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Commit 572abf66 authored by peastman's avatar peastman
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Merge pull request #1368 from swails/scee 

Compare 1-4 scaling factors by looking at size of difference
parents ed2b92e2 bb92e3c0
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Showing with 6348 additions and 41 deletions
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 572abf66
......@@ -345,7 +345,7 @@ class ForceField(object):
index += 1
return torsion
class _SystemData:
class _SystemData(object):
"""Inner class used to encapsulate data about the system being created."""
def __init__(self):
self.atomType = {}
......@@ -371,7 +371,7 @@ class ForceField(object):
self.constraints[key] = distance
system.addConstraint(atom1, atom2, distance)
class _TemplateData:
class _TemplateData(object):
"""Inner class used to encapsulate data about a residue template definition."""
def __init__(self, name):
self.name = name
......@@ -413,7 +413,7 @@ class ForceField(object):
atom = self.getAtomIndexByName(atom_name)
self.addExternalBond(atom)
class _TemplateAtomData:
class _TemplateAtomData(object):
"""Inner class used to encapsulate data about an atom in a residue template definition."""
def __init__(self, name, type, element, parameters={}):
self.name = name
......@@ -423,7 +423,7 @@ class ForceField(object):
self.bondedTo = []
self.externalBonds = 0
class _BondData:
class _BondData(object):
"""Inner class used to encapsulate data about a bond."""
def __init__(self, atom1, atom2):
self.atom1 = atom1
......@@ -431,7 +431,7 @@ class ForceField(object):
self.isConstrained = False
self.length = 0.0
class _VirtualSiteData:
class _VirtualSiteData(object):
"""Inner class used to encapsulate data about a virtual site."""
def __init__(self, node, atomIndices):
attrib = node.attrib
......@@ -464,7 +464,7 @@ class ForceField(object):
else:
self.excludeWith = self.atoms[0]
class _AtomType:
class _AtomType(object):
"""Inner class used to record atom types and associated properties."""
def __init__(self, name, atomClass, mass, element):
self.name = name
......@@ -472,7 +472,7 @@ class ForceField(object):
self.mass = mass
self.element = element
class _AtomTypeParameters:
class _AtomTypeParameters(object):
"""Inner class used to record parameter values for atom types."""
def __init__(self, forcefield, forceName, atomTag, paramNames):
self.ff = forcefield
......@@ -1163,7 +1163,7 @@ def _createResidueTemplate(residue):
# to the System. The static method should be added to the parsers map.
## @private
class HarmonicBondGenerator:
class HarmonicBondGenerator(object):
"""A HarmonicBondGenerator constructs a HarmonicBondForce."""
def __init__(self, forcefield):
......@@ -1214,7 +1214,7 @@ parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement
## @private
class HarmonicAngleGenerator:
class HarmonicAngleGenerator(object):
"""A HarmonicAngleGenerator constructs a HarmonicAngleForce."""
def __init__(self, forcefield):
......@@ -1287,7 +1287,7 @@ parsers["HarmonicAngleForce"] = HarmonicAngleGenerator.parseElement
## @private
class PeriodicTorsion:
class PeriodicTorsion(object):
"""A PeriodicTorsion records the information for a periodic torsion definition."""
def __init__(self, types):
......@@ -1300,7 +1300,7 @@ class PeriodicTorsion:
self.k = []
## @private
class PeriodicTorsionGenerator:
class PeriodicTorsionGenerator(object):
"""A PeriodicTorsionGenerator constructs a PeriodicTorsionForce."""
def __init__(self, forcefield):
......@@ -1398,7 +1398,7 @@ parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement
## @private
class RBTorsion:
class RBTorsion(object):
"""An RBTorsion records the information for a Ryckaert-Bellemans torsion definition."""
def __init__(self, types, c):
......@@ -1409,7 +1409,7 @@ class RBTorsion:
self.c = c
## @private
class RBTorsionGenerator:
class RBTorsionGenerator(object):
"""An RBTorsionGenerator constructs an RBTorsionForce."""
def __init__(self, forcefield):
......@@ -1501,7 +1501,7 @@ parsers["RBTorsionForce"] = RBTorsionGenerator.parseElement
## @private
class CMAPTorsion:
class CMAPTorsion(object):
"""A CMAPTorsion records the information for a CMAP torsion definition."""
def __init__(self, types, map):
......@@ -1513,7 +1513,7 @@ class CMAPTorsion:
self.map = map
## @private
class CMAPTorsionGenerator:
class CMAPTorsionGenerator(object):
"""A CMAPTorsionGenerator constructs a CMAPTorsionForce."""
def __init__(self, forcefield):
......@@ -1593,9 +1593,11 @@ parsers["CMAPTorsionForce"] = CMAPTorsionGenerator.parseElement
## @private
class NonbondedGenerator:
class NonbondedGenerator(object):
"""A NonbondedGenerator constructs a NonbondedForce."""
