Merge remote-tracking branch 'upstream/master' into forcefield

plugins/amoeba/serialization/tests/TestSerializeAmoebaBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaBondForce force1;
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalBondCubic(12.3);
     force1.setAmoebaGlobalBondQuartic(98.7);
     force1.addBond(0, 1, 1.0, 2.0);
@@ -60,6 +61,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaBondForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getAmoebaGlobalBondCubic(), force2.getAmoebaGlobalBondCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalBondQuartic(), force2.getAmoebaGlobalBondQuartic());
     ASSERT_EQUAL(force1.getNumBonds(), force2.getNumBonds());

plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaGeneralizedKirkwoodForce force1;
+    force1.setForceGroup(3);
     force1.setSolventDielectric(  80.0);
     force1.setSoluteDielectric(   1.0);
     //force1.setDielectricOffset(   0.09);
@@ -64,6 +65,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaGeneralizedKirkwoodForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getSolventDielectric(),    force2.getSolventDielectric());
     ASSERT_EQUAL(force1.getSoluteDielectric(),     force2.getSoluteDielectric());
     //ASSERT_EQUAL(force1.getDielectricOffset(),     force2.getDielectricOffset());

plugins/amoeba/serialization/tests/TestSerializeAmoebaInPlaneAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,6 +46,7 @@ void testSerialization() {
 
     AmoebaInPlaneAngleForce force1;
 
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalInPlaneAngleCubic(12.3);
     force1.setAmoebaGlobalInPlaneAngleQuartic(98.7);
     force1.setAmoebaGlobalInPlaneAnglePentic(91.7);
@@ -65,6 +66,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaInPlaneAngleForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleCubic(),    force2.getAmoebaGlobalInPlaneAngleCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleQuartic(),  force2.getAmoebaGlobalInPlaneAngleQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAnglePentic(),   force2.getAmoebaGlobalInPlaneAnglePentic());

plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -59,6 +59,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaMultipoleForce force1;
+    force1.setForceGroup(3);
     force1.setNonbondedMethod(AmoebaMultipoleForce::NoCutoff);
     force1.setCutoffDistance(0.9);
     force1.setAEwald(0.544);
@@ -74,6 +75,12 @@ void testSerialization() {
     force1.setMutualInducedTargetEpsilon(1.0e-05); 
     //force1.setElectricConstant(138.93); 
     force1.setEwaldErrorTolerance(1.0e-05); 
+    
+    vector<double> coeff;
+    coeff.push_back(0.0);
+    coeff.push_back(-0.1);
+    coeff.push_back(1.1);
+    force1.setExtrapolationCoefficients(coeff);
 
     std::vector<std::string> covalentTypes;
     getCovalentTypes(covalentTypes);
@@ -105,6 +112,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaMultipoleForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getCutoffDistance(),                force2.getCutoffDistance());
     ASSERT_EQUAL(force1.getNonbondedMethod(),               force2.getNonbondedMethod());
     ASSERT_EQUAL(force1.getAEwald(),                        force2.getAEwald());
@@ -125,6 +133,8 @@ void testSerialization() {
         ASSERT_EQUAL(gridDimension1[jj], gridDimension2[jj]);
     }
     
+    ASSERT_EQUAL_CONTAINERS(force1.getExtrapolationCoefficients(), force2.getExtrapolationCoefficients());
+    
     ASSERT_EQUAL(force1.getNumMultipoles(),  force2.getNumMultipoles());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumMultipoles()); ii++) {
 

plugins/amoeba/serialization/tests/TestSerializeAmoebaOutOfPlaneBendForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,6 +46,7 @@ void testSerialization() {
 
     AmoebaOutOfPlaneBendForce force1;
 
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalOutOfPlaneBendCubic(12.3);
     force1.setAmoebaGlobalOutOfPlaneBendQuartic(98.7);
     force1.setAmoebaGlobalOutOfPlaneBendPentic(91.7);
@@ -65,6 +66,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaOutOfPlaneBendForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendCubic(), force2.getAmoebaGlobalOutOfPlaneBendCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendQuartic(), force2.getAmoebaGlobalOutOfPlaneBendQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendPentic(), force2.getAmoebaGlobalOutOfPlaneBendPentic());

plugins/amoeba/serialization/tests/TestSerializeAmoebaPiTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaPiTorsionForce force1;
+    force1.setForceGroup(3);
     force1.addPiTorsion(0, 1, 3, 4, 5, 6, 2.0);
     force1.addPiTorsion(0, 2, 3, 5, 12, 13, 2.1);
     force1.addPiTorsion(2, 3, 5, 6, 81, 91, 2.2);
@@ -58,6 +59,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaPiTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getNumPiTorsions(), force2.getNumPiTorsions());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumPiTorsions()); ii++) {
         int a1, a2, a3, a4, a5, a6, b1, b2, b3, b4, b5, b6;

plugins/amoeba/serialization/tests/TestSerializeAmoebaStretchBendForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaStretchBendForce force1;
+    force1.