Merge pull request #189 from peastman/pdbx

Fixed exception loading PDBx/mmCIF files with missing blocks

pdbfixer/pdbfixer.py

@@ -306,9 +306,10 @@ class PDBFixer(object):
         # Load the sequence data.
         # Load the sequence data.
 
 
         sequenceData = block.getObj('entity_poly_seq')
         sequenceData = block.getObj('entity_poly_seq')
+        sequences = {}
+        if sequenceData is not None:
             entityIdCol = sequenceData.getAttributeIndex('entity_id')
             entityIdCol = sequenceData.getAttributeIndex('entity_id')
             residueCol = sequenceData.getAttributeIndex('mon_id')
             residueCol = sequenceData.getAttributeIndex('mon_id')
-        sequences = {}
             for row in sequenceData.getRowList():
             for row in sequenceData.getRowList():
                 entityId = row[entityIdCol]
                 entityId = row[entityIdCol]
                 residue = row[residueCol]
                 residue = row[residueCol]
@@ -320,9 +321,10 @@ class PDBFixer(object):
         # convert from entities to chains.
         # convert from entities to chains.
 
 
         asymData = block.getObj('struct_asym')
         asymData = block.getObj('struct_asym')
+        self.sequences = []
+        if asymData is not None:
             asymIdCol = asymData.getAttributeIndex('id')
             asymIdCol = asymData.getAttributeIndex('id')
             entityIdCol = asymData.getAttributeIndex('entity_id')
             entityIdCol = asymData.getAttributeIndex('entity_id')
-        self.sequences = []
             for row in asymData.getRowList():
             for row in asymData.getRowList():
                 asymId = row[asymIdCol]
                 asymId = row[asymIdCol]
                 entityId = row[entityIdCol]
                 entityId = row[entityIdCol]
@@ -332,11 +334,12 @@ class PDBFixer(object):
         # Load the modified residues.
         # Load the modified residues.
 
 
         modData = block.getObj('pdbx_struct_mod_residue')
         modData = block.getObj('pdbx_struct_mod_residue')
+        self.modifiedResidues = []
+        if modData is not None:
             asymIdCol = modData.getAttributeIndex('label_asym_id')
             asymIdCol = modData.getAttributeIndex('label_asym_id')
             resNameCol = modData.getAttributeIndex('label_comp_id')
             resNameCol = modData.getAttributeIndex('label_comp_id')
             resNumCol = modData.getAttributeIndex('auth_seq_id')
             resNumCol = modData.getAttributeIndex('auth_seq_id')
             standardResCol = modData.getAttributeIndex('parent_comp_id')
             standardResCol = modData.getAttributeIndex('parent_comp_id')
-        self.modifiedResidues = []
             if -1 not in (asymIdCol, resNameCol, resNumCol, standardResCol):
             if -1 not in (asymIdCol, resNameCol, resNumCol, standardResCol):
                 for row in modData.getRowList():
                 for row in modData.getRowList():
                     self.modifiedResidues.append(ModifiedResidue(row[asymIdCol], int(row[resNumCol]), row[resNameCol], row[standardResCol]))
                     self.modifiedResidues.append(ModifiedResidue(row[asymIdCol], int(row[resNumCol]), row[resNameCol], row[standardResCol]))