Skip to content

Commit

Permalink
Add support for CCD length > 3 characters
Browse files Browse the repository at this point in the history
  • Loading branch information
Ezra Peisach committed May 28, 2023
1 parent 040522a commit 6f6f48c
Show file tree
Hide file tree
Showing 5 changed files with 389 additions and 7 deletions.
5 changes: 0 additions & 5 deletions pylintrc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -503,8 +503,3 @@ min-public-methods=2


[EXCEPTIONS]

# Exceptions that will emit a warning when being caught. Defaults to
# "BaseException, Exception".
overgeneral-exceptions=BaseException,
Exception
14 changes: 13 additions & 1 deletion wwpdb/utils/oe_util/build/OeChemCompIoUtils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,19 @@ def getFromIdList(self, idList, use3D=True, coordType="model", setTitle=True):
hashd = idU[-1]
pth = os.path.join(self.__topCachePath, hashd, idU + '.cif')
else:
hashd = idU[0]
hashd = self.__getCcdHash(idU)
pth = os.path.join(self.__topCachePath, hashd, idU, idU + '.cif')
pathList.append(pth)
return self.getFromPathList(pathList, use3D=use3D, coordType=coordType, setTitle=setTitle)

def __getCcdHash(self, idCode):
"""Returns the hash code for a CCD id. Currently first letter"""
if not idCode:
return None

if len(idCode) > 3:
hash_key = idCode.upper()[-2:]
else:
hash_key = idCode.upper()[0]

return hash_key
3 changes: 2 additions & 1 deletion wwpdb/utils/tests_oe_util/OeChemCompIoUtilsTests.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ def setUp(self):

self.__topCachePath = os.path.join(self.__here, "ligand-dict-v3")
self.__pathList = [os.path.join(self.__datadir, "ATP.cif"), os.path.join(self.__datadir, "GTP.cif"), os.path.join(self.__datadir, "ARG.cif")]
self.__idList = ["MSE", "GTP", "TRP"]
self.__idList = ["MSE", "GTP", "TRP", "XXATP"]

