Merge pull request #1182 from peastman/residueparams

[WIP] Per-atom parameters can be taken from residue templates

docs-source/usersguide/application.rst

@@ -1843,7 +1843,7 @@ The :code:`<ForceField>` tag contains the following children:
 * Zero or more tags defining specific forces
 
 
-The order of these tags does not matter.  They are described in details below.
+The order of these tags does not matter.  They are described in detail below.
 
 <AtomTypes>
 ===========
@@ -1927,9 +1927,9 @@ as in the following example:
 
 Each :code:`<VirtualSite>` tag indicates an atom in the residue that should
 be represented with a virtual site.  The :code:`type` attribute may equal
-:code:`"average2"`\ , :code:`"average3"`\ , or :code:`"outOfPlane"`\ , which
-correspond to the TwoParticleAverageSite, ThreeParticleAverageSite, and
-OutOfPlaneSite classes respectively.  The :code:`index` attribute gives the
+:code:`"average2"`\ , :code:`"average3"`\ , :code:`"outOfPlane"`\ , or
+:code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite,
+OutOfPlaneSite, and LocalCoordinatesSite classes respectively.  The :code:`index` attribute gives the
 index (starting from 0) of the atom to represent with a virtual site.  The atoms
 it is calculated based on are specified by :code:`atom1`\ , :code:`atom2`\ ,
 and (for virtual site classes that involve three atoms) :code:`atom3`\ .  The
@@ -1938,7 +1938,10 @@ parameters for calculating the site position.  For a TwoParticleAverageSite,
 they are :code:`weight1` and :code:`weight2`\ .  For a
 ThreeParticleAverageSite, they are :code:`weight1`\ , :code:`weight2`\ , and
 \ :code:`weight3`\ . For an OutOfPlaneSite, they are :code:`weight12`\ ,
-:code:`weight13`\ , and :code:`weightCross`\ .
+:code:`weight13`\ , and :code:`weightCross`\ . For a LocalCoordinatesSite, they
+are :code:`wo1`\ , :code:`wo2`\ , :code:`wo3`\ , :code:`wx1`\ , :code:`wx2`\ ,
+:code:`wx3`\ , :code:`wy1`\ , :code:`wy2`\ , :code:`wy3`\ , :code:`p1`\ ,
+:code:`p2`\ , and :code:`p3`\ .
 
 
 <HarmonicBondForce>
@@ -2496,8 +2499,9 @@ The following operators are supported: + (add), - (subtract), * (multiply), /
 
 The following standard functions are supported: sqrt, exp, log, sin, cos, sec,
 csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs,
-step. step(x) = 0 if x < 0, 1 otherwise.  Some custom forces allow additional
-functions to be defined from tabulated values.
+floor, ceil, step, delta, select. step(x) = 0 if x < 0, 1 otherwise.
+delta(x) = 1 if x is 0, 0 otherwise.  select(x,y,z) = z if x = 0, y otherwise.
+Some custom forces allow additional functions to be defined from tabulated values.
 
 Numbers may be given in either decimal or exponential form.  All of the
 following are valid numbers: 5, -3.1, 1e6, and 3.12e-2.
@@ -2521,8 +2525,8 @@ values.  All uses of a value must appear *before* that value’s definition.
 
 .. _tabulated-functions:
 
-TabulatedFunctions
-==================
+Tabulated Functions
+===================
 
 Some forces, such as CustomNonbondedForce and CustomGBForce, allow you to define
 tabulated functions.  To define a function, include a :code:`<Function>` tag inside the
@@ -2569,6 +2573,47 @@ successive values separated by white space.  See the API documentation for more
 details.
 
