Merge branch 'master' of github.com:leeping/openmm

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -41,9 +41,9 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 import os
 import os.path
-import copy
 import re
 import math
+import warnings
 
 try:
     import numpy
@@ -52,6 +52,7 @@ except:
 
 import simtk.unit as units
 import simtk.openmm
+from simtk.openmm.app import element as elem
 import customgbforces as customgb
 
 #=============================================================================================
@@ -428,15 +429,25 @@ class PrmtopLoader(object):
         charges=self.getCharges()
         nonbondTerms = self.getNonbondTerms()
         for ii in range(0,len(dihedralPointers),5):
-             if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
-                 iAtom = int(dihedralPointers[ii])//3
-                 lAtom = int(dihedralPointers[ii+3])//3
-                 chargeProd = charges[iAtom]*charges[lAtom]
-                 (rVdwI, epsilonI) = nonbondTerms[iAtom]
-                 (rVdwL, epsilonL) = nonbondTerms[lAtom]
-                 rMin = (rVdwI+rVdwL)
-                 epsilon = math.sqrt(epsilonI*epsilonL)
-                 returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon))
+            if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
+                iAtom = int(dihedralPointers[ii])//3
+                lAtom = int(dihedralPointers[ii+3])//3
+                iidx = int(dihedralPointers[ii+4]) - 1
+                chargeProd = charges[iAtom]*charges[lAtom]
+                (rVdwI, epsilonI) = nonbondTerms[iAtom]
+                (rVdwL, epsilonL) = nonbondTerms[lAtom]
+                rMin = (rVdwI+rVdwL)
+                epsilon = math.sqrt(epsilonI*epsilonL)
+                try:
+                    iScee = float(self._raw_data["SCEE_SCALE_FACTOR"][iidx])
+                except KeyError:
+                    iScee = 1.2
+                try:
+                    iScnb = float(self._raw_data["SCNB_SCALE_FACTOR"][iidx])
+                except KeyError:
+                    iScnb = 2.0
+
+                returnList.append((iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb))
         return returnList
 
     def getExcludedAtoms(self):
@@ -462,34 +473,74 @@ class PrmtopLoader(object):
             self._excludedAtoms.append(atomList)
         return self._excludedAtoms
 
-    def getGBParms(self, symbls=None):
+    def getGBParms(self, gbmodel, elements):
         """Return list giving GB params, Radius and screening factor"""
-        try:
-            return self._gb_List
-        except AttributeError:
-            pass
-        self._gb_List=[]
-        radii=self._raw_data["RADII"]
-        screen=self._raw_data["SCREEN"]
+        gb_List=[]
+        radii=[float(r) for r in self._raw_data["RADII"]]
+        screen=[float(s) for s in self._raw_data["SCREEN"]]
+        if gbmodel == 'GBn2':
+            alpha = [0 for i in self._raw_data['RADII']]
+            beta = [0 for i in self._raw_data['RADII']]
+            gamma = [0 for i in self._raw_data['RADII']]
         # Update screening parameters for GBn if specified
-        if symbls:
-            for (i, symbl) in enumerate(symbls):
-                if symbl[0] == ('c' or 'C'):
+        if gbmodel == 'GBn':
+            if elements is None:
+                raise Exception('GBn model requires element information')
+            for i, element in enumerate(elements):
+                if element is elem.carbon:
                     screen[i] = 0.48435382330
-                elif symbl[0] == ('h' or 'H'):
+                elif element is elem.hydrogen:
                     screen[i] = 1.09085413633
-                elif symbl[0] == ('n' or 'N'):
+                elif element is elem.nitrogen:
                     screen[i] = 0.700147318409
-                elif symbl[0] == ('o' or 'O'):
+                elif element is elem.oxygen:
                     screen[i] = 1.06557401132
-                elif symbl[0] == ('s' or 'S'):
+                elif element is elem.sulfur:
                     screen[i] = 0.602256336067
                 else:
                     screen[i] = 0.5
+        if gbmodel == 'GBn2':
+            if elements is None:
+                raise Exception('GBn2 model requires element information')
+            for i, element in enumerate(elements):
+                if element is elem.carbon:
+                    screen[i] = 1.058554
+                    alpha[i] = 0.733756
+                    beta[i] = 0.506378
+                    gamma[i] = 0.205844
+                elif element is elem.hydrogen:
+                    screen[i] = 1.425952
+                    alpha[i] = 0.788440
+                    beta[i] = 0.798699
+                    gamma[i] = 0.437334
+                elif element is elem.nitrogen:
+                    screen[i] = 0.733599
+                    alpha[i] = 0.503364
+                    beta[i] = 0.316828
+                    gamma[i] = 0.192915
+                elif element is elem.oxygen:
+                    screen[i] = 1.061039
+                    alpha[i] = 0.867814
+                    beta[i] = 0.876635
+                    gamma[i] = 0.387882
+                elif element is elem.sulfur:
+                    screen[i] = -0.703469
+                    alpha[i] = 0.867814
+                    beta[i] = 0.876635
+                    gamma[i] = 0.387882
+                else: # not optimized
+                    screen[i] = 0.5
+                    alpha[i] = 1.0
+                    beta[i] = 0.8
+                    gamma[i] = 4.85
         lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
-        for iAtom in range(len(radii)):
-            self._gb_List.append((float(radii[iAtom])*lengthConversionFactor, float(screen[iAtom])))
-        return self._gb_List
+        if gbmodel == 'GBn2':
+            for rad, scr, alp, bet, gam in zip(radii, screen, alpha, beta, gamma):
+                gb_List.append((rad*lengthConversionFactor, scr, alp, bet, gam))
+        else:
+            for rad, scr in zip(radii, screen):
+                gb_List.append((rad*lengthConversionFactor, scr))
+        return gb_List
 
     def getBoxBetaAndDimensions(self):
         """Return periodic boundary box beta angle and dimensions"""
@@ -502,11 +553,21 @@ class PrmtopLoader(object):
                 units.Quantity(y, units.angstrom),
                 units.Quantity(z, units.angstrom))
 
+    @property
+    def has_scee_scnb(self):
+        return ("SCEE_SCALE_FACTOR" in self._raw_data and "SCNB_SCALE_FACTOR" in self._raw_data)
+
+    @property
+    def has_atomic_number(self):
+        return 'ATOMIC_NUMBER' in self._raw_data
+
 #=============================================================================================
 # AMBER System builder (based on, but not identical to, systemManager from 'zander')
 #=============================================================================================
 
-def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5, nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=1.2, scnb=2.0, mm=None, verbose=False, EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True):
+def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None, soluteDielectric=1.0, solventDielectric=78.5,
+                    nonbondedCutoff=None, nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False,
+                    EwaldErrorTolerance=None, flexibleConstraints=True, rigidWater=True, elements=None):
     """
     Create an OpenMM System from an Amber prmtop file.
 