def tearDown(self):
pass
Expand Down Expand Up @@ -77,6 +77,7 @@ def testMakeFromIds(self):
oeU = OeChemCompIoUtils(topCachePath=self.__topCachePath, verbose=self.__verbose, log=self.__lfh)
oemList = oeU.getFromIdList(self.__idList, use3D=True, coordType="model")
for oem in oemList:
self.__lfh.write("CcId = %s\n" % oem.getCcId())
self.__lfh.write("Title = %s\n" % oem.getTitle())
self.__lfh.write("SMILES (canonical) = %s\n" % oem.getCanSMILES())
self.__lfh.write("SMILES (isomeric) = %s\n" % oem.getIsoSMILES())
Expand Down
187 changes: 187 additions & 0 deletions wwpdb/utils/tests_oe_util/data/XXATP.cif
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,187 @@
data_XXATP
#
_chem_comp.id XXATP
_chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 N5 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 507.181
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XXATP
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1B0U
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
XXATP HOG2 2HOG H 0 0 N N N 47.590 43.767 57.197 2.100 -0.546 -8.725 HOG2 XXATP 32
XXATP HOG3 3HOG H 0 0 N N N 46.180 44.800 58.946 -0.616 -1.048 -7.522 HOG3 XXATP 33
XXATP HOB2 2HOB H 0 0 N N N 44.228 45.447 54.456 -1.554 -0.952 -5.132 HOB2 XXATP 34
XXATP HOA2 2HOA H 0 0 N N N 43.423 41.710 52.660 0.752 1.455 -1.563 HOA2 XXATP 35
XXATP H8 H8 H 0 1 N N N 47.836 41.390 51.499 1.334 1.357 3.044 H8 XXATP 44
XXATP HN61 1HN6 H 0 0 N N N 52.491 41.565 47.460 3.938 0.548 8.562 HN61 XXATP 45
XXATP HN62 2HN6 H 0 0 N N N 51.940 42.252 48.852 4.015 1.303 7.064 HN62 XXATP 46
XXATP H2 H2 H 0 1 N N N 52.036 37.229 48.759 0.166 -2.014 8.490 H2 XXATP 47
XXATP "H5'1" 1H5* H 0 0 N N N 47.666 40.570 53.221 -2.678 0.312 -0.296 "H5'1" XXATP 36
XXATP "H5'2" 2H5* H 0 0 N N N 46.587 40.459 54.656 -1.263 1.259 0.221 "H5'2" XXATP 37
XXATP "H4'" H4* H 0 1 N N N 45.665 38.327 53.639 -2.275 -1.304 1.550 "H4'" XXATP 38
XXATP "H3'" H3* H 0 1 N N N 48.234 39.870 54.375 -2.651 1.649 2.078 "H3'" XXATP 39
XXATP "HO3'" *HO3 H 0 0 N N N 48.532 38.283 55.898 -4.515 0.788 3.094 "HO3'" XXATP 40
XXATP "H2'" H2* H 0 1 N N N 49.788 38.422 53.212 -1.646 1.537 4.157 "H2'" XXATP 41
XXATP "HO2'" *HO2 H 0 0 N N N 49.196 36.267 52.822 -3.667 0.662 4.867 "HO2'" XXATP 42
XXATP "H1'" H1* H 0 1 N N N 48.203 37.474 51.117 -1.119 -1.430 3.931 "H1'" XXATP 43
XXATP PG PG P 0 1 N N N 46.107 45.182 56.950 1.200 -0.226 -6.850 PG XXATP 1
XXATP O1G O1G O 0 1 N N N 45.779 46.330 56.052 1.740 1.140 -6.672 O1G XXATP 2
XXATP O2G O2G O 0 1 N N N 47.382 44.497 56.626 2.123 -1.036 -7.891 O2G XXATP 3
XXATP O3G O3G O 0 1 N N N 45.972 45.530 58.375 -0.302 -0.139 -7.421 O3G XXATP 4
XXATP PB PB P 0 1 N N R 43.911 43.740 55.655 0.255 -0.130 -4.446 PB XXATP 5
XXATP O1B O1B O 0 1 N N N 42.975 42.722 55.986 0.810 1.234 -4.304 O1B XXATP 6
XXATP O2B O2B O 0 1 N N N 43.603 44.767 54.678 -1.231 -0.044 -5.057 O2B XXATP 7
XXATP O3B O3B O 0 1 N N N 45.041 44.015 56.738 1.192 -0.990 -5.433 O3B XXATP 8
XXATP PA PA P 0 1 N N R 45.228 42.669 53.257 -0.745 0.068 -2.071 PA XXATP 9
XXATP O1A O1A O 0 1 N N N 46.380 43.396 52.788 -2.097 0.143 -2.669 O1A XXATP 10
XXATP O2A O2A O 0 1 N N N 44.183 42.190 52.351 -0.125 1.549 -1.957 O2A XXATP 11
XXATP O3A O3A O 0 1 N N N 44.917 42.716 54.789 0.203 -0.840 -3.002 O3A XXATP 12
XXATP "O5'" O5* O 0 1 N N N 46.172 41.568 53.302 -0.844 -0.587 -0.604 "O5'" XXATP 13
XXATP "C5'" C5* C 0 1 N N N 46.609 40.422 53.542 -1.694 0.260 0.170 "C5'" XXATP 14
XXATP "C4'" C4* C 0 1 N N R 46.520 38.989 53.364 -1.831 -0.309 1.584 "C4'" XXATP 15