 
+Residue Template Parameters
+===========================
+
+In forces that use an :code:`<Atom>` tag to define parameters for atom types or
+classes, there is an alternate mechanism you can also use: defining those
+parameter values in the residue template.  This is useful for situations that
+come up in certain force fields.  For example, :code:`NonbondedForce` and
+:code:`GBSAOBCForce` each have a :code:`charge` attribute.  If you only have to
+define the charge of each atom type once, that is more convenient and avoids
+potential bugs.  Also, many force fields have a different charge for each atom
+type, but Lennard-Jones parameters that are the same for all types in a class.
+It would be preferable not to have to repeat those parameter values many times
+over.
+
+When writing a residue template, you can add arbitrary additional attributes
+to each :code:`<Atom>` tag.  For example, you might include a :code:`charge`
+attribute as follows:
+
+.. code-block:: xml
+
+   <Atom name="CA" type="53" charge="0.0381"/>
+
+When writing the tag for a force, you can then include a
+:code:`<UseAttributeFromResidue>` tag inside it.  This indicates that a
+specified attribute should be taken from the residue template.  Finally, you
+simply omit that attribute in the force's own :code:`<Atom>` tags.  For example:
+
+.. code-block:: xml
+
+    <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+     <UseAttributeFromResidue name="charge"/>
+     <Atom class="CX" sigma="0.339966950842" epsilon="0.4577296"/>
+     ...
+    </NonbondedForce>
+
+Notice that the :code:`charge` attribute is missing, and that the parameters
+are specified by class, not by type.  This means that sigma and epsilon only
+need to be specified once for each class.  The atom charges, which are different
+for each type, are taken from the residue template instead.
+
+
 Using Multiple Files
 ********************
 

wrappers/python/simtk/openmm/app/forcefield.py

@@ -150,7 +150,11 @@ class ForceField(object):
                 resName = residue.attrib['name']
                 template = ForceField._TemplateData(resName)
                 for atom in residue.findall('Atom'):
-                    template.atoms.append(ForceField._TemplateAtomData(atom.attrib['name'], atom.attrib['type'], self._atomTypes[atom.attrib['type']][2]))
+                    params = {}
+                    for key in atom.attrib:
+                        if key not in ('name', 'type'):
+                            params[key] = _convertParameterToNumber(atom.attrib[key])
+                    template.atoms.append(ForceField._TemplateAtomData(atom.attrib['name'], atom.attrib['type'], self._atomTypes[atom.attrib['type']][2], params))
                 for site in residue.findall('VirtualSite'):
                     template.virtualSites.append(ForceField._VirtualSiteData(site))
                 for bond in residue.findall('Bond'):
@@ -256,6 +260,7 @@ class ForceField(object):
         """Inner class used to encapsulate data about the system being created."""
         def __init__(self):
             self.atomType = {}
+            self.atomParameters = {}
             self.atoms = []
             self.excludeAtomWith = []
             self.virtualSites = {}
@@ -282,10 +287,11 @@ class ForceField(object):
 
     class _TemplateAtomData:
         """Inner class used to encapsulate data about an atom in a residue template definition."""
-        def __init__(self, name, type, element):
+        def __init__(self, name, type, element, parameters={}):
             self.name = name
             self.type = type
             self.element = element
+            self.parameters = parameters
             self.bondedTo = []
             self.externalBonds = 0
 
@@ -325,6 +331,77 @@ class ForceField(object):
             else:
                 self.excludeWith = self.atoms[0]
 