@@ -520,8 +581,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
       soluteDielectric (float) - The solute dielectric constant to use in the implicit solvent model (default: 1.0)
       solventDielectric (float) - The solvent dielectric constant to use in the implicit solvent model (default: 78.5)
       nonbondedCutoff (float) - if specified, will set nonbondedCutoff (default: None)
-      scnb (float) - 1-4 Lennard-Jones scaling factor (default: 1.2)
-      scee (float) - 1-4 electrostatics scaling factor (default: 2.0)
+      scnb (float) - 1-4 Lennard-Jones scaling factor (default: taken from prmtop or 1.2 if not present there)
+      scee (float) - 1-4 electrostatics scaling factor (default: taken from prmtop or 2.0 if not present there)
       mm - if specified, this module will be used in place of pyopenmm (default: None)
       verbose (boolean) - if True, print out information on progress (default: False)
       flexibleConstraints (boolean) - if True, flexible bonds will be added in addition ot constrained bonds
@@ -571,6 +632,10 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     if prmtop.getIfBox()>1:
         raise Exception("only standard periodic boxes are currently supported")
 
+    if prmtop.has_scee_scnb and (scee is not None or scnb is not None):
+        warnings.warn("1-4 scaling parameters in topology file are being ignored. "
+            "This is not recommended unless you know what you are doing.")
+
     # Use pyopenmm implementation of OpenMM by default.
     if mm is None:
         mm = simtk.openmm
@@ -615,7 +680,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     if shake == 'h-angles':
         numConstrainedBonds = system.getNumConstraints()
         atomConstraints = [[]]*system.getNumParticles()
-        for i in range(system.getNumConstraints()):
+        for i in range(numConstrainedBonds):
             c = system.getConstraintParameters(i)
             distance = c[2].value_in_unit(units.nanometer)
             atomConstraints[c[0]].append((c[1], distance))
@@ -712,9 +777,12 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     # Add 1-4 Interactions
     excludedAtomPairs = set()
     sigmaScale = 2**(-1./6.)
-    for (iAtom, lAtom, chargeProd, rMin, epsilon) in prmtop.get14Interactions():
-        chargeProd /= scee
-        epsilon /= scnb
+    _scee, _scnb = scee, scnb
+    for (iAtom, lAtom, chargeProd, rMin, epsilon, iScee, iScnb) in prmtop.get14Interactions():
+        if scee is None: _scee = iScee
+        if scnb is None: _scnb = iScnb
+        chargeProd /= _scee
+        epsilon /= _scnb
         sigma = rMin * sigmaScale
         force.addException(iAtom, lAtom, chargeProd, sigma, epsilon)
         excludedAtomPairs.add(min((iAtom, lAtom), (lAtom, iAtom)))
@@ -792,25 +860,32 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     if gbmodel is not None:
         if verbose: print "Adding GB parameters..."
         charges = prmtop.getCharges()
-        symbls = None
-        if gbmodel == 'GBn':
-            symbls = prmtop.getAtomTypes()
-        gb_parms = prmtop.getGBParms(symbls)
+        cutoff = None
+        if nonbondedMethod != 'NoCutoff':
+            cutoff = nonbondedCutoff
+            if units.is_quantity(cutoff):
+                cutoff = cutoff.value_in_unit(units.nanometers)
+        gb_parms = prmtop.getGBParms(gbmodel, elements)
         if gbmodel == 'HCT':
-            gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE')
+            gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
         elif gbmodel == 'OBC1':
-            gb = customgb.GBSAOBC1Force(solventDielectric, soluteDielectric, 'ACE')
+            gb = customgb.GBSAOBC1Force(solventDielectric, soluteDielectric, 'ACE', cutoff)
         elif gbmodel == 'OBC2':
             gb = mm.GBSAOBCForce()
             gb.setSoluteDielectric(soluteDielectric)
             gb.setSolventDielectric(solventDielectric)
         elif gbmodel == 'GBn':
-            gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE')
+            gb = customgb.GBSAGBnForce(solventDielectric, soluteDielectric, 'ACE', cutoff)
+        elif gbmodel == 'GBn2':
+            gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff)
         else:
             raise Exception("Illegal value specified for implicit solvent model")
         for iAtom in range(prmtop.getNumAtoms()):
             if gbmodel == 'OBC2':
                 gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
+            elif gbmodel == 'GBn2':
+                gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],
+                                gb_parms[iAtom][2], gb_parms[iAtom][3], gb_parms[iAtom][4]])
             else:
                 gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
         system.addForce(gb)
@@ -824,6 +899,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             gb.setCutoffDistance(nonbondedCutoff)
         else:
             raise Exception("Illegal nonbonded method for use with GBSA")
+        # This applies the reaction field dielectric to the NonbondedForce
+        # created above. Do not bind force to another name before this!
         force.setReactionFieldDielectric(1.0)
 
     # TODO: Add GBVI terms?

wrappers/python/simtk/openmm/app/internal/customgbforces.py

@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org.
 
 Portions copyright (c) 2012 University of Virginia and the Authors.
 Authors: Christoph Klein, Michael R. Shirts
-Contributors:
+Contributors: Jason M. Swails
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -29,8 +29,9 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 
+from __future__ import division
+
 from simtk.openmm import CustomGBForce
-import sys, pdb, pickle
 
 d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
     2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
@@ -188,20 +189,35 @@ for i in range (len(d0)):
     m0[i]=m0[i]*10
 
 
+def _createEnergyTerms(force, SA, cutoff):
+    # Add the energy terms to the CustomGBForce.  These are identical for all the GB models.
+    
+    force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
+    if SA=='ACE':
+        force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
+    elif SA is not None:
+        raise ValueError('Unknown surface area method: '+SA)
+    if cutoff is None:
+        force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
+                            "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
+    else:
+        force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
+                            "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
+
 """
 Amber Equivalent: igb = 1
 """
 
 
-def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
+def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
 
     custom = CustomGBForce()
 