XXATP "O4'" O4* O 0 1 N N N 46.785 38.908 51.948 -0.542 -0.355 2.234 "O4'" XXATP 16
XXATP "C3'" C3* C 0 1 N N S 47.808 38.874 54.112 -2.683 0.630 2.465 "C3'" XXATP 17
XXATP "O3'" O3* O 0 1 N N N 47.713 38.357 55.423 -4.033 0.165 2.534 "O3'" XXATP 18
XXATP "C2'" C2* C 0 1 N N R 48.719 38.116 53.139 -2.011 0.555 3.856 "C2'" XXATP 19
XXATP "O2'" O2* O 0 1 N N N 48.632 36.737 53.425 -2.926 0.043 4.827 "O2'" XXATP 20
XXATP "C1'" C1* C 0 1 N N R 48.133 38.409 51.721 -0.830 -0.418 3.647 "C1'" XXATP 21
XXATP N9 N9 N 0 1 Y N N 48.846 39.464 50.986 0.332 0.015 4.425 N9 XXATP 22
XXATP C8 C8 C 0 1 Y N N 48.616 40.842 50.945 1.302 0.879 4.012 C8 XXATP 23
XXATP N7 N7 N 0 1 Y N N 49.425 41.489 50.165 2.184 1.042 4.955 N7 XXATP 24
XXATP C5 C5 C 0 1 Y N N 50.232 40.470 49.664 1.833 0.300 6.033 C5 XXATP 25
XXATP C6 C6 C 0 1 Y N N 51.308 40.466 48.731 2.391 0.077 7.303 C6 XXATP 26
XXATP N6 N6 N 0 1 N N N 51.721 41.568 48.129 3.564 0.706 7.681 N6 XXATP 27
XXATP N1 N1 N 0 1 Y N N 51.912 39.274 48.447 1.763 -0.747 8.135 N1 XXATP 28
XXATP C2 C2 C 0 1 Y N N 51.493 38.151 49.029 0.644 -1.352 7.783 C2 XXATP 29
XXATP N3 N3 N 0 1 Y N N 50.491 38.016 49.900 0.088 -1.178 6.602 N3 XXATP 30
XXATP C4 C4 C 0 1 Y N N 49.892 39.253 50.171 0.644 -0.371 5.704 C4 XXATP 31
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
XXATP PG O1G DOUB N N 1
XXATP PG O2G SING N N 2
XXATP PG O3G SING N N 3
XXATP PG O3B SING N N 4
XXATP O2G HOG2 SING N N 5
XXATP O3G HOG3 SING N N 6
XXATP PB O1B DOUB N N 7
XXATP PB O2B SING N N 8
XXATP PB O3B SING N N 9
XXATP PB O3A SING N N 10
XXATP O2B HOB2 SING N N 11
XXATP PA O1A DOUB N N 12
XXATP PA O2A SING N N 13
XXATP PA O3A SING N N 14
XXATP PA "O5'" SING N N 15
XXATP O2A HOA2 SING N N 16
XXATP "O5'" "C5'" SING N N 17
XXATP "C5'" "C4'" SING N N 18
XXATP "C5'" "H5'1" SING N N 19
XXATP "C5'" "H5'2" SING N N 20
XXATP "C4'" "O4'" SING N N 21
XXATP "C4'" "C3'" SING N N 22
XXATP "C4'" "H4'" SING N N 23
XXATP "O4'" "C1'" SING N N 24
XXATP "C3'" "O3'" SING N N 25
XXATP "C3'" "C2'" SING N N 26
XXATP "C3'" "H3'" SING N N 27
XXATP "O3'" "HO3'" SING N N 28
XXATP "C2'" "O2'" SING N N 29
XXATP "C2'" "C1'" SING N N 30
XXATP "C2'" "H2'" SING N N 31
XXATP "O2'" "HO2'" SING N N 32
XXATP "C1'" N9 SING N N 33
XXATP "C1'" "H1'" SING N N 34
XXATP N9 C8 SING Y N 35
XXATP N9 C4 SING Y N 36
XXATP C8 N7 DOUB Y N 37
XXATP C8 H8 SING N N 38
XXATP N7 C5 SING Y N 39
XXATP C5 C6 SING Y N 40
XXATP C5 C4 DOUB Y N 41
XXATP C6 N6 SING N N 42
XXATP C6 N1 DOUB Y N 43
XXATP N6 HN61 SING N N 44
XXATP N6 HN62 SING N N 45
XXATP N1 C2 SING Y N 46
XXATP C2 N3 DOUB Y N 47
XXATP C2 H2 SING N N 48
XXATP N3 C4 SING Y N 49
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
XXATP SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O"
XXATP SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O"
XXATP SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O"
XXATP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N"
XXATP SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N"
XXATP InChI InChI 1.03 "InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1"
XXATP InChIKey InChI 1.03 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
XXATP "SYSTEMATIC NAME" ACDLabs 10.04
;adenosine 5'-(tetrahydrogen triphosphate)
;
XXATP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
_pdbx_chem_comp_audit.annotator
_pdbx_chem_comp_audit.details
XXATP "Create component" 1999-07-08 EBI ? ?
XXATP "Modify descriptor" 2011-06-04 RCSB ? ?
#
Loading

0 comments on commit 6f6f48c

Please sign in to comment.