+    class _AtomTypeParameters:
+        """Inner class used to record parameter values for atom types."""
+        def __init__(self, forcefield, forceName, atomTag, paramNames):
+            self.ff = forcefield
+            self.forceName = forceName
+            self.atomTag = atomTag
+            self.paramNames = paramNames
+            self.paramsForType = {}
+            self.extraParamsForType = {}
+
+        def registerAtom(self, parameters, expectedParams=None):
+            if expectedParams is None:
+                expectedParams = self.paramNames
+            types = self.ff._findAtomTypes(parameters, 1)
+            if None not in types:
+                values = {}
+                extraValues = {}
+                for key in parameters:
+                    if key in expectedParams:
+                        values[key] = _convertParameterToNumber(parameters[key])
+                    else:
+                        extraValues[key] = parameters[key]
+                if len(values) < len(expectedParams):
+                    for key in expectedParams:
+                        if key not in values:
+                            raise ValueError('%s: No value specified for "%s"' % (self.forceName, key))
+                for t in types[0]:
+                    self.paramsForType[t] = values
+                    self.extraParamsForType[t] = extraValues
+
+        def parseDefinitions(self, element):
+            """"Load the definitions from an XML element."""
+            expectedParams = list(self.paramNames)
+            excludedParams = [node.attrib['name'] for node in element.findall('UseAttributeFromResidue')]
+            for param in excludedParams:
+                if param not in expectedParams:
+                    raise ValueError('%s: <UseAttributeFromResidue> specified an invalid attribute: %s' % (self.forceName, param))
+                expectedParams.remove(param)
+            for atom in element.findall(self.atomTag):
+                for param in excludedParams:
+                    if param in atom.attrib:
+                        raise ValueError('%s: The attribute "%s" appeared in both <%s> and <UseAttributeFromResidue> tags' % (self.forceName, param, self.atomTag))
+                self.registerAtom(atom.attrib, expectedParams)
+
+        def getAtomParameters(self, atom, data):
+            """Get the parameter values for a particular atom."""
+            t = data.atomType[atom]
+            p = data.atomParameters[atom]
+            if t in self.paramsForType:
+                values = self.paramsForType[t]
+                result = [None]*len(self.paramNames)
+                for i, name in enumerate(self.paramNames):
+                    if name in values:
+                        result[i] = values[name]
+                    elif name in p:
+                        result[i] = p[name]
+                    else:
+                        raise ValueError('%s: No value specified for "%s"' % (self.forceName, name))
+                return result
+            else:
+                raise ValueError('%s: No parameters defined for atom type %s' % (self.forceName, t))
+
+        def getExtraParameters(self, atom, data):
+            """Get extra parameter values for an atom that appeared in the <Atom> tag but were not included in paramNames."""
+            t = data.atomType[atom]
+            if t in self.paramsForType:
+                return self.extraParamsForType[t]
+            else:
+                raise ValueError('%s: No parameters defined for atom type %s' % (self.forceName, t))
+
+
     def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
                      constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, **args):
         """Construct an OpenMM System representing a Topology with this force field.
@@ -385,6 +462,7 @@ class ForceField(object):
                 matchAtoms = dict(zip(matches, res.atoms()))
                 for atom, match in zip(res.atoms(), matches):
                     data.atomType[atom] = template.atoms[match].type
+                    data.atomParameters[atom] = template.atoms[match].parameters
                     for site in template.virtualSites:
                         if match == site.index:
                             data.virtualSites[atom] = (site, [matchAtoms[i].index for i in site.atoms], matchAtoms[site.excludeWith].index)
@@ -1138,14 +1216,10 @@ class NonbondedGenerator:
         self.ff = forcefield
         self.coulomb14scale = coulomb14scale
         self.lj14scale = lj14scale
-        self.typeMap = {}
+        self.params = ForceField._AtomTypeParameters(forcefield, 'NonbondedForce', 'Atom', ('charge', 'sigma', 'epsilon'))
 
     def registerAtom(self, parameters):
-        types = self.ff._findAtomTypes(parameters, 1)
-        if None not in types:
-            values = (_convertParameterToNumber(parameters['charge']), _convertParameterToNumber(parameters['sigma']), _convertParameterToNumber(parameters['epsilon']))
-            for t in types[0]:
-                self.typeMap[t] = values
+        self.params.registerAtom(parameters)
 
