Minor improvements to correctly handle more PDB files

pdbfixer.py

@@ -46,13 +46,13 @@ import math
 substitutions = {
     '2AS':'ASP', '3AH':'HIS', '5HP':'GLU', 'ACL':'ARG', 'AGM':'ARG', 'AIB':'ALA', 'ALM':'ALA', 'ALO':'THR', 'ALY':'LYS', 'ARM':'ARG',
     'ASA':'ASP', 'ASB':'ASP', 'ASK':'ASP', 'ASL':'ASP', 'ASQ':'ASP', 'AYA':'ALA', 'BCS':'CYS', 'BHD':'ASP', 'BMT':'THR', 'BNN':'ALA',
-    'BUC':'CYS', 'BUG':'LEU', 'C5C':'CYS', 'C6C':'CYS', 'CCS':'CYS', 'CEA':'CYS', 'CGU':'GLU', 'CHG':'ALA', 'CLE':'LEU', 'CME':'CYS',
+    'BUC':'CYS', 'BUG':'LEU', 'C5C':'CYS', 'C6C':'CYS', 'CAS':'CYS', 'CCS':'CYS', 'CEA':'CYS', 'CGU':'GLU', 'CHG':'ALA', 'CLE':'LEU', 'CME':'CYS',
     'CSD':'ALA', 'CSO':'CYS', 'CSP':'CYS', 'CSS':'CYS', 'CSW':'CYS', 'CSX':'CYS', 'CXM':'MET', 'CY1':'CYS', 'CY3':'CYS', 'CYG':'CYS',
     'CYM':'CYS', 'CYQ':'CYS', 'DAH':'PHE', 'DAL':'ALA', 'DAR':'ARG', 'DAS':'ASP', 'DCY':'CYS', 'DGL':'GLU', 'DGN':'GLN', 'DHA':'ALA',
     'DHI':'HIS', 'DIL':'ILE', 'DIV':'VAL', 'DLE':'LEU', 'DLY':'LYS', 'DNP':'ALA', 'DPN':'PHE', 'DPR':'PRO', 'DSN':'SER', 'DSP':'ASP',
     'DTH':'THR', 'DTR':'TRP', 'DTY':'TYR', 'DVA':'VAL', 'EFC':'CYS', 'FLA':'ALA', 'FME':'MET', 'GGL':'GLU', 'GL3':'GLY', 'GLZ':'GLY',
     'GMA':'GLU', 'GSC':'GLY', 'HAC':'ALA', 'HAR':'ARG', 'HIC':'HIS', 'HIP':'HIS', 'HMR':'ARG', 'HPQ':'PHE', 'HTR':'TRP', 'HYP':'PRO',
-    'IIL':'ILE', 'IYR':'TYR', 'KCX':'LYS', 'LLP':'LYS', 'LLY':'LYS', 'LTR':'TRP', 'LYM':'LYS', 'LYZ':'LYS', 'MAA':'ALA', 'MEN':'ASN',
+    'IAS':'ASP', 'IIL':'ILE', 'IYR':'TYR', 'KCX':'LYS', 'LLP':'LYS', 'LLY':'LYS', 'LTR':'TRP', 'LYM':'LYS', 'LYZ':'LYS', 'MAA':'ALA', 'MEN':'ASN',
     'MHS':'HIS', 'MIS':'SER', 'MLE':'LEU', 'MPQ':'GLY', 'MSA':'GLY', 'MSE':'MET', 'MVA':'VAL', 'NEM':'HIS', 'NEP':'HIS', 'NLE':'LEU',
     'NLN':'LEU', 'NLP':'LEU', 'NMC':'GLY', 'OAS':'SER', 'OCS':'CYS', 'OMT':'MET', 'PAQ':'TYR', 'PCA':'GLU', 'PEC':'CYS', 'PHI':'PHE',
     'PHL':'PHE', 'PR3':'CYS', 'PRR':'ALA', 'PTR':'TYR', 'PYX':'CYS', 'SAC':'SER', 'SAR':'GLY', 'SCH':'CYS', 'SCS':'CYS', 'SCY':'CYS',
@@ -145,8 +145,11 @@ class PDBFixer(object):
                 # Create the new residue and add existing heavy atoms.
                                 
                 newResidue = newTopology.addResidue(residue.name, newChain)
+                addResiduesAfter = (residue == chainResidues[-1] and (chain.index, indexInChain+1) in self.missingResidues)
                 for atom in residue.atoms():
                     if not heavyAtomsOnly or (atom.element is not None and atom.element != hydrogen):
+                        if atom.name == 'OXT' and (chain.index, indexInChain+1) in self.missingResidues:
+                            continue # Remove terminal oxygen, since we'll add more residues after this one
                         newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
                         existingAtomMap[atom] = newAtom
                         newPositions.append(self.positions[atom.index])
@@ -417,7 +420,7 @@ class PDBFixer(object):
                 
                 for i in range(10):
                     context.setParameter('C', 0.15*(i+1))
-                    integrator.step(1000)
+                    integrator.step(200)
                     d = self._findNearestDistance(context, newTopology, newAtoms)
                     if d > nearest:
                         nearest = d