-    custom.addPerParticleParameter("q");
-    custom.addPerParticleParameter("radius");
-    custom.addPerParticleParameter("scale");
-    custom.addGlobalParameter("solventDielectric", solventDielectric);
-    custom.addGlobalParameter("soluteDielectric", soluteDielectric);
+    custom.addPerParticleParameter("q")
+    custom.addPerParticleParameter("radius")
+    custom.addPerParticleParameter("scale")
+    custom.addGlobalParameter("solventDielectric", solventDielectric)
+    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
     custom.addGlobalParameter("offset", 0.009)
     custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                   "U=r+sr2;"
@@ -212,30 +228,21 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
 
     custom.addComputedValue("B", "1/(1/or-I);"
                                   "or=radius-offset", CustomGBForce.SingleParticle)
-
-
-    custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
-    if SA=='ACE':
-        custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
-    elif SA is not None:
-        raise ValueError('Unknown surface area method: '+SA)
-    custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
-                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
-
+    _createEnergyTerms(custom, SA, cutoff)
     return custom
 
 """
 Amber Equivalents: igb = 2
 """
-def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
+def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
 
     custom = CustomGBForce()
 
-    custom.addPerParticleParameter("q");
-    custom.addPerParticleParameter("radius");
-    custom.addPerParticleParameter("scale");
-    custom.addGlobalParameter("solventDielectric", solventDielectric);
-    custom.addGlobalParameter("soluteDielectric", soluteDielectric);
+    custom.addPerParticleParameter("q")
+    custom.addPerParticleParameter("radius")
+    custom.addPerParticleParameter("scale")
+    custom.addGlobalParameter("solventDielectric", solventDielectric)
+    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
     custom.addGlobalParameter("offset", 0.009)
     custom.addComputedValue("I",  "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                   "U=r+sr2;"
@@ -246,29 +253,21 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
 
     custom.addComputedValue("B", "1/(1/or-tanh(0.8*psi+2.909125*psi^3)/radius);"
                                   "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
-
-    custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
-    if SA=='ACE':
-        custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
-    elif SA is not None:
-        raise ValueError('Unknown surface area method: '+SA)
-    custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
-                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
-
+    _createEnergyTerms(custom, SA, cutoff)
     return custom
 
 """
 Amber Equivalents: igb = 5
 """
-def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
+def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
 
     custom = CustomGBForce()
 
-    custom.addPerParticleParameter("q");
-    custom.addPerParticleParameter("radius");
-    custom.addPerParticleParameter("scale");
-    custom.addGlobalParameter("solventDielectric", solventDielectric);
-    custom.addGlobalParameter("soluteDielectric", soluteDielectric);
+    custom.addPerParticleParameter("q")
+    custom.addPerParticleParameter("radius")
+    custom.addPerParticleParameter("scale")
+    custom.addGlobalParameter("solventDielectric", solventDielectric)
+    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
     custom.addGlobalParameter("offset", 0.009)
     custom.addComputedValue("I",  "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
                                   "U=r+sr2;"
@@ -279,21 +278,13 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None):
 
     custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
                                   "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
-
-    custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
-    if SA=='ACE':
-        custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
-    elif SA is not None:
-        raise ValueError('Unknown surface area method: '+SA)
-    custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
-                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
-
+    _createEnergyTerms(custom, SA, cutoff)
     return custom
 
 """
 Amber Equivalents: igb = 7
 """
-def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
+def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
 
 
     """
@@ -306,12 +297,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
 
     custom = CustomGBForce()
 
-    custom.addPerParticleParameter("q");
-    custom.addPerParticleParameter("radius");
-    custom.addPerParticleParameter("scale");
+    custom.addPerParticleParameter("q")
+    custom.addPerParticleParameter("radius")
+    custom.addPerParticleParameter("scale")
 
-    custom.addGlobalParameter("solventDielectric", solventDielectric);
-    custom.addGlobalParameter("soluteDielectric", soluteDielectric);
+    custom.addGlobalParameter("solventDielectric", solventDielectric)
+    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
     custom.addGlobalParameter("offset", 0.009)
     custom.addGlobalParameter("neckScale", 0.361825)
     custom.addGlobalParameter("neckCut", 0.68)
@@ -331,13 +322,52 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None):
 
     custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
                               "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
+    _createEnergyTerms(custom, SA, cutoff)
+    return custom
 
-    custom.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce.SingleParticle)
-    if SA=='ACE':
-        custom.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
-    elif SA is not None:
-        raise ValueError('Unknown surface area method: '+SA)
-    custom.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
-                           "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
+"""
+Amber Equivalents: igb = 8
+"""
+def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
 
+
+    """
+    Indexing for tables:
+        input: radius1, radius2
+        index = (radius2*200-20)*21 + (radius1*200-20)
+        output: index of desired value in row-by-row, 1D version of Tables 3 & 4
+    """
+
+
+    custom = CustomGBForce()
+
+    custom.addPerParticleParameter("q")
+    custom.addPerParticleParameter("radius")
+    custom.addPerParticleParameter("scale")
+    custom.addPerParticleParameter("alpha")
+    custom.addPerParticleParameter("beta")
+    custom.addPerParticleParameter("gamma")
+
+    custom.addGlobalParameter("solventDielectric", solventDielectric)
+    custom.addGlobalParameter("soluteDielectric", soluteDielectric)
+    custom.addGlobalParameter("offset", 0.0195141)
+    custom.addGlobalParameter("neckScale", 0.826836)
+    custom.addGlobalParameter("neckCut", 0.68)
+
+    custom.addFunction("getd0", d0, 0, 440)
+    custom.addFunction("getm0", m0, 0, 440)
+
+    custom.addComputedValue("I",  "Ivdw+neckScale*Ineck;"
+                                  "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
+                                  "index = (radius2*200-20)*21 + (radius1*200-20);"
+                                  "Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
+                                  "U=r+sr2;"
+                                  "L=max(or1, D);"
+                                  "D=abs(r-sr2);"
+                                  "sr2 = scale2*or2;"
+                                  "or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
+
+    custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
+                              "psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
+    _createEnergyTerms(custom, SA, cutoff)
     return custom

wrappers/python/simtk/openmm/app/internal/pdbstructure.py

@@ -8,7 +8,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2012 Stanford University and the Authors.
+Portions copyright (c) 2012-2013 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
@@ -138,6 +138,8 @@ class PdbStructure(object):
         self.default_model = None
         self.models_by_number = {}
         self._unit_cell_dimensions = None
+        self.sequences = []
+        self.modified_residues = []
         # read file
         self._load(input_stream)
 
