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Commit abc801dd authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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fixes

parent 406105ef
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Showing with 22 additions and 22 deletions
wrappers/python/simtk/openmm/app/forcefield.py
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...@@ -1888,48 +1888,48 @@ class PeriodicTorsionGenerator(object): ...@@ -1888,48 +1888,48 @@ class PeriodicTorsionGenerator(object):
for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))): for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
if t2[0] in types2 and t3[0] in types3 and t4[0] in types4: if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
# topology atom indexes # topology atom indexes
a1 = torsion[t2[1]] a2 = torsion[t2[1]]
a2 = torsion[t3[1]] a3 = torsion[t3[1]]
a4 = torsion[t4[1]] a4 = torsion[t4[1]]
# residue indexes # residue indexes
r1 = data.atoms[a1].residue.index
r2 = data.atoms[a2].residue.index r2 = data.atoms[a2].residue.index
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index r4 = data.atoms[a4].residue.index
# template atom indexes # template atom indexes
ta1 = data.atomTemplateIndexes[data.atoms[a1]]
ta2 = data.atomTemplateIndexes[data.atoms[a2]] ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]] ta4 = data.atomTemplateIndexes[data.atoms[a4]]
# elements # elements
e1 = data.atoms[a1].element
e2 = data.atoms[a2].element e2 = data.atoms[a2].element
e3 = data.atoms[a3].element
e4 = data.atoms[a4].element e4 = data.atoms[a4].element
# the following for AMBER only - TODO: decide how to pass this in ffxml's # the following for AMBER only - TODO: decide how to pass this in ffxml's
if isAmber: if isAmber:
if not hasWildcard: if not hasWildcard:
if t2[0] == t4[0] and (r1 > r4 or (r1 == r4 and ta1 > ta4)): if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a1, a4) = (a4, a1)
if t3[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2) (a2, a4) = (a4, a2)
if t2[0] == t3[0] and (r1 > r2 or (r1 == r2 and ta1 > ta2)): if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a1, a2) = (a2, a1) (a3, a4) = (a4, a3)
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2)
else: else:
if e1 == e4 and (r1 > r4 or (r1 == r4 and ta1 > ta4)):
(a1, a4) = (a4, a1)
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)): if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2) (a2, a4) = (a4, a2)
if (r1 > r2 or (r1 == r2 and ta1 > ta2)): if e3 == e4 and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a1, a2) = (a2, a1) (a3, a4) = (a4, a3)
if r2 > r3 or (r2 == r3 and ta2 > ta3):
(a2, a3) = (a3, a2)
# the following is OpenMM default # the following is OpenMM default
else: else:
if t2[0] == t4[0] and (r1 > r4 or (r1 == r4 and ta1 > ta4)): if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a1, a4) = (a4, a1)
if t3[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2) (a2, a4) = (a4, a2)
if t2[0] == t3[0] and (r1 > r2 or (r1 == r2 and ta1 > ta2)): if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a1, a2) = (a2, a1) (a3, a4) = (a4, a3)
if hasTwoWildcards and (r1 > r2 or (r1 == r2 and ta1 > ta2)): if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a1, a2) = (a2, a1) (a2, a3) = (a3, a2)
match = (a1, a2, torsion[0], a4, tordef) elif hasTwoWildcards and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2)
match = (a2, a3, torsion[0], a4, tordef)
break break
if match is not None: if match is not None:
(a1, a2, a3, a4, tordef) = match (a1, a2, a3, a4, tordef) = match
......
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