     @staticmethod
     def parseElement(element, ff):
@@ -1158,8 +1232,7 @@ class NonbondedGenerator:
             generator = existing[0]
             if generator.coulomb14scale != float(element.attrib['coulomb14scale']) or generator.lj14scale != float(element.attrib['lj14scale']):
                 raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales')
-        for atom in element.findall('Atom'):
-            generator.registerAtom(atom.attrib)
+        generator.params.parseDefinitions(element)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
@@ -1171,12 +1244,8 @@ class NonbondedGenerator:
             raise ValueError('Illegal nonbonded method for NonbondedForce')
         force = mm.NonbondedForce()
         for atom in data.atoms:
-            t = data.atomType[atom]
-            if t in self.typeMap:
-                values = self.typeMap[t]
-                force.addParticle(values[0], values[1], values[2])
-            else:
-                raise ValueError('No nonbonded parameters defined for atom type '+t)
+            values = self.params.getAtomParameters(atom, data)
+            force.addParticle(values[0], values[1], values[2])
         force.setNonbondedMethod(methodMap[nonbondedMethod])
         force.setCutoffDistance(nonbondedCutoff)
         if 'ewaldErrorTolerance' in args:
@@ -1225,14 +1294,10 @@ class GBSAOBCGenerator:
 
     def __init__(self, forcefield):
         self.ff = forcefield
-        self.typeMap = {}
+        self.params = ForceField._AtomTypeParameters(forcefield, 'GBSAOBCForce', 'Atom', ('charge', 'radius', 'scale'))
 
     def registerAtom(self, parameters):
-        types = self.ff._findAtomTypes(parameters, 1)
-        if None not in types:
-            values = (_convertParameterToNumber(parameters['charge']), _convertParameterToNumber(parameters['radius']), _convertParameterToNumber(parameters['scale']))
-            for t in types[0]:
-                self.typeMap[t] = values
+        self.params.registerAtom(parameters)
 
     @staticmethod
     def parseElement(element, ff):
@@ -1243,8 +1308,7 @@ class GBSAOBCGenerator:
         else:
             # Multiple <GBSAOBCForce> tags were found, probably in different files.  Simply add more types to the existing one.
             generator = existing[0]
-        for atom in element.findall('Atom'):
-            generator.registerAtom(atom.attrib)
+        generator.params.parseDefinitions(element)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
@@ -1254,12 +1318,8 @@ class GBSAOBCGenerator:
             raise ValueError('Illegal nonbonded method for GBSAOBCForce')
         force = mm.GBSAOBCForce()
         for atom in data.atoms:
-            t = data.atomType[atom]
-            if t in self.typeMap:
-                values = self.typeMap[t]
-                force.addParticle(values[0], values[1], values[2])
-            else:
-                raise ValueError('No GBSAOBC parameters defined for atom type '+t)
+            values = self.params.getAtomParameters(atom, data)
+            force.addParticle(values[0], values[1], values[2])
         force.setNonbondedMethod(methodMap[nonbondedMethod])
         force.setCutoffDistance(nonbondedCutoff)
         if 'soluteDielectric' in args:
@@ -1577,7 +1637,6 @@ class CustomNonbondedGenerator:
         self.ff = forcefield
         self.energy = energy
         self.bondCutoff = bondCutoff
-        self.typeMap = {}
         self.globalParams = {}
         self.perParticleParams = []
         self.functions = []
@@ -1590,12 +1649,8 @@ class CustomNonbondedGenerator:
             generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
         for param in element.findall('PerParticleParameter'):
             generator.perParticleParams.append(param.attrib['name'])
-        for atom in element.findall('Atom'):
-            types = ff._findAtomTypes(atom.attrib, 1)
-            if None not in types:
-                values = [float(atom.attrib[param]) for param in generator.perParticleParams]
-                for t in types[0]:
-                    generator.typeMap[t] = values
+        generator.params = ForceField._AtomTypeParameters(ff, 'CustomNonbondedForce', 'Atom', generator.perParticleParams)
+        generator.params.parseDefinitions(element)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
@@ -1622,11 +1677,8 @@ class CustomNonbondedGenerator:
             elif type == 'Discrete3D':
                 force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
         for atom in data.atoms:
-            t = data.atomType[atom]
-            if t in self.typeMap:
-                force.addParticle(self.typeMap[t])
-            else:
-                raise ValueError('No CustomNonbonded parameters defined for atom type '+t)
+            values = self.params.getAtomParameters(atom, data)
+            force.addParticle(values)
         force.setNonbondedMethod(methodMap[nonbondedMethod])
         force.setCutoffDistance(nonbondedCutoff)
         sys.addForce(force)
@@ -1671,7 +1723,6 @@ class CustomGBGenerator:
 