@@ -172,6 +174,13 @@ class PdbStructure(object):
                     except:
                         pass
                 self._current_model.connects.append(atoms)
+            elif (pdb_line.find("SEQRES") == 0):
+                chain_id = pdb_line[11]
+                if len(self.sequences) == 0 or chain_id != self.sequences[-1].chain_id:
+                    self.sequences.append(Sequence(chain_id))
+                self.sequences[-1].residues.extend(pdb_line[19:].split())
+            elif (pdb_line.find("MODRES") == 0):
+                self.modified_residues.append(ModifiedResidue(pdb_line[16], int(pdb_line[18:22]), pdb_line[12:15].strip(), pdb_line[24:27].strip()))
         self._finalize()
 
     def write(self, output_stream=sys.stdout):
@@ -266,6 +275,21 @@ class PdbStructure(object):
         return self._unit_cell_dimensions
 
 
+class Sequence(object):
+    """Sequence holds the sequence of a chain, as specified by SEQRES records."""
+    def __init__(self, chain_id):
+        self.chain_id = chain_id
+        self.residues = []
+
+class ModifiedResidue(object):
+    """ModifiedResidue holds information about a modified residue, as specified by a MODRES record."""
+    def __init__(self, chain_id, number, residue_name, standard_name):
+        self.chain_id = chain_id
+        self.number = number
+        self.residue_name = residue_name
+        self.standard_name = standard_name
+
+
 class Model(object):
     """Model holds one model of a PDB structure.
 
@@ -412,7 +436,7 @@ class Chain(object):
         self._finalize()
 
     def get_residue(self, residue_number, insertion_code=' '):
-        return residues_by_num_icode[str(residue_number) + insertion_code]
+        return self.residues_by_num_icode[str(residue_number) + insertion_code]
 
     def __contains__(self, residue_number):
         return self.residues_by_number.__contains__(residue_number)
@@ -892,7 +916,6 @@ if __name__=='__main__':
     import doctest, sys
     doctest.testmod(sys.modules[__name__])
 
-    import sys
     import os
     import gzip
     import re

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

@@ -37,7 +37,7 @@ from simtk.openmm.app import Topology, PDBFile, ForceField
 from simtk.openmm.app.forcefield import HAngles, _createResidueSignature, _matchResidue, DrudeGenerator
 from simtk.openmm.app.topology import Residue
 from simtk.openmm.vec3 import Vec3
-from simtk.openmm import System, Context, NonbondedForce, VerletIntegrator, LocalEnergyMinimizer
+from simtk.openmm import System, Context, NonbondedForce, CustomNonbondedForce, HarmonicBondForce, HarmonicAngleForce, VerletIntegrator, LocalEnergyMinimizer
 from simtk.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm
 import element as elem
 import os
@@ -519,7 +519,7 @@ class Modeller(object):
                     terminal = hydrogen.attrib['terminal']
                 data.hydrogens.append(Modeller._Hydrogen(hydrogen.attrib['name'], hydrogen.attrib['parent'], maxph, atomVariants, terminal))
 
-    def addHydrogens(self, forcefield, pH=7.0, variants=None, platform=None):
+    def addHydrogens(self, forcefield=None, pH=7.0, variants=None, platform=None):
         """Add missing hydrogens to the model.
 
         Some residues can exist in multiple forms depending on the pH and properties of the local environment.  These
@@ -561,7 +561,8 @@ class Modeller(object):
         additional definitions for other residue types.
 
         Parameters:
-         - forcefield (ForceField) the ForceField to use for determining the positions of hydrogens
+         - forcefield (ForceField=None) the ForceField to use for determining the positions of hydrogens.  If this is None,
+           positions will be picked which are generally reasonable but not optimized for any particular ForceField.
          - pH (float=7.0) the pH based on which to select variants
          - variants (list=None) an optional list of variants to use.  If this is specified, its length must equal the number
            of residues in the model.  variants[i] is the name of the variant to use for residue i (indexed starting at 0).
@@ -753,14 +754,45 @@ class Modeller(object):
             if bond[0] in newAtoms and bond[1] in newAtoms:
                 newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
 
-        # The hydrogens were added at random positions.  Now use the ForceField to fix them up.
-
-        system = forcefield.createSystem(newTopology, rigidWater=False)
-        atoms = list(newTopology.atoms())
-        for i in range(system.getNumParticles()):
-            if atoms[i].element != elem.hydrogen:
-                # This is a heavy atom, so make it immobile.
-                system.setParticleMass(i, 0)
+        # The hydrogens were added at random positions.  Now perform an energy minimization to fix them up.
+
+        if forcefield is not None:
+            # Use the ForceField the user specified.
+            
+            system = forcefield.createSystem(newTopology, rigidWater=False)
+            atoms = list(newTopology.atoms())
+            for i in range(system.getNumParticles()):
+                if atoms[i].element != elem.hydrogen:
+                    # This is a heavy atom, so make it immobile.
+                    system.setParticleMass(i, 0)
+        else:
+            # Create a System that restrains the distance of each hydrogen from its parent atom
+            # and causes hydrogens to spread out evenly.
+            
+            system = System()
+            nonbonded = CustomNonbondedForce('1/((r/0.1)^4+1)')
+            bonds = HarmonicBondForce()
+            angles = HarmonicAngleForce()
+            system.addForce(nonbonded)
+            system.addForce(bonds)
+            system.addForce(angles)
+            for atom in newTopology.atoms():
+                nonbonded.addParticle([])
+                if atom.element != elem.hydrogen:
+                    system.addParticle(0.0)
+                else:
+                    system.addParticle(1.0)
+            for atom1, atom2 in newTopology.bonds():
+                if atom1.element == elem.hydrogen or atom2.element == elem.hydrogen:
+                    bonds.addBond(atom1.index, atom2.index, 0.1, 100000.0)
+            for residue in newTopology.residues():
+                if residue.name == 'HOH':
+                    atoms = list(residue.atoms())
+                    oindex = [i for i in range(len(atoms)) if atoms[i].element == elem.oxygen]
+                    if len(atoms) == 3 and len(oindex) == 1:
+                        hindex = list(set([0,1,2])-set(oindex))
+                        angles.addAngle(atoms[hindex[0]].index, atoms[oindex[0]].index, atoms[hindex[1]].index, 1.824, 836.8)
+            
         if platform is None:
             context = Context(system, VerletIntegrator(0.0))
         else:

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

@@ -36,7 +36,8 @@ import sys
 import math
 import xml.etree.ElementTree as etree
 from copy import copy
-from simtk.openmm import Vec3
+from datetime import date
+from simtk.openmm import Vec3, Platform
 from simtk.openmm.app.internal.pdbstructure import PdbStructure
 from simtk.openmm.app import Topology
 from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity
@@ -70,7 +71,13 @@ class PDBFile(object):
 
