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Commit 883cb72c authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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add new code to RBTorsion and CustomTorsion

parent 4f11c10f
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Showing with 151 additions and 36 deletions
wrappers/python/simtk/openmm/app/forcefield.py
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...@@ -1736,6 +1736,7 @@ def _createResidueTemplate(residue): ...@@ -1736,6 +1736,7 @@ def _createResidueTemplate(residue):
template.addExternalBondByName(atom2.name) template.addExternalBondByName(atom2.name)
return template return template
# The following classes are generators that know how to create Force subclasses and add them to a System that is being # The following classes are generators that know how to create Force subclasses and add them to a System that is being
# created. Each generator class must define two methods: 1) a static method that takes an etree Element and a ForceField, # created. Each generator class must define two methods: 1) a static method that takes an etree Element and a ForceField,
# and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it # and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it
...@@ -2062,12 +2063,16 @@ parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement ...@@ -2062,12 +2063,16 @@ parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement
class RBTorsion(object): class RBTorsion(object):
"""An RBTorsion records the information for a Ryckaert-Bellemans torsion definition.""" """An RBTorsion records the information for a Ryckaert-Bellemans torsion definition."""
def __init__(self, types, c): def __init__(self, types, c, ordering='default'):
self.types1 = types[0] self.types1 = types[0]
self.types2 = types[1] self.types2 = types[1]
self.types3 = types[2] self.types3 = types[2]
self.types4 = types[3] self.types4 = types[3]
self.c = c self.c = c
if ordering == 'default' or ordering == 'amber':
self.ordering = ordering
else:
raise ValueError('Illegal ordering type for RBTorsion (%s,%s,%s,%s)' % (types[0], types[1], types[2], types[3]))
## @private ## @private
class RBTorsionGenerator(object): class RBTorsionGenerator(object):
...@@ -2093,6 +2098,9 @@ class RBTorsionGenerator(object): ...@@ -2093,6 +2098,9 @@ class RBTorsionGenerator(object):
for torsion in element.findall('Improper'): for torsion in element.findall('Improper'):
types = ff._findAtomTypes(torsion.attrib, 4) types = ff._findAtomTypes(torsion.attrib, 4)
if None not in types: if None not in types:
if 'ordering' in element.attrib:
generator.improper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)], element.attrib['ordering']))
else:
generator.improper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)])) generator.improper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
...@@ -2141,6 +2149,7 @@ class RBTorsionGenerator(object): ...@@ -2141,6 +2149,7 @@ class RBTorsionGenerator(object):
if type1 in types1: if type1 in types1:
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:
if tordef.ordering == 'default':
if hasWildcard: if hasWildcard:
# Workaround to be more consistent with AMBER. It uses wildcards to define most of its # Workaround to be more consistent with AMBER. It uses wildcards to define most of its
# impropers, which leaves the ordering ambiguous. It then follows some bizarre rules # impropers, which leaves the ordering ambiguous. It then follows some bizarre rules
...@@ -2155,8 +2164,57 @@ class RBTorsionGenerator(object): ...@@ -2155,8 +2164,57 @@ class RBTorsionGenerator(object):
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
match = (a1, a2, torsion[0], torsion[t4[1]], tordef) match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
else: else:
# There are no wildcards, so the order is unambiguous. - # There are no wildcards, so the order is unambiguous.
match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef) - match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
break
elif tordef.ordering == 'amber':
# topology atom indexes
a2 = torsion[t2[1]]
a3 = torsion[t3[1]]
a4 = torsion[t4[1]]
# residue indexes
r2 = data.atoms[a2].residue.index
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
# template atom indexes
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
# elements
e2 = data.atoms[a2].element
e3 = data.atoms[a3].element
e4 = data.atoms[a4].element
if not hasWildcard:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(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)):
(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)):
(a2, a3) = (a3, a2)
else:
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(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)):
(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):
(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
...@@ -2618,12 +2676,16 @@ parsers["CustomAngleForce"] = CustomAngleGenerator.parseElement ...@@ -2618,12 +2676,16 @@ parsers["CustomAngleForce"] = CustomAngleGenerator.parseElement
class CustomTorsion(object): class CustomTorsion(object):
"""A CustomTorsion records the information for a custom torsion definition.""" """A CustomTorsion records the information for a custom torsion definition."""
def __init__(self, types, paramValues): def __init__(self, types, paramValues, ordering='default'):
self.types1 = types[0] self.types1 = types[0]
self.types2 = types[1] self.types2 = types[1]
self.types3 = types[2] self.types3 = types[2]
self.types4 = types[3] self.types4 = types[3]
self.paramValues = paramValues self.paramValues = paramValues
if ordering == 'default' or ordering == 'amber':
self.ordering = ordering
else:
raise ValueError('Illegal ordering type for CustomTorsion (%s,%s,%s,%s)' % (types[0], types[1], types[2], types[3]))
## @private ## @private
class CustomTorsionGenerator(object): class CustomTorsionGenerator(object):
...@@ -2652,6 +2714,9 @@ class CustomTorsionGenerator(object): ...@@ -2652,6 +2714,9 @@ class CustomTorsionGenerator(object):
for torsion in element.findall('Improper'): for torsion in element.findall('Improper'):
types = ff._findAtomTypes(torsion.attrib, 4) types = ff._findAtomTypes(torsion.attrib, 4)
if None not in types: if None not in types:
if 'ordering' in element.attrib:
generator.improper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams], element.attrib['ordering']))
else:
generator.improper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams])) generator.improper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args): def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
...@@ -2699,6 +2764,7 @@ class CustomTorsionGenerator(object): ...@@ -2699,6 +2764,7 @@ class CustomTorsionGenerator(object):
if type1 in types1: if type1 in types1:
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:
if tordef.ordering == 'default':
if hasWildcard: if hasWildcard:
# Workaround to be more consistent with AMBER. It uses wildcards to define most of its # Workaround to be more consistent with AMBER. It uses wildcards to define most of its
# impropers, which leaves the ordering ambiguous. It then follows some bizarre rules # impropers, which leaves the ordering ambiguous. It then follows some bizarre rules
...@@ -2713,8 +2779,57 @@ class CustomTorsionGenerator(object): ...@@ -2713,8 +2779,57 @@ class CustomTorsionGenerator(object):
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
match = (a1, a2, torsion[0], torsion[t4[1]], tordef) match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
else: else:
# There are no wildcards, so the order is unambiguous. - # There are no wildcards, so the order is unambiguous.
match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef) - match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
break
elif tordef.ordering == 'amber':
# topology atom indexes
a2 = torsion[t2[1]]
a3 = torsion[t3[1]]
a4 = torsion[t4[1]]
# residue indexes
r2 = data.atoms[a2].residue.index
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
# template atom indexes
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
# elements
e2 = data.atoms[a2].element
e3 = data.atoms[a3].element
e4 = data.atoms[a4].element
if not hasWildcard:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(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)):
(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)):
(a2, a3) = (a3, a2)
else:
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(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)):
(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):
(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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