     def __init__(self, forcefield):
         self.ff = forcefield
-        self.typeMap = {}
         self.globalParams = {}
         self.perParticleParams = []
         self.computedValues = []
@@ -1686,12 +1737,8 @@ class CustomGBGenerator:
             generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
         for param in element.findall('PerParticleParameter'):
             generator.perParticleParams.append(param.attrib['name'])
-        for atom in element.findall('Atom'):
-            types = ff._findAtomTypes(atom.attrib, 1)
-            if None not in types:
-                values = [float(atom.attrib[param]) for param in generator.perParticleParams]
-                for t in types[0]:
-                    generator.typeMap[t] = values
+        generator.params = ForceField._AtomTypeParameters(ff, 'CustomGBForce', 'Atom', generator.perParticleParams)
+        generator.params.parseDefinitions(element)
         computationMap = {"SingleParticle" : mm.CustomGBForce.SingleParticle,
                           "ParticlePair" : mm.CustomGBForce.ParticlePair,
                           "ParticlePairNoExclusions" : mm.CustomGBForce.ParticlePairNoExclusions}
@@ -1742,11 +1789,8 @@ class CustomGBGenerator:
             elif type == 'Discrete3D':
                 force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
         for atom in data.atoms:
-            t = data.atomType[atom]
-            if t in self.typeMap:
-                force.addParticle(self.typeMap[t])
-            else:
-                raise ValueError('No CustomGB parameters defined for atom type '+t)
+            values = self.params.getAtomParameters(atom, data)
+            force.addParticle(values)
         force.setNonbondedMethod(methodMap[nonbondedMethod])
         force.setCutoffDistance(nonbondedCutoff)
         sys.addForce(force)
@@ -1764,7 +1808,6 @@ class CustomManyParticleGenerator:
         self.energy = energy
         self.permutationMode = permutationMode
         self.bondCutoff = bondCutoff
-        self.typeMap = {}
         self.globalParams = {}
         self.perParticleParams = []
         self.functions = []
@@ -1782,12 +1825,8 @@ class CustomManyParticleGenerator:
             generator.perParticleParams.append(param.attrib['name'])
         for param in element.findall('TypeFilter'):
             generator.typeFilters.append((int(param.attrib['index']), [int(x) for x in param.attrib['types'].split(',')]))
-        for atom in element.findall('Atom'):
-            types = ff._findAtomTypes(atom.attrib, 1)
-            if None not in types:
-                values = [float(atom.attrib[param]) for param in generator.perParticleParams]
-                for t in types[0]:
-                    generator.typeMap[t] = (values, int(atom.attrib['filterType']))
+        generator.params = ForceField._AtomTypeParameters(ff, 'CustomManyParticleForce', 'Atom', generator.perParticleParams)
+        generator.params.parseDefinitions(element)
 
     def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
         methodMap = {NoCutoff:mm.CustomManyParticleForce.NoCutoff,
@@ -1817,12 +1856,9 @@ class CustomManyParticleGenerator:
             elif type == 'Discrete3D':
                 force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
         for atom in data.atoms:
-            t = data.atomType[atom]
-            if t in self.typeMap:
-                values = self.typeMap[t]
-                force.addParticle(values[0], values[1])
-            else:
-                raise ValueError('No CustomManyParticle parameters defined for atom type '+t)
+            values = self.params.getAtomParameters(atom, data)
+            type = int(self.params.getExtraParameters(atom, data)['filterType'])
+            force.addParticle(values, type)
         force.setNonbondedMethod(methodMap[nonbondedMethod])
         force.setCutoffDistance(nonbondedCutoff)
         sys.addForce(force)
@@ -3083,8 +3119,6 @@ class AmoebaVdwGenerator:
         self.vdw14Scale = vdw14Scale
         self.vdw15Scale = vdw15Scale
 
-        self.typeMap = {}
-
     #=============================================================================================
 
