Reconciled fix for 2lrr and 2mff

wwPDB · Feb 20, 2024 · c6c0840 · c6c0840
1 parent 9cb1530
commit c6c0840
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Showing 6 changed files with 31 additions and 30 deletions.
diff --git a/wwpdb/utils/nmr/mr/BiosymMRParserListener.py b/wwpdb/utils/nmr/mr/BiosymMRParserListener.py
@@ -1035,9 +1035,9 @@ def assignCoordPolymerSequence(self, refChainId, seqId, compId, atomId):
         compId = translateToStdResName(_compId, ccU=self.__ccU)
 
         if self.__reasons is not None:
-            if 'non_poly_remap' in self.__reasons and compId in self.__reasons['non_poly_remap']\
-               and seqId in self.__reasons['non_poly_remap'][compId]:
-                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], str(refChainId), seqId, compId)
+            if 'non_poly_remap' in self.__reasons and _compId in self.__reasons['non_poly_remap']\
+               and seqId in self.__reasons['non_poly_remap'][_compId]:
+                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], str(refChainId), seqId, _compId)
                 refChainId = fixedChainId
                 preferNonPoly = True
             if 'branched_remap' in self.__reasons and seqId in self.__reasons['branched_remap']:

diff --git a/wwpdb/utils/nmr/mr/CyanaMRParserListener.py b/wwpdb/utils/nmr/mr/CyanaMRParserListener.py
@@ -2100,15 +2100,15 @@ def assignCoordPolymerSequence(self, seqId, compId, atomId):
         compId = translateToStdResName(_compId, ccU=self.__ccU)
 
         if self.__reasons is not None:
-            if 'ambig_atom_id_remap' in self.__reasons and compId in self.__reasons['ambig_atom_id_remap']\
-               and atomId in self.__reasons['ambig_atom_id_remap'][compId]:
-                return self.atomIdListToChainAssign(self.__reasons['ambig_atom_id_remap'][compId][atomId])
-            if 'unambig_atom_id_remap' in self.__reasons and compId in self.__reasons['unambig_atom_id_remap']\
-               and atomId in self.__reasons['unambig_atom_id_remap'][compId]:
-                atomId = self.__reasons['unambig_atom_id_remap'][compId][atomId][0]  # select representative one
-            if 'non_poly_remap' in self.__reasons and compId in self.__reasons['non_poly_remap']\
-               and seqId in self.__reasons['non_poly_remap'][compId]:
-                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], None, seqId, compId)
+            if 'ambig_atom_id_remap' in self.__reasons and _compId in self.__reasons['ambig_atom_id_remap']\
+               and atomId in self.__reasons['ambig_atom_id_remap'][_compId]:
+                return self.atomIdListToChainAssign(self.__reasons['ambig_atom_id_remap'][_compId][atomId])
+            if 'unambig_atom_id_remap' in self.__reasons and _compId in self.__reasons['unambig_atom_id_remap']\
+               and atomId in self.__reasons['unambig_atom_id_remap'][_compId]:
+                atomId = self.__reasons['unambig_atom_id_remap'][_compId][atomId][0]  # select representative one
+            if 'non_poly_remap' in self.__reasons and _compId in self.__reasons['non_poly_remap']\
+               and seqId in self.__reasons['non_poly_remap'][_compId]:
+                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], None, seqId, _compId)
                 preferNonPoly = True
             if 'branched_remap' in self.__reasons and seqId in self.__reasons['branched_remap']:
                 fixedChainId, fixedSeqId = retrieveRemappedChainId(self.__reasons['branched_remap'], seqId)
@@ -2412,15 +2412,15 @@ def assignCoordPolymerSequenceWithChainId(self, refChainId, seqId, compId, atomI
         compId = translateToStdResName(_compId, ccU=self.__ccU)
 
         if self.__reasons is not None:
-            if 'ambig_atom_id_remap' in self.__reasons and compId in self.__reasons['ambig_atom_id_remap']\
-               and atomId in self.__reasons['ambig_atom_id_remap'][compId]:
-                return self.atomIdListToChainAssign(self.__reasons['ambig_atom_id_remap'][compId][atomId])
-            if 'unambig_atom_id_remap' in self.__reasons and compId in self.__reasons['unambig_atom_id_remap']\
-               and atomId in self.__reasons['unambig_atom_id_remap'][compId]:
-                atomId = self.__reasons['unambig_atom_id_remap'][compId][atomId][0]  # select representative one
-            if 'non_poly_remap' in self.__reasons and compId in self.__reasons['non_poly_remap']\
-               and seqId in self.__reasons['non_poly_remap'][compId]:
-                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], str(refChainId), seqId, compId)
+            if 'ambig_atom_id_remap' in self.__reasons and _compId in self.__reasons['ambig_atom_id_remap']\
+               and atomId in self.__reasons['ambig_atom_id_remap'][_compId]:
+                return self.atomIdListToChainAssign(self.__reasons['ambig_atom_id_remap'][_compId][atomId])
+            if 'unambig_atom_id_remap' in self.__reasons and _compId in self.__reasons['unambig_atom_id_remap']\
+               and atomId in self.__reasons['unambig_atom_id_remap'][_compId]:
+                atomId = self.__reasons['unambig_atom_id_remap'][_compId][atomId][0]  # select representative one
+            if 'non_poly_remap' in self.__reasons and _compId in self.__reasons['non_poly_remap']\
+               and seqId in self.__reasons['non_poly_remap'][_compId]:
+                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], str(refChainId), seqId, _compId)
                 refChainId = fixedChainId
                 preferNonPoly = True
             if 'branched_remap' in self.__reasons and seqId in self.__reasons['branched_remap']:

diff --git a/wwpdb/utils/nmr/mr/CyanaMRReader.py b/wwpdb/utils/nmr/mr/CyanaMRReader.py
@@ -278,6 +278,7 @@ def parse(self, mrFilePath, cifFilePath=None, isFilePath=True,
     reader.setDebugMode(True)
     reader.parse('../../tests-nmr/mock-data-remediation/2lrr/2lrr-trimmed.mr',
                  '../../tests-nmr/mock-data-remediation/2lrr/2lrr.cif')
+
     reader = CyanaMRReader(True)
     reader.setDebugMode(True)
     reader.parse('../../tests-nmr/mock-data-remediation/2kym/2kym-corrected.mr',

diff --git a/wwpdb/utils/nmr/mr/DynamoMRParserListener.py b/wwpdb/utils/nmr/mr/DynamoMRParserListener.py
@@ -1351,9 +1351,9 @@ def assignCoordPolymerSequence(self, refChainId, seqId, compId, atomId, index=No
         compId = translateToStdResName(_compId, ccU=self.__ccU)
 
         if self.__reasons is not None:
-            if 'non_poly_remap' in self.__reasons and compId in self.__reasons['non_poly_remap']\
-               and seqId in self.__reasons['non_poly_remap'][compId]:
-                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], refChainId, seqId, compId)
+            if 'non_poly_remap' in self.__reasons and _compId in self.__reasons['non_poly_remap']\
+               and seqId in self.__reasons['non_poly_remap'][_compId]:
+                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], refChainId, seqId, _compId)
                 refChainId = fixedChainId
                 preferNonPoly = True
             if 'branched_remap' in self.__reasons and seqId in self.__reasons['branched_remap']:

diff --git a/wwpdb/utils/nmr/mr/IsdMRParserListener.py b/wwpdb/utils/nmr/mr/IsdMRParserListener.py
@@ -858,9 +858,9 @@ def assignCoordPolymerSequence(self, seqId, compId, atomId):
         compId = translateToStdResName(_compId, ccU=self.__ccU)
 
         if self.__reasons is not None:
-            if 'non_poly_remap' in self.__reasons and compId in self.__reasons['non_poly_remap']\
-               and seqId in self.__reasons['non_poly_remap'][compId]:
-                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], None, seqId, compId)
+            if 'non_poly_remap' in self.__reasons and _compId in self.__reasons['non_poly_remap']\
+               and seqId in self.__reasons['non_poly_remap'][_compId]:
+                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], None, seqId, _compId)
                 preferNonPoly = True
             if 'branched_remap' in self.__reasons and seqId in self.__reasons['branched_remap']:
                 fixedChainId, fixedSeqId = retrieveRemappedChainId(self.__reasons['branched_remap'], seqId)

diff --git a/wwpdb/utils/nmr/mr/SybylMRParserListener.py b/wwpdb/utils/nmr/mr/SybylMRParserListener.py
@@ -864,9 +864,9 @@ def assignCoordPolymerSequence(self, seqId, compId, atomId):
         compId = translateToStdResName(_compId, ccU=self.__ccU)
 
         if self.__reasons is not None:
-            if 'non_poly_remap' in self.__reasons and compId in self.__reasons['non_poly_remap']\
-               and seqId in self.__reasons['non_poly_remap'][compId]:
-                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], None, seqId, compId)
+            if 'non_poly_remap' in self.__reasons and _compId in self.__reasons['non_poly_remap']\
+               and seqId in self.__reasons['non_poly_remap'][_compId]:
+                fixedChainId, fixedSeqId = retrieveRemappedNonPoly(self.__reasons['non_poly_remap'], None, seqId, _compId)
                 preferNonPoly = True
             if 'branched_remap' in self.__reasons and seqId in self.__reasons['branched_remap']:
                 fixedChainId, fixedSeqId = retrieveRemappedChainId(self.__reasons['branched_remap'], seqId)