         # Load the PDB file
 
-        pdb = PdbStructure(open(file), load_all_models=True)
+        if isinstance(file, PdbStructure):
+            pdb = file
+        else:
+            inputfile = file
+            if isinstance(file, str):
+                inputfile = open(file)
+            pdb = PdbStructure(inputfile, load_all_models=True)
         PDBFile._loadNameReplacementTables()
 
         # Build the topology
@@ -140,7 +147,8 @@ class PDBFile(object):
         for connect in pdb.models[0].connects:
             i = connect[0]
             for j in connect[1:]:
-                connectBonds.append((atomByNumber[i], atomByNumber[j]))
+                if i in atomByNumber and j in atomByNumber:
+                    connectBonds.append((atomByNumber[i], atomByNumber[j]))
         if len(connectBonds) > 0:
             # Only add bonds that don't already exist.
             existingBonds = set(top.bonds())
@@ -235,6 +243,7 @@ class PDBFile(object):
          - topology (Topology) The Topology defining the molecular system being written
          - file (file=stdout) A file to write the file to
         """
+        print >>file, "REMARK   1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today()))
         boxSize = topology.getUnitCellDimensions()
         if boxSize is not None:
             size = boxSize.value_in_unit(angstroms)
@@ -278,11 +287,15 @@ class PDBFile(object):
                     else:
                         atomName = atom.name
                     coords = positions[posIndex]
-                    line = "ATOM  %5d %-4s %3s %s%4d    %s%s%s  1.00  0.00" % (
+                    if atom.element is not None:
+                        symbol = atom.element.symbol
+                    else:
+                        symbol = ' '
+                    line = "ATOM  %5d %-4s %3s %s%4d    %s%s%s  1.00  0.00          %2s  " % (
                         atomIndex%100000, atomName, resName, chainName,
                         (resIndex+1)%10000, _format_83(coords[0]),
-                        _format_83(coords[1]), _format_83(coords[2]))
-                    assert len(line) == 66, 'Fixed width overflow detected'
+                        _format_83(coords[1]), _format_83(coords[2]), symbol)
+                    assert len(line) == 80, 'Fixed width overflow detected'
                     print >>file, line
                     posIndex += 1
                     atomIndex += 1
@@ -300,6 +313,56 @@ class PDBFile(object):
          - topology (Topology) The Topology defining the molecular system being written
          - file (file=stdout) A file to write the file to
         """
+        # Identify bonds that should be listed as CONECT records.
+        
+        standardResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR',
+                            'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL',
+                            'A', 'G', 'C', 'U', 'I', 'DA', 'DG', 'DC', 'DT', 'DI', 'HOH']
+        conectBonds = []
+        for atom1, atom2 in topology.bonds():
+            if atom1.residue.name not in standardResidues or atom2.residue.name not in standardResidues:
+                conectBonds.append((atom1, atom2))
+            elif atom1.name == 'SG' and atom2.name == 'SG' and atom1.residue.name == 'CYS' and atom2.residue.name == 'CYS':
+                conectBonds.append((atom1, atom2))
+        if len(conectBonds) > 0:
+            
+            # Work out the index used in the PDB file for each atom.
+            
+            atomIndex = {}
+            nextAtomIndex = 0
+            prevChain = None
+            for chain in topology.chains():
+                for atom in chain.atoms():
+                    if atom.residue.chain != prevChain:
+                        nextAtomIndex += 1
+                        prevChain = atom.residue.chain
+                    atomIndex[atom] = nextAtomIndex
+                    nextAtomIndex += 1
+            
+            # Record which other atoms each atom is bonded to.
+            
+            atomBonds = {}
+            for atom1, atom2 in conectBonds:
+                index1 = atomIndex[atom1]
+                index2 = atomIndex[atom2]
+                if index1 not in atomBonds:
+                    atomBonds[index1] = []
+                if index2 not in atomBonds:
+                    atomBonds[index2] = []
+                atomBonds[index1].append(index2)
+                atomBonds[index2].append(index1)
+            
+            # Write the CONECT records.
+            
+            for index1 in sorted(atomBonds):
+                bonded = atomBonds[index1]
+                while len(bonded) > 4:
+                    print >>file, "CONECT%5d%5d%5d%5d" % (index1, bonded[0], bonded[1], bonded[2])
+                    del bonded[:4]
+                line = "CONECT%5d" % index1
+                for index2 in bonded:
+                    line = "%s%5d" % (line, index2)
+                print >>file, line
         print >>file, "END"
 
 

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

@@ -79,5 +79,6 @@ class PDBReporter(object):
         self._nextModel += 1
 
     def __del__(self):
-        PDBFile.writeFooter(self._topology, self._out)
+        if self._topology is not None:
+            PDBFile.writeFooter(self._topology, self._out)
         self._out.close()

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

@@ -31,9 +31,10 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
+import bz2
+import gzip
 import simtk.openmm as mm
 import simtk.unit as unit
-from simtk.openmm.app import PDBFile
 import math
 
 class StateDataReporter(object):
@@ -67,7 +68,14 @@ class StateDataReporter(object):
         self._reportInterval = reportInterval
         self._openedFile = isinstance(file, str)
         if self._openedFile:
-            self._out = open(file, 'w', 0)
+            # Detect the desired compression scheme from the filename extension
+            # and open all files unbuffered
+            if file.endswith('.gz'):
+                self._out = gzip.GzipFile(fileobj=open(file, 'wb', 0))
+            elif file.endswith('.bz2'):
+                self._out = bz2.BZ2File(file, 'w', 0)
+            else:
+                self._out = open(file, 'w', 0)
         else:
             self._out = file
         self._step = step
@@ -109,7 +117,10 @@ class StateDataReporter(object):
             self._initializeConstants(simulation)
             headers = self._constructHeaders()
             print >>self._out, '#"%s"' % ('"'+self._separator+'"').join(headers)
-            self._out.flush()
+            try:
+                self._out.flush()
+            except AttributeError:
+                pass
             self._hasInitialized = True
 
         # Check for errors.
@@ -120,7 +131,10 @@ class StateDataReporter(object):
 
         # Write the values.
         print >>self._out, self._separator.join(str(v) for v in values)
-        self._out.flush()
+        try:
+            self._out.flush()
+        except AttributeError:
+            pass
 
     def _constructReportValues(self, simulation, state):
         """Query the simulation for the current state of our observables of interest.

wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in

@@ -616,6 +616,7 @@ EXCLUDE_SYMLINKS       = NO
 
 EXCLUDE_PATTERNS       = */tests/* \
                          */openmmapi/src/* \
+                         */internal/* \
                          */.svn/* \
                          *OpenMMFortranModule.f90 \
                          *OpenMMCWrapper.h

wrappers/python/src/swig_doxygen/swigInputBuilder.py

-#!/bin/env python
+#!/usr/bin/env python
 #
 #
  

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -14,20 +14,7 @@ DOC_STRINGS = {("Context", "setPositions") :
 # Do not generate wrappers for the following methods.
 # Indexed by (className, [methodName [, numParams]])
 SKIP_METHODS = [('State',),
-                ('Stream',),
                 ('Vec3',),
-                ('AmoebaGeneralizedKirkwoodForceImpl',),
-                ('AmoebaAngleForceImpl',),
-                ('AmoebaBondForceImpl',),
-                ('AmoebaInPlaneAngleForceImpl',),
-                ('AmoebaMultipoleForceImpl',),
-                ('AmoebaOutOfPlaneBendForceImpl',),
-                ('AmoebaPiTorsionForceImpl',),
-                ('AmoebaStretchBendForceImpl',),
-                ('AmoebaTorsionTorsionForceImpl',),
-                ('AmoebaVdwForceImpl',),
-                ('AmoebaWcaDispersionForceImpl',),
-                ('AndersenThermostatImpl',),
                 ('AngleInfo',),
                 ('ApplyAndersenThermostatKernel',),
                 ('ApplyConstraintsKernel',),
@@ -63,30 +50,14 @@ SKIP_METHODS = [('State',),
                 ('CalcNonbondedForceKernel',),
                 ('CalcPeriodicTorsionForceKernel',),
                 ('CalcRBTorsionForceKernel',),
-                ('CMAPTorsionForceImpl',),
-                ('CMMotionRemoverImpl',),
                 ('ComputationInfo',),
                 ('ConstraintInfo',),
-                ('ContextImpl',),
                 ('CudaKernelFactory',),
                 ('CudaStreamFactory',),
-                ('CustomAngleForceImpl',),
-                ('CustomBondForceImpl',),
-                ('CustomCompoundBondForceImpl',),
-                ('CustomExternalForceImpl',),
-                ('CustomGBForceImpl',),
-                ('CustomHbondForceImpl',),
-                ('CustomNonbondedForceImpl',),
-                ('CustomTorsionForceImpl',),
                 ('ExceptionInfo',),
                 ('ExclusionInfo',),
-                ('ForceImpl',),
                 ('FunctionInfo',),
-                ('GBSAOBCForceImpl',),
-                ('GBVIForceImpl',),
                 ('GlobalParameterInfo',),
-                ('HarmonicAngleForceImpl',),
-                ('HarmonicBondForceImpl',),
                 ('InitializeForcesKernel',),
                 ('IntegrateBrownianStepKernel',),
                 ('IntegrateLangevinStepKernel',),
@@ -97,24 +68,18 @@ SKIP_METHODS = [('State',),
                 ('Kernel',),
                 ('KernelFactory',),
                 ('KernelImpl',),
-                ('MonteCarloBarostatImpl',),
-                ('MonteCarloAnisotropicBarostatImpl',),
                 ('MultipoleInfo',),
-                ('NonbondedForceImpl',),
                 ('OutOfPlaneBendInfo',),
                 ('ParameterInfo',),
                 ('ParticleInfo',),
-                ('PeriodicTorsionForceImpl',),
                 ('PeriodicTorsionInfo',),
                 ('PerParticleParameterInfo',),
                 ('PiTorsionInfo',),
                 ('PlatformData',),
-                ('RBTorsionForceImpl',),
                 ('RBTorsionInfo',),
                 ('RemoveCMMotionKernel',),
                 ('SplineFitter',),
                 ('StreamFactory',),
-                ('StreamImpl',),
                 ('StretchBendInfo',),
                 ('TorsionInfo',),
                 ('TorsionTorsionGridInfo',),
@@ -139,7 +104,6 @@ SKIP_METHODS = [('State',),
                 ('Platform', 'registerKernelFactory'),
                 ('IntegrateRPMDStepKernel',),
                 ('RPMDIntegrator',  'getState'),
-                ('DrudeForceImpl',),
                 ('CalcDrudeForceKernel',),
                 ('IntegrateDrudeLangevinStepKernel',),
                 ('IntegrateDrudeSCFStepKernel',),
@@ -159,6 +123,8 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
                   ('AmoebaMultipoleForce', 'addParticle', 'molecularDipole'),
                   ('AmoebaMultipoleForce', 'addParticle', 'molecularQuadrupole'),
                   ('AmoebaMultipoleForce', 'setCovalentMap', 'covalentAtoms'),
+                  ('AmoebaMultipoleForce', 'getElectrostaticPotential', 'context'),
+                  ('AmoebaMultipoleForce', 'getInducedDipoles', 'context'),
 ]
 
 # SWIG assumes the target language shadow class owns the C++ class
@@ -283,6 +249,7 @@ UNITS = {
 #("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( None, ('unit.kilojoule_per_mole')),
 #("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( ('unit.kilojoule_per_mole'), ()),
 ("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( None, ()),
+("AmoebaMultipoleForce",                 "getInducedDipoles")                             :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getSystemMultipoleMoments")                     :  ( None, ()),
 
 ("AmoebaOutOfPlaneBendForce",            "getNumOutOfPlaneBends")                         :  ( None, ()),

wrappers/python/src/swig_doxygen/swig_lib/python/extend.i

@@ -7,15 +7,21 @@
                             int enforcePeriodic,
                             int groups) {
     State state;
-    Py_BEGIN_ALLOW_THREADS
+    PyThreadState* _savePythonThreadState = PyEval_SaveThread();
     int types = 0;
     if (getPositions) types |= State::Positions;
     if (getVelocities) types |= State::Velocities;
     if (getForces) types |= State::Forces;
     if (getEnergy) types |= State::Energy;
     if (getParameters) types |= State::Parameters;
-    state = self->getState(types, enforcePeriodic, groups);
-    Py_END_ALLOW_THREADS
+    try {
+        state = self->getState(types, enforcePeriodic, groups);
+    }
+    catch (...) {
+        PyEval_RestoreThread(_savePythonThreadState);
+        throw;
+    }
+    PyEval_RestoreThread(_savePythonThreadState);
     return _convertStateToLists(state);
   }
 