     @staticmethod
@@ -3097,31 +3131,10 @@ class AmoebaVdwGenerator:
         generator = AmoebaVdwGenerator(element.attrib['type'], element.attrib['radiusrule'], element.attrib['radiustype'], element.attrib['radiussize'], element.attrib['epsilonrule'],
                                         float(element.attrib['vdw-13-scale']), float(element.attrib['vdw-14-scale']), float(element.attrib['vdw-15-scale']))
         forceField._forces.append(generator)
+        generator.params = ForceField._AtomTypeParameters(forceField, 'AmoebaVdwForce', 'Vdw', ('sigma', 'epsilon', 'reduction'))
+        generator.params.parseDefinitions(element)
         two_six = 1.122462048309372
 
-        # types[] = [ sigma, epsilon, reductionFactor, class ]
-        # sigma is modified based on radiustype and radiussize
-
-        for atom in element.findall('Vdw'):
-            types = forceField._findAtomTypes(atom.attrib, 1)
-            if None not in types:
-
-                values = [float(atom.attrib['sigma']), float(atom.attrib['epsilon']), float(atom.attrib['reduction'])]
-
-
-                if (generator.radiustype == 'SIGMA'):
-                    values[0] *= two_six
-
-                if (generator.radiussize == 'DIAMETER'):
-                    values[0] *= 0.5
-
-                for t in types[0]:
-                    generator.typeMap[t] = values
-
-            else:
-                outputString = "AmoebaVdwGenerator: error getting type: %s" % (atom.attrib['class'])
-                raise ValueError(outputString)
-
     #=============================================================================================
 
     # Return a set containing the indices of particles bonded to particle with index=particleIndex
@@ -3199,28 +3212,25 @@ class AmoebaVdwGenerator:
             force = existing[0]
 
         # add particles to force
-        # throw error if particle type not available
 
+        sigmaScale = 1
+        if self.radiustype == 'SIGMA':
+            sigmaScale = 1.122462048309372
+        if self.radiussize == 'DIAMETER':
+            sigmaScale = 0.5
         for (i, atom) in enumerate(data.atoms):
-            t = data.atomType[atom]
-            if t in self.typeMap:
-
-                values = self.typeMap[t]
-
-                # ivIndex = index of bonded partner for hydrogens; otherwise ivIndex = particle index
-
-                ivIndex = i
-                mass = sys.getParticleMass(i)/unit.dalton
-                if (mass < 1.9 and len(data.atomBonds[i]) == 1):
-                    bondIndex = data.atomBonds[i][0]
-                    if (data.bonds[bondIndex].atom1 == i):
-                        ivIndex = data.bonds[bondIndex].atom2
-                    else:
-                        ivIndex = data.bonds[bondIndex].atom1
+            values = self.params.getAtomParameters(atom, data)
+            # ivIndex = index of bonded partner for hydrogens; otherwise ivIndex = particle index
+
+            ivIndex = i
+            if atom.element == elem.hydrogen and len(data.atomBonds[i]) == 1:
+                bondIndex = data.atomBonds[i][0]
+                if (data.bonds[bondIndex].atom1 == i):
+                    ivIndex = data.bonds[bondIndex].atom2
+                else:
+                    ivIndex = data.bonds[bondIndex].atom1
 
-                force.addParticle(ivIndex, values[0], values[1], values[2])
-            else:
-                raise ValueError('No vdw type for atom %s' % (atom.name))
+            force.addParticle(ivIndex, values[0]*sigmaScale, values[1], values[2])
 
         # set combining rules
 
@@ -3937,8 +3947,6 @@ class AmoebaWcaDispersionGenerator:
         self.dispoff = dispoff
         self.shctd = shctd
 
-        self.typeMap = {}
-
     #=========================================================================================
 
