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Commit aaf535b8 authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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add ordering attribute to impropers

parent 18253db9
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Showing with 23 additions and 18 deletions
wrappers/python/simtk/openmm/app/forcefield.py
View file @ aaf535b8
...@@ -1802,6 +1802,7 @@ class PeriodicTorsion(object): ...@@ -1802,6 +1802,7 @@ class PeriodicTorsion(object):
self.periodicity = [] self.periodicity = []
self.phase = [] self.phase = []
self.k = [] self.k = []
self.ordering = 'default'
## @private ## @private
class PeriodicTorsionGenerator(object): class PeriodicTorsionGenerator(object):
...@@ -1817,9 +1818,15 @@ class PeriodicTorsionGenerator(object): ...@@ -1817,9 +1818,15 @@ class PeriodicTorsionGenerator(object):
if torsion is not None: if torsion is not None:
self.proper.append(torsion) self.proper.append(torsion)
def registerImproperTorsion(self, parameters): def registerImproperTorsion(self, parameters, ordering='default'):
torsion = self.ff._parseTorsion(parameters) torsion = self.ff._parseTorsion(parameters)
if torsion is not None: if torsion is not None:
if ordering == 'default':
pass
elif ordering == 'amber':
torsion.ordering = ordering
else:
raise ValueError('Illegal ordering type for improper torsion %s' % torsion)
self.improper.append(torsion) self.improper.append(torsion)
@staticmethod @staticmethod
...@@ -1833,7 +1840,7 @@ class PeriodicTorsionGenerator(object): ...@@ -1833,7 +1840,7 @@ class PeriodicTorsionGenerator(object):
for torsion in element.findall('Proper'): for torsion in element.findall('Proper'):
generator.registerProperTorsion(torsion.attrib) generator.registerProperTorsion(torsion.attrib)
for torsion in element.findall('Improper'): for torsion in element.findall('Improper'):
generator.registerImproperTorsion(torsion.attrib) generator.registerImproperTorsion(torsion.attrib, element.attrib['ordering'])
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
existing = [sys.getForce(i) for i in range(sys.getNumForces())] existing = [sys.getForce(i) for i in range(sys.getNumForces())]
...@@ -1903,14 +1910,12 @@ class PeriodicTorsionGenerator(object): ...@@ -1903,14 +1910,12 @@ class PeriodicTorsionGenerator(object):
e2 = data.atoms[a2].element e2 = data.atoms[a2].element
e3 = data.atoms[a3].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 if tordef.ordering == 'default':
if isAmber:
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 r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]] ta2 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]] 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)
...@@ -1920,38 +1925,38 @@ class PeriodicTorsionGenerator(object): ...@@ -1920,38 +1925,38 @@ class PeriodicTorsionGenerator(object):
ta4 = data.atomTemplateIndexes[data.atoms[a4]] 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: elif hasTwoWildcards and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)): (a2, a3) = (a3, a2)
elif tordef.ordering == 'amber':
if not hasWildcard:
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 r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]] ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]] ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if e3 == e4 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 r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]] ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]] ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if 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)
# the following is OpenMM default
else: else:
if t2[0] == t4[0] 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 r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a3]] ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]] ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t3[0] == t4[0] 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 r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]] ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]] ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)): if r2 > r3 or (r2 == r3 and ta2 > ta3):
(a2, a3) = (a3, a2)
elif hasTwoWildcards and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2) (a2, a3) = (a3, a2)
match = (a2, a3, torsion[0], a4, tordef) match = (a2, a3, torsion[0], a4, tordef)
break break
......
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