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Commit e5ffa905 authored by Jason Swails's avatar Jason Swails
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Have the CHARMM parsers use the Topology API additions.

parent b0ecf372
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wrappers/python/simtk/openmm/app/charmmpsffile.py
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...@@ -777,11 +777,12 @@ class CharmmPsfFile(object): ...@@ -777,11 +777,12 @@ class CharmmPsfFile(object):
# Add each chain (separate 'system's) and residue # Add each chain (separate 'system's) and residue
for atom in self.atom_list: for atom in self.atom_list:
if atom.system != last_chain: if atom.system != last_chain:
chain = topology.addChain() chain = topology.addChain(atom.system)
last_chain = atom.system last_chain = atom.system
if atom.residue.idx != last_residue: if atom.residue.idx != last_residue:
last_residue = atom.residue.idx last_residue = atom.residue.idx
residue = topology.addResidue(atom.residue.resname, chain) residue = topology.addResidue(atom.residue.resname, chain,
str(atom.residue.idx))
if atom.type is not None: if atom.type is not None:
# This is the most reliable way of determining the element # This is the most reliable way of determining the element
atomic_num = atom.type.atomic_number atomic_num = atom.type.atomic_number
......
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