     @staticmethod
@@ -3957,19 +3965,8 @@ class AmoebaWcaDispersionGenerator:
                                                   element.attrib['dispoff'],
                                                   element.attrib['shctd'])
         forceField._forces.append(generator)
-
-        # typeMap[] = [ radius, epsilon ]
-
-        for atom in element.findall('WcaDispersion'):
-            types = forceField._findAtomTypes(atom.attrib, 1)
-            if None not in types:
-
-                values = [float(atom.attrib['radius']), float(atom.attrib['epsilon'])]
-                for t in types[0]:
-                    generator.typeMap[t] = values
-            else:
-                outputString = "AmoebaWcaDispersionGenerator: error getting type: %s" % (atom.attrib['class'])
-                raise ValueError(outputString)
+        generator.params = ForceField._AtomTypeParameters(forceField, 'AmoebaWcaDispersionForce', 'WcaDispersion', ('radius', 'epsilon'))
+        generator.params.parseDefinitions(element)
 
     #=========================================================================================
 
@@ -3997,14 +3994,9 @@ class AmoebaWcaDispersionGenerator:
         force.setAwater( float(self.awater ))
         force.setShctd(  float(self.shctd  ))
 
-        for (i, atom) in enumerate(data.atoms):
-            t = data.atomType[atom]
-            if t in self.typeMap:
-
-                values = self.typeMap[t]
-                force.addParticle(values[0], values[1])
-            else:
-                raise ValueError('No WcaDispersion type for atom %s of %s %d' % (atom.name, atom.residue.name, atom.residue.index))
+        for atom in data.atoms:
+            values = self.params.getAtomParameters(atom, data)
+            force.addParticle(values[0], values[1])
 
 parsers["AmoebaWcaDispersionForce"] = AmoebaWcaDispersionGenerator.parseElement
 

wrappers/python/tests/TestForceField.py

@@ -6,6 +6,10 @@ 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:
+    from cStringIO import StringIO
 
 class TestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method."""
@@ -144,7 +148,8 @@ class TestForceField(unittest.TestCase):
         context = Context(system, integrator)
         context.setPositions(pdb.positions)
         state1 = context.getState(getForces=True)
-        state2 = XmlSerializer.deserialize(open('systems/lysozyme-implicit-forces.xml').read())
+        with open('systems/lysozyme-implicit-forces.xml') as input:
+            state2 = XmlSerializer.deserialize(input.read())
         numDifferences = 0
         for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
             diff = norm(f1-f2)
@@ -197,7 +202,51 @@ class TestForceField(unittest.TestCase):
         for i in range(3):
             self.assertEqual(vectors[i], self.pdb1.topology.getPeriodicBoxVectors()[i])
             self.assertEqual(vectors[i], system.getDefaultPeriodicBoxVectors()[i])
-        
+
+    def test_ResidueAttributes(self):
+        """Test a ForceField that gets per-particle parameters from residue attributes."""
+
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="tip3p-O" class="OW" element="O" mass="15.99943"/>
+  <Type name="tip3p-H" class="HW" element="H" mass="1.007947"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="HOH">
+   <Atom name="O" type="tip3p-O" charge="-0.834"/>
+   <Atom name="H1" type="tip3p-H" charge="0.417"/>
+   <Atom name="H2" type="tip3p-H" charge="0.417"/>
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+  </Residue>
+ </Residues>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <UseAttributeFromResidue name="charge"/>
+  <Atom type="tip3p-O" sigma="0.315" epsilon="0.635"/>
+  <Atom type="tip3p-H" sigma="1" epsilon="0"/>
+ </NonbondedForce>
+</ForceField>"""
+        ff = ForceField(StringIO(xml))
+
+        # Build a water box.
+        modeller = Modeller(Topology(), [])
+        modeller.addSolvent(ff, boxSize=Vec3(3, 3, 3)*nanometers)
+
+        # Create a system and make sure all nonbonded parameters are correct.
+        system = ff.createSystem(modeller.topology)
+        nonbonded = [f for f in system.getForces() if isinstance(f, NonbondedForce)][0]
+        atoms = list(modeller.topology.atoms())
+        for i in range(len(atoms)):
+            params = nonbonded.getParticleParameters(i)
+            if atoms[i].element == elem.oxygen:
+                self.assertEqual(params[0], -0.834*elementary_charge)
+                self.assertEqual(params[1], 0.315*nanometers)
+                self.assertEqual(params[2], 0.635*kilojoule_per_mole)
+            else:
+                self.assertEqual(params[0], 0.417*elementary_charge)
+                self.assertEqual(params[1], 1.0*nanometers)
+                self.assertEqual(params[2], 0.0*kilojoule_per_mole)
 