@@ -150,15 +156,21 @@ Parameters:
                             int enforcePeriodic,
                             int groups) {
     State state;
-    Py_BEGIN_ALLOW_THREADS
+    PyThreadState* _savePythonThreadState = PyEval_SaveThread();
     int types = 0;
     if (getPositions) types |= State::Positions;
     if (getVelocities) types |= State::Velocities;
     if (getForces) types |= State::Forces;
     if (getEnergy) types |= State::Energy;
     if (getParameters) types |= State::Parameters;
-    state = self->getState(copy, types, enforcePeriodic, groups);
-    Py_END_ALLOW_THREADS
+    try {
+        state = self->getState(copy, types, enforcePeriodic, groups);
+    }
+    catch (...) {
+        PyEval_RestoreThread(_savePythonThreadState);
+        throw;
+    }
+    PyEval_RestoreThread(_savePythonThreadState);
     return _convertStateToLists(state);
   }
 

wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i

 
 /* Convert python list of tuples to C++ std::vector of Vec3 objects */
-%typemap(in) std::vector<Vec3>& (std::vector<OpenMM::Vec3> vVec) {
+%typemap(in) const std::vector<Vec3>& (std::vector<OpenMM::Vec3> vVec) {
   // typemap -- %typemap(in) std::vector<Vec3>& (std::vector<OpenMM::Vec3> vVec)
   int i, pLength, itemLength;
   double x, y, z;
@@ -34,6 +34,32 @@
   $1 = &vVec;
 }
 
+/* The following two typemaps cause a non-const vector<Vec3>& to become a return value. */
+%typemap(in, numinputs=0) std::vector<Vec3>& (std::vector<Vec3> temp) {
+    $1 = &temp;
+}
+
+%typemap(argout) std::vector<Vec3>& {
+    int i, n;
+    PyObject *pyList;
+
+    n=(*$1).size(); 
+    pyList=PyList_New(n);
+    PyObject* mm = PyImport_AddModule("simtk.openmm");
+    PyObject* vec3 = PyObject_GetAttrString(mm, "Vec3");
+    for (i=0; i<n; i++) {
+        OpenMM::Vec3& v = (*$1).at(i);
+        PyObject* args = Py_BuildValue("(d,d,d)", v[0], v[1], v[2]);
+        PyObject* pyVec = PyObject_CallObject(vec3, args);
+        Py_DECREF(args);
+        PyList_SET_ITEM(pyList, i, pyVec);
+    }
+    $result = pyList;
+}
+
+/* const vector<Vec3> should NOT become an output. */
+%typemap(argout) const std::vector<Vec3>& {
+}
 
 /* Convert python tuple to C++ Vec3 object*/
 %typemap(typecheck) Vec3 {

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -3,6 +3,7 @@ from validateConstraints import *
 from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
+import simtk.openmm.app.element as elem
 
 class TestAmberPrmtopFile(unittest.TestCase):
 
@@ -93,42 +94,59 @@ class TestAmberPrmtopFile(unittest.TestCase):
             self.assertTrue(any(isinstance(f, force_type) for f in forces))
 
     def test_ImplicitSolventParameters(self):
-        """Test that solventDielectric and soluteDielectric are passed correctly 
-        for the different types of implicit solvent.
-
-        """
+        """Test that parameters are set correctly for the different types of implicit solvent."""
+        methodMap = {NoCutoff:NonbondedForce.NoCutoff,
+                     CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic}
         for implicitSolvent_value in [HCT, OBC1, OBC2, GBn]:
-            system = self.prmtop2.createSystem(implicitSolvent=implicitSolvent_value, 
-                                               solventDielectric=50.0, 
-                                               soluteDielectric = 0.9)
-            found_matching_solvent_dielectric=False
-            found_matching_solute_dielectric=False
-            if implicitSolvent_value in set([HCT, OBC1, GBn]):
-                for force in system.getForces():
-                    if isinstance(force, CustomGBForce):
-                        for j in range(force.getNumGlobalParameters()):
-                            if (force.getGlobalParameterName(j) == 'solventDielectric' and
-                               force.getGlobalParameterDefaultValue(j) == 50.0):
+            for method in methodMap:
+                system = self.prmtop2.createSystem(implicitSolvent=implicitSolvent_value, 
+                                    solventDielectric=50.0, soluteDielectric=0.9, nonbondedMethod=method)
+                found_matching_solvent_dielectric=False
+                found_matching_solute_dielectric=False
+                if implicitSolvent_value in set([HCT, OBC1, GBn]):
+                    for force in system.getForces():
+                        if isinstance(force, CustomGBForce):
+                            self.assertEqual(force.getNonbondedMethod(), methodMap[method])
+                            for j in range(force.getNumGlobalParameters()):
+                                if (force.getGlobalParameterName(j) == 'solventDielectric' and
+                                   force.getGlobalParameterDefaultValue(j) == 50.0):
+                                    found_matching_solvent_dielectric = True
+                                if (force.getGlobalParameterName(j) == 'soluteDielectric' and
+                                   force.getGlobalParameterDefaultValue(j) == 0.9):
+                                    found_matching_solute_dielectric = True
+                        if isinstance(force, NonbondedForce):
+                            self.assertEqual(force.getReactionFieldDielectric(), 1.0)
+                            self.assertEqual(force.getNonbondedMethod(), methodMap[method])
+                    self.assertTrue(found_matching_solvent_dielectric and 
+                                    found_matching_solute_dielectric)
+                else:
+                    for force in system.getForces():
+                        if isinstance(force, GBSAOBCForce):
+                            self.assertEqual(force.getNonbondedMethod(), methodMap[method])
+                            if force.getSolventDielectric() == 50.0:
                                 found_matching_solvent_dielectric = True
-                            if (force.getGlobalParameterName(j) == 'soluteDielectric' and
-                               force.getGlobalParameterDefaultValue(j) == 0.9):
+                            if force.getSoluteDielectric() == 0.9:
                                 found_matching_solute_dielectric = True
-                    if isinstance(force, NonbondedForce):
-                        self.assertEqual(force.getReactionFieldDielectric(), 1.0)
-                self.assertTrue(found_matching_solvent_dielectric and 
-                                found_matching_solute_dielectric)
-            else:
-                for force in system.getForces():
-                    if isinstance(force, GBSAOBCForce):
-                        if force.getSolventDielectric() == 50.0:
-                            found_matching_solvent_dielectric = True
-                        if force.getSoluteDielectric() == 0.9:
-                            found_matching_solute_dielectric = True
-                    if isinstance(force, NonbondedForce):
-                        self.assertEqual(force.getReactionFieldDielectric(), 1.0)
-                self.assertTrue(found_matching_solvent_dielectric and 
-                                found_matching_solute_dielectric)
+                        if isinstance(force, NonbondedForce):
+                            self.assertEqual(force.getReactionFieldDielectric(), 1.0)
+                            self.assertEqual(force.getNonbondedMethod(), methodMap[method])
+                    self.assertTrue(found_matching_solvent_dielectric and 
+                                    found_matching_solute_dielectric)
+
+    def test_HydrogenMass(self):
+        """Test that altering the mass of hydrogens works correctly."""
+        
+        topology = self.prmtop1.topology
+        hydrogenMass = 4*amu
+        system1 = self.prmtop1.createSystem()
+        system2 = self.prmtop1.createSystem(hydrogenMass=hydrogenMass)
+        for atom in topology.atoms():
+            if atom.element == elem.hydrogen:
+                self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
+                self.assertEqual(hydrogenMass, system2.getParticleMass(atom.index))
+        totalMass1 = sum([system1.getParticleMass(i) for i in range(system1.getNumParticles())]).value_in_unit(amu)
+        totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
+        self.assertAlmostEqual(totalMass1, totalMass2)
 
