.direct_space_asu.reference_table module", "cctbx.sgtbx.direct_space_asu.short_cuts module", "cctbx.sgtbx.harker module", "cctbx.sgtbx.lattice_symmetry module", "cctbx.sgtbx.literal_description module", "cctbx.sgtbx.plane_groups module", "cctbx.sgtbx.pointgroup_tools module", "cctbx.sgtbx.rational_matrices_point_groups module", "cctbx.sgtbx.reticular_pg_tools module", "cctbx.sgtbx.reticular_twin_laws module", "cctbx.sgtbx.show_cosets module", "cctbx.sgtbx.sub_lattice_tools module", "cctbx.sgtbx.subgroups module", "cctbx.sgtbx.symbol_confidence module", "cctbx.sgtbx.sys_abs_equiv module", "cctbx.source_generators package", "cctbx.source_generators.eltbx package", "cctbx.source_generators.eltbx.generate_henke_cpp module", "cctbx.source_generators.eltbx.generate_sasaki_cpp module", "cctbx.source_generators.flex_fwd_h module", "cctbx.statistics module", "cctbx.symmetry_search module", "cctbx.translation_search module", "cctbx.uctbx package", "cctbx.uctbx.determine_unit_cell package", "cctbx.uctbx.gruber_1973 module", "cctbx.uctbx.gruber_1973_table_1 module", "cctbx.uctbx.krivy_gruber_1976 module", "cctbx.uctbx.reduction_base module", "cctbx.web package", "cctbx.web.all_axes module", "cctbx.web.asu_gallery package", "cctbx.web.asu_gallery.guide_to_notation module", "cctbx.web.asu_gallery.jv_asu module", "cctbx.web.asu_gallery.jv_index module", "cctbx.web.asu_gallery.jvx module", "cctbx.web.asu_gallery.web_links module", "cctbx.web.browse_settings module", "cctbx.web.cgi_utils module", "cctbx.web.change_basis module", "cctbx.web.change_hand module", "cctbx.web.change_setting module", "cctbx.web.dispatcher module", "cctbx.web.emma module", "cctbx.web.explore_symmetry module", "cctbx.web.frac_cart module", "cctbx.web.io_utils module", "cctbx.web.iotbx_cif_validate module", "cctbx.web.lattice_symmetry module", "cctbx.web.libtbx_help module", "cctbx.web.multiple_cell module", "cctbx.web.phase_o_phrenia module", "cctbx.web.replay module", "cctbx.web.shelx module", "cctbx.web.structure_factors module", "cctbx.web.structure_factors_pdb module", "cctbx.web.wyckoff module", "cctbx.xray package", "cctbx.xray.ext module", "cctbx.xray.minimization module", "cctbx.xray.observation_types module", "cctbx.xray.observations package", "cctbx.xray.scatterer module", "cctbx.xray.structure module", "cctbx.xray.structure_factors package", "cctbx.xray.structure_factors.from_scatterers module", "cctbx.xray.structure_factors.from_scatterers_direct module", "cctbx.xray.structure_factors.from_scatterers_direct_parallel module", "cctbx.xray.structure_factors.from_scatterers_fft module", "cctbx.xray.structure_factors.global_counters module", "cctbx.xray.structure_factors.gradient_flags module", "cctbx.xray.structure_factors.gradients module", "cctbx.xray.structure_factors.gradients_base module", "cctbx.xray.structure_factors.gradients_direct module", "cctbx.xray.structure_factors.gradients_fft module", "cctbx.xray.structure_factors.manager module", "cctbx.xray.structure_factors.misc module", "cctbx.xray.target_functors module", "cctbx.xray.targets package", "cctbx.xray.targets.r1 module", "cctbx.xray.weighting_schemes module", "cctbx", "dxtbx.model", "dxtbx.serialize", "dxtbx package", "CCTBX development history", "Computational Crystallography Toolbox", "Installation overview", "iotbx - file readers and writers", "iotbx.cif", "iotbx.file_reader - generic file input", "iotbx.managers", "iotbx.ncs package", "iotbx.pdb", "iotbx.pdb tutorial: pdb_truncate_to_ala", "iotbx.reflection_file_reader - generic reflection file input", "iotbx.shelx", "iotbx.xds", "libtbx 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module", "mmtbx.kinemage package", "mmtbx.ligands package", "mmtbx.maps package", "mmtbx.masks package", "mmtbx.max_lik package", "mmtbx.monomer_library package", "mmtbx.ncs", "mmtbx.pdbtools - model manipulation utilities", "mmtbx.polygon package", "mmtbx.real_space package", "mmtbx.refinement package", "mmtbx.refinement.ensemble_refinement package", "mmtbx.refinement.real_space package", "mmtbx.rotamer package", "mmtbx.rsr package", "mmtbx.scaling package", "mmtbx.secondary_structure package", "mmtbx.secondary_structure.build package", "mmtbx.solvent package", "mmtbx.tls package", "mmtbx.torsion_restraints package", "mmtbx.twinning package", "mmtbx.utils package", "mmtbx.validation package", "mmtbx.validation.molprobity package", "mmtbx.wwpdb package", "mmtbx", "scitbx - general-purpose scientific programming infrastructure", "scitbx.array_family.flex", "scitbx.lbfgs", "scitbx.lstbx", "scitbx.matrix", "Tour of the cctbx", "xfel", "xfel package", "xfel.cftbx package", 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