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Commit 28c28ead authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
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Fix issue with bond enumeration.

parent 4f352019
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Showing with 3 additions and 3 deletions
wrappers/python/simtk/openmm/app/forcefield.py
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...@@ -586,9 +586,9 @@ class ForceField(object): ...@@ -586,9 +586,9 @@ class ForceField(object):
bondedToAtom = [] bondedToAtom = []
for atom in topology.atoms(): for atom in topology.atoms():
bondedToAtom.append(set()) bondedToAtom.append(set())
for bond in topology.bonds(): for (atom1, atom2) in topology.bonds():
bondedToAtom[bond.atom1.index].add(bond.atom2.index) bondedToAtom[atom1.index].add(atom2.index)
bondedToAtom[bond.atom2.index].add(bond.atom1.index) bondedToAtom[atom2.index].add(atom1.index)
def getUnmatchedResidues(self, topology): def getUnmatchedResidues(self, topology):
"""Return a list of Residue objects from specified topology for which no forcefield templates are available. """Return a list of Residue objects from specified topology for which no forcefield templates are available.
......
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