 if __name__ == '__main__':
     unittest.main()
-

wrappers/python/tests/TestDesmondDMSFile.py

+import os
+import unittest
+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+import simtk.openmm.app.element as elem
+
+class TestDesmondDMSFile(unittest.TestCase):
+    def setUp(self):
+        """Set up the tests by loading the input files."""
+
+        # alanine dipeptide with explicit water
+        path = os.path.join(os.path.dirname(__file__), 'systems/alanine-dipeptide-explicit-amber99SBILDN-tip3p.dms')
+        self.dms = DesmondDMSFile(path)
+    
+    def test_NonbondedMethod(self):
+        """Test all five options for the nonbondedMethod parameter."""
+
+        methodMap = {NoCutoff:NonbondedForce.NoCutoff, 
+                     CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic, 
+                     CutoffPeriodic:NonbondedForce.CutoffPeriodic, 
+                     Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
+        for method in methodMap:
+            system = self.dms.createSystem(nonbondedMethod=method)
+            forces = system.getForces()
+            self.assertTrue(any(isinstance(f, NonbondedForce) and 
+                                f.getNonbondedMethod()==methodMap[method] 
+                                for f in forces))
+                                
+    def test_Cutoff(self):
+        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
+
+        for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
+            system = self.dms.createSystem(nonbondedMethod=method, 
+                                            nonbondedCutoff=2*nanometer)
+            cutoff_distance = 0.0*nanometer
+            cutoff_check = 2.0*nanometer
+            for force in system.getForces():
+                if isinstance(force, NonbondedForce):
+                    cutoff_distance = force.getCutoffDistance()
+            self.assertEqual(cutoff_distance, cutoff_check)
+
+    def test_EwaldErrorTolerance(self):
+        """Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
+
+        for method in [Ewald, PME]:
+            system = self.dms.createSystem(nonbondedMethod=method,
+                                            ewaldErrorTolerance=1e-6)
+            tolerance = 0
+            tolerance_check = 1e-6
+            for force in system.getForces():
+                if isinstance(force, NonbondedForce):
+                    tolerance = force.getEwaldErrorTolerance()
+            self.assertEqual(tolerance, tolerance_check)
+
+    def test_RemoveCMMotion(self):
+        """Test both options (True and False) for the removeCMMotion parameter."""
+
+        for b in [True, False]:
+            system = self.dms.createSystem(removeCMMotion=b)
+            self.assertEqual(any(isinstance(f, CMMotionRemover) for f in system.getForces()), b)
+
+    def test_HydrogenMass(self):
+        """Test that altering the mass of hydrogens works correctly."""
+        
+        topology = self.dms.topology
+        hydrogenMass = 4*amu
+        system1 = self.dms.createSystem()
+        system2 = self.dms.createSystem(hydrogenMass=hydrogenMass)
+        for atom in topology.atoms():
+            if atom.element == elem.hydrogen:
+                self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
+                self.assertEqual(hydrogenMass, system2.getParticleMass(atom.index))
+        totalMass1 = sum([system1.getParticleMass(i) for i in range(system1.getNumParticles())]).value_in_unit(amu)
+        totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
+        self.assertAlmostEqual(totalMass1, totalMass2)

wrappers/python/tests/TestForceField.py

@@ -3,6 +3,7 @@ from validateConstraints import *
 from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
+import simtk.openmm.app.element as elem
 
 class TestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method."""
@@ -104,6 +105,20 @@ class TestForceField(unittest.TestCase):
         self.assertTrue(found_matching_solvent_dielectric and 
                         found_matching_solute_dielectric)
 
+    def test_HydrogenMass(self):
+        """Test that altering the mass of hydrogens works correctly."""
+        
+        topology = self.pdb1.topology
+        hydrogenMass = 4*amu
+        system1 = self.forcefield1.createSystem(topology)
+        system2 = self.forcefield1.createSystem(topology, hydrogenMass=hydrogenMass)
+        for atom in topology.atoms():
+            if atom.element == elem.hydrogen:
+                self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
+                self.assertEqual(hydrogenMass, system2.getParticleMass(atom.index))
+        totalMass1 = sum([system1.getParticleMass(i) for i in range(system1.getNumParticles())]).value_in_unit(amu)
+        totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
+        self.assertAlmostEqual(totalMass1, totalMass2)
 
 
 if __name__ == '__main__':

wrappers/python/tests/TestGromacsTopFile.py

@@ -3,6 +3,7 @@ from validateConstraints import *
 from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
+import simtk.openmm.app.element as elem
 
 class TestGromacsTopFile(unittest.TestCase):
 
@@ -103,6 +104,21 @@ class TestGromacsTopFile(unittest.TestCase):
         self.assertTrue(found_matching_solvent_dielectric and 
                         found_matching_solute_dielectric)
 
+    def test_HydrogenMass(self):
+        """Test that altering the mass of hydrogens works correctly."""
+        
+        topology = self.top1.topology
+        hydrogenMass = 4*amu
+        system1 = self.top1.createSystem()
+        system2 = self.top1.createSystem(hydrogenMass=hydrogenMass)
+        for atom in topology.atoms():
+            if atom.element == elem.hydrogen:
+                self.assertNotEqual(hydrogenMass, system1.getParticleMass(atom.index))
+                self.assertEqual(hydrogenMass, system2.getParticleMass(atom.index))
+        totalMass1 = sum([system1.getParticleMass(i) for i in range(system1.getNumParticles())]).value_in_unit(amu)
+        totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
+        self.assertAlmostEqual(totalMass1, totalMass2)
+
 if __name__ == '__main__':
     unittest.main()