 class AmoebaTestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method with the AMOEBA forcefield."""
@@ -270,6 +319,22 @@ class AmoebaTestForceField(unittest.TestCase):
         self.assertAlmostEqual(constraints[(0,2)], hoDist)
         self.assertAlmostEqual(constraints[(1,2)], hohDist)
 
+    def test_Forces(self):
+        """Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
+
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        forcefield = ForceField('amoeba2013.xml', 'amoeba2013_gk.xml')
+        system = forcefield.createSystem(pdb.topology, polarization='direct')
+        integrator = VerletIntegrator(0.001)
+        context = Context(system, integrator)
+        context.setPositions(pdb.positions)
+        state1 = context.getState(getForces=True)
+        with open('systems/alanine-dipeptide-amoeba-forces.xml') as input:
+            state2 = XmlSerializer.deserialize(input.read())
+        for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
+            diff = norm(f1-f2)
+            self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
+
 if __name__ == '__main__':
     unittest.main()
 

wrappers/python/tests/systems/alanine-dipeptide-amoeba-forces.xml

+<?xml version="1.0" ?>
+<State time="0" type="State" version="1">
+	<PeriodicBoxVectors>
+		<A x="2" y="0" z="0"/>
+		<B x="0" y="2" z="0"/>
+		<C x="0" y="0" z="2"/>
+	</PeriodicBoxVectors>
+	<Forces>
+		<Force x="-60.899006905648534" y="-704.8991281062977" z=".0364180169671772"/>
+		<Force x="1179.7263311404506" y="629.2168542831286" z="1.563821009034657"/>
+		<Force x="-484.4401097634541" y="135.94210610096957" z="558.0155391926069"/>
+		<Force x="-484.1625627429897" y="136.02915381525668" z="-557.7203977673528"/>
+		<Force x="-804.8403408476064" y="-857.579131840898" z="118.43755474210333"/>
+		<Force x="84.24441920455223" y="-421.86322192608037" z="120.734742628977"/>
+		<Force x="666.4942549112259" y="-479.03339298154526" z="19.66166555862896"/>
+		<Force x="-518.9062723002917" y="686.3850843706331" z=".7311137123231983"/>
+		<Force x="-105.62094199225953" y="710.9845370176521" z="-508.0677463920413"/>
+		<Force x="285.6690654282444" y="-111.35548608152155" z="847.8096733172159"/>
+		<Force x="-396.4822698774795" y="24.462223992557014" z="297.9581483103431"/>
+		<Force x="-168.22340166944585" y="110.99779797739818" z="-824.0916382722021"/>
+		<Force x="805.7023041833917" y="15.738288953519556" z="-340.2263402925698"/>
+		<Force x="366.3025998383222" y="-647.7535895818237" z="-273.83047817845636"/>
+		<Force x="-649.7310636705703" y="-495.52797252280067" z="317.36013856851315"/>
+		<Force x="-480.120788018345" y="172.44477988154952" z="-16.235455767965004"/>
+		<Force x="-486.20230228601736" y="982.6376366390087" z="127.20818643942287"/>
+		<Force x="820.5730252078641" y="-78.71234329038225" z="109.31395566365498"/>
+		<Force x="355.03388135028814" y="-1391.2776654673507" z=".9942543092954484"/>
+		<Force x="-511.3467906691061" y="677.7717086552518" z=".008253291392112616"/>
+		<Force x="293.66157422204157" y="452.68343054060256" z="502.83463917630775"/>
+		<Force x="293.5683952568295" y="452.70832957117113" z="-502.49604726620026"/>
+	</Forces>
+</State>