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Commit 6412e52f authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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add updates of r and ta

parent abc801dd
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wrappers/python/simtk/openmm/app/forcefield.py
View file @ 6412e52f
...@@ -1908,23 +1908,47 @@ class PeriodicTorsionGenerator(object): ...@@ -1908,23 +1908,47 @@ class PeriodicTorsionGenerator(object):
if not hasWildcard: if not hasWildcard:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)): if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2) (a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)): if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3) (a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)): if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2) (a2, a3) = (a3, a2)
else: else:
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)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if e3 == e4 and (r3 > r4 or (r3 == r4 and ta3 > ta4)): if e3 == e4 and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3) (a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if r2 > r3 or (r2 == r3 and ta2 > ta3): if r2 > r3 or (r2 == r3 and ta2 > ta3):
(a2, a3) = (a3, a2) (a2, a3) = (a3, a2)
# the following is OpenMM default # the following is OpenMM default
else: else:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)): if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2) (a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)): if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3) (a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)): if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2) (a2, a3) = (a3, a2)
elif hasTwoWildcards and (r2 > r3 or (r2 == r3 and ta2 > ta3)): elif hasTwoWildcards and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
......
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