SCALETOL = 1e-5
def __init__(self, forcefield, coulomb14scale, lj14scale):
self.ff = forcefield
self.coulomb14scale = coulomb14scale
......@@ -1614,7 +1616,8 @@ class NonbondedGenerator:
else:
# Multiple <NonbondedForce> tags were found, probably in different files. Simply add more types to the existing one.
generator = existing[0]
if generator.coulomb14scale != float(element.attrib['coulomb14scale']) or generator.lj14scale != float(element.attrib['lj14scale']):
if abs(generator.coulomb14scale - float(element.attrib['coulomb14scale'])) > NonbondedGenerator.SCALETOL or \
abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL:
raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales')
generator.params.parseDefinitions(element)
......@@ -1673,7 +1676,7 @@ parsers["NonbondedForce"] = NonbondedGenerator.parseElement
## @private
class GBSAOBCGenerator:
class GBSAOBCGenerator(object):
"""A GBSAOBCGenerator constructs a GBSAOBCForce."""
def __init__(self, forcefield):
......@@ -1723,7 +1726,7 @@ parsers["GBSAOBCForce"] = GBSAOBCGenerator.parseElement
## @private
class CustomBondGenerator:
class CustomBondGenerator(object):
"""A CustomBondGenerator constructs a CustomBondForce."""
def __init__(self, forcefield):
......@@ -1771,7 +1774,7 @@ parsers["CustomBondForce"] = CustomBondGenerator.parseElement
## @private
class CustomAngleGenerator:
class CustomAngleGenerator(object):
"""A CustomAngleGenerator constructs a CustomAngleForce."""
def __init__(self, forcefield):
......@@ -1823,7 +1826,7 @@ parsers["CustomAngleForce"] = CustomAngleGenerator.parseElement
## @private
class CustomTorsion:
class CustomTorsion(object):
"""A CustomTorsion records the information for a custom torsion definition."""
def __init__(self, types, paramValues):
......@@ -1834,7 +1837,7 @@ class CustomTorsion:
self.paramValues = paramValues
## @private
class CustomTorsionGenerator:
class CustomTorsionGenerator(object):
"""A CustomTorsionGenerator constructs a CustomTorsionForce."""
def __init__(self, forcefield):
......@@ -1932,7 +1935,7 @@ parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement
## @private
class CustomNonbondedGenerator:
class CustomNonbondedGenerator(object):
"""A CustomNonbondedGenerator constructs a CustomNonbondedForce."""
def __init__(self, forcefield, energy, bondCutoff):
......@@ -2020,7 +2023,7 @@ parsers["CustomNonbondedForce"] = CustomNonbondedGenerator.parseElement
## @private
class CustomGBGenerator:
class CustomGBGenerator(object):
"""A CustomGBGenerator constructs a CustomGBForce."""
def __init__(self, forcefield):
......@@ -2101,7 +2104,7 @@ parsers["CustomGBForce"] = CustomGBGenerator.parseElement
## @private
class CustomManyParticleGenerator:
class CustomManyParticleGenerator(object):
"""A CustomManyParticleGenerator constructs a CustomManyParticleForce."""
def __init__(self, forcefield, particlesPerSet, energy, permutationMode, bondCutoff):
......@@ -2226,7 +2229,7 @@ def countConstraint(data):
print("Constraints bond=%d angle=%d total=%d" % (bondCount, angleCount, (bondCount+angleCount)))
## @private
class AmoebaBondGenerator:
class AmoebaBondGenerator(object):
#=============================================================================================
......@@ -2329,7 +2332,7 @@ def addAngleConstraint(angle, idealAngle, data, sys):
#=============================================================================================
## @private
class AmoebaAngleGenerator:
class AmoebaAngleGenerator(object):
#=============================================================================================
"""An AmoebaAngleGenerator constructs a AmoebaAngleForce."""
......@@ -2518,7 +2521,7 @@ parsers["AmoebaAngleForce"] = AmoebaAngleGenerator.parseElement
#=============================================================================================
## @private
class AmoebaOutOfPlaneBendGenerator:
class AmoebaOutOfPlaneBendGenerator(object):
#=============================================================================================
......@@ -2792,7 +2795,7 @@ parsers["AmoebaOutOfPlaneBendForce"] = AmoebaOutOfPlaneBendGenerator.parseElemen
#=============================================================================================
## @private
class AmoebaTorsionGenerator:
class AmoebaTorsionGenerator(object):
#=============================================================================================
"""An AmoebaTorsionGenerator constructs a AmoebaTorsionForce."""
......@@ -2901,7 +2904,7 @@ parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement
#=============================================================================================
## @private
class AmoebaPiTorsionGenerator:
class AmoebaPiTorsionGenerator(object):
#=============================================================================================
......@@ -3015,7 +3018,7 @@ parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement
#=============================================================================================
## @private
class AmoebaTorsionTorsionGenerator:
class AmoebaTorsionTorsionGenerator(object):
#=============================================================================================
"""An AmoebaTorsionTorsionGenerator constructs a AmoebaTorsionTorsionForce."""
......@@ -3257,7 +3260,7 @@ parsers["AmoebaTorsionTorsionForce"] = AmoebaTorsionTorsionGenerator.parseElemen
#=============================================================================================
## @private
class AmoebaStretchBendGenerator:
class AmoebaStretchBendGenerator(object):
#=============================================================================================
"""An AmoebaStretchBendGenerator constructs a AmoebaStretchBendForce."""
......@@ -3401,7 +3404,7 @@ parsers["AmoebaStretchBendForce"] = AmoebaStretchBendGenerator.parseElement
#=============================================================================================
## @private
class AmoebaVdwGenerator:
class AmoebaVdwGenerator(object):
"""A AmoebaVdwGenerator constructs a AmoebaVdwForce."""
......@@ -3567,7 +3570,7 @@ parsers["AmoebaVdwForce"] = AmoebaVdwGenerator.parseElement
#=============================================================================================
## @private
class AmoebaMultipoleGenerator:
class AmoebaMultipoleGenerator(object):
#=============================================================================================
......@@ -4234,7 +4237,7 @@ parsers["AmoebaMultipoleForce"] = AmoebaMultipoleGenerator.parseElement
#=============================================================================================
## @private
class AmoebaWcaDispersionGenerator:
class AmoebaWcaDispersionGenerator(object):
"""A AmoebaWcaDispersionGenerator constructs a AmoebaWcaDispersionForce."""
......@@ -4307,7 +4310,7 @@ parsers["AmoebaWcaDispersionForce"] = AmoebaWcaDispersionGenerator.parseElement
#=============================================================================================
## @private
class AmoebaGeneralizedKirkwoodGenerator:
class AmoebaGeneralizedKirkwoodGenerator(object):
"""A AmoebaGeneralizedKirkwoodGenerator constructs a AmoebaGeneralizedKirkwoodForce."""
......@@ -4575,7 +4578,7 @@ parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.p
#=============================================================================================
## @private
class AmoebaUreyBradleyGenerator:
class AmoebaUreyBradleyGenerator(object):
#=============================================================================================
"""An AmoebaUreyBradleyGenerator constructs a AmoebaUreyBradleyForce."""
......@@ -4649,7 +4652,7 @@ parsers["AmoebaUreyBradleyForce"] = AmoebaUreyBradleyGenerator.parseElement
## @private
class DrudeGenerator:
class DrudeGenerator(object):
"""A DrudeGenerator constructs a DrudeForce."""
def __init__(self, forcefield):
......
wrappers/python/tests/TestForceField.py
View file @ 572abf66
......@@ -6,10 +6,11 @@ from simtk.unit import *
import simtk.openmm.app.element as elem
import simtk.openmm.app.forcefield as forcefield
import math
if sys.version_info >= (3, 0):
from io import StringIO
else:
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
import os
class TestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method."""
......@@ -573,5 +574,10 @@ class AmoebaTestForceField(unittest.TestCase):
self.assertEqual(len(ff._forces[0].proper), 1)
self.assertEqual(len(ff._forces[0].improper), 1)
def test_ScalingFactorCombining(self):
""" Tests that FFs can be combined if their scaling factors are very close """
forcefield = ForceField('amber99sb.xml', os.path.join('systems', 'test_amber_ff.xml'))
# This would raise an exception if it didn't work
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/systems/test_amber_ff.xml 0 → 100644
View file @ 572abf66
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