Drop 'nm-res-ccp' file type because CCPN can export NEF

wwPDB · Nov 29, 2024 · c10eba7 · c10eba7
1 parent fee3dfa
commit c10eba7
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Showing 4 changed files with 38 additions and 9 deletions.
diff --git a/wwpdb/utils/nmr/NmrDpReport.py b/wwpdb/utils/nmr/NmrDpReport.py
@@ -84,7 +84,7 @@
 # 29-Jan-2024  M. Yokochi - add 'ambiguous_dihedral_angle' warning type (NMR restraint remediation, 6sy2)
 # 21-Feb-2024  M. Yokochi - add support for discontinuous model_id (NMR restraint remediation, 2n6j)
 # 01-May-2024  M. Yokochi - merge cs/mr sequence extensions containing unknown residues (e.g UNK, DN, N) if necessary (NMR restraint remediation, 6fw4)
-# 07-Nov-2024  M. Yokochi - add 'nm-pea-ccp', 'nm-pea-pip', 'nm-pea-vie', 'nm-pea-spa', 'nm-pea-top', and 'nm-pea-xea' file types for NMR spectral peak remediation
+# 07-Nov-2024  M. Yokochi - add 'nm-pea-ari', 'nm-pea-pip', 'nm-pea-vie', 'nm-pea-spa', 'nm-pea-top', 'nm-pea-xea', and 'nm-pea-xwi' file types for NMR spectral peak remediation
 # 14-Nov-2024  M. Yokochi - add 'nm-aux-cha' file type for CHARMM extended CRD (CARD) file acting as CHARMM topology definition
 # 19-Nov-2024  M. Yokochi - add support for pH titration data (NMR restraint remediation)
 # 22-Nov-2024  M. Yokochi - add 'nm-res-noa' file type for CYANA NOA (NOE Assignment) file
@@ -1756,8 +1756,8 @@ def __init__(self, verbose=True, log=sys.stdout):
                            'nm-res-cya', 'nm-res-dyn', 'nm-res-gro', 'nm-res-isd', 'nm-res-mr',
                            'nm-res-noa', 'nm-res-oth', 'nm-res-ros', 'nm-res-sax', 'nm-res-syb',
                            'nm-res-xpl',
-                           'nm-pea-any', 'nm-pea-ccp', 'nm-pea-pip', 'nm-pea-spa', 'nm-pea-top',
-                           'nm-pea-vie', 'nm-pea-xea')
+                           'nm-pea-any', 'nm-pea-ari', 'nm-pea-pip', 'nm-pea-spa', 'nm-pea-top',
+                           'nm-pea-vie', 'nm-pea-xea', 'nm-pea-xwi')
         self.content_types = ('model',
                               'nmr-data-nef', 'nmr-data-str',
                               'nmr-chemical-shifts', 'nmr-restraints', 'nmr-peaks')

diff --git a/wwpdb/utils/nmr/mr/DynamoMRParserListener.py b/wwpdb/utils/nmr/mr/DynamoMRParserListener.py
@@ -232,7 +232,6 @@ class DynamoMRParserListener(ParseTreeListener):
     __verbose = None
     __lfh = None
     __debug = False
-    __remediate = False
 
     __createSfDict = False
     __omitDistLimitOutlier = True

diff --git a/wwpdb/utils/nmr/mr/ParserListenerUtil.py b/wwpdb/utils/nmr/mr/ParserListenerUtil.py
@@ -1948,6 +1948,25 @@
 
 REMEDIATE_BACKBONE_ANGLE_NAME_PAT = re.compile(r'pseudo (PHI|PSI|OMEGA) \(0, (0|1|\-1), (0|1|\-1), 0\)')
 
+SPECTRAL_DIM_TEMPLATE = {'axis_code': None,
+                         'spectrometer_frequency': None,
+                         'atom_type': None,
+                         'atom_isotope_number': None,
+                         'spectral_region': None,
+                         'magnetization_linkage_id': None,
+                         'sweep_width': None,
+                         'sweep_width_unit': None,
+                         'value_first_point': None,
+                         'absolute_peak_positions': None,
+                         'acquisition': None,
+                         'center_frequency_offset': None,
+                         'encoding_code': None,
+                         'encoded_reduced_dimension_id': None
+                         }
+
+SPECTRAL_DIM_TRANSFER_TEMPLATE = {'indirect': None,
+                                  'type': None}
+
 
 def toRegEx(string):
     """ Return regular expression for a given string including XPLOR-NIH wildcard format.
@@ -6744,9 +6763,9 @@ def getRestraintName(mrSubtype, title=False):
     if mrSubtype.startswith('pccr'):
         return "Paramagnetic CCR restraints" if title else "paramagnetic CCR restraints"
     if mrSubtype.startswith('ccr_d_csa'):
-        return "CCR D-CSA restraints" if title else "CCR D-CSA restraints"
+        return "CCR D-CSA restraints"
     if mrSubtype.startswith('ccr_dd'):
-        return "CCR D-D restraints" if title else "CCR D-D restraints"
+        return "CCR D-D restraints"
     if mrSubtype.startswith('geo'):
         return "Coordinate geometry restraints" if title else "coordinate geometry restraints"
     if mrSubtype.startswith('noepk'):
@@ -6768,6 +6787,13 @@ def getRestraintName(mrSubtype, title=False):
     if mrSubtype == 'ph_param_data':
         return "pH titration data"
 
+    if mrSubtype == 'peak2d':
+        return "2D spectral peak list"
+    if mrSubtype == 'peak3d':
+        return "3D spectral peak list"
+    if mrSubtype == 'peak4d':
+        return "4D spectral peak list"
+
     raise KeyError(f'Internal restraint subtype {mrSubtype!r} is not defined.')
 
 
@@ -6799,6 +6825,9 @@ def contentSubtypeOf(mrSubtype):
     if mrSubtype in ('plane', 'adist', 'rama', 'radi', 'diff', 'nbase', 'ang', 'pang', 'geo'):
         return 'other_restraint'
 
+    if mrSubtype.startswth('peak'):
+        return 'spectral_peak'
+
     raise KeyError(f'Internal restraint subtype {mrSubtype!r} is not defined.')
 
 
@@ -6830,7 +6859,8 @@ def incListIdCounter(mrSubtype, listIdCounter, reduced=True):
                          'ccr_dd_restraint': 0,
                          'fchiral_restraint': 0,
                          'saxs_restraint': 0,
-                         'other_restraint': 0
+                         'other_restraint': 0,
+                         'spectral_peak': 0
                          }
 
     contentSubtype = (contentSubtypeOf(mrSubtype) if reduced else mrSubtype) if mrSubtype is not None else 'other_restraint'
@@ -6871,7 +6901,8 @@ def decListIdCounter(mrSubtype, listIdCounter, reduced=True):
                          'ccr_dd_restraint': 0,
                          'fchiral_restraint': 0,
                          'saxs_restraint': 0,
-                         'other_restraint': 0
+                         'other_restraint': 0,
+                         'spectral_peak': 0
                          }
 
     contentSubtype = (contentSubtypeOf(mrSubtype) if reduced else mrSubtype) if mrSubtype is not None else 'other_restraint'

diff --git a/wwpdb/utils/tests-nmr/json-schema/nmr-data-procesing-report-schema-v4.json b/wwpdb/utils/tests-nmr/json-schema/nmr-data-procesing-report-schema-v4.json
@@ -40,7 +40,6 @@
             "nm-res-xpl",
             "nm-pea-any",
             "nm-pea-ari",
-            "nm-pea-ccp",
             "nm-pea-pip",
             "nm-pea-spa",
             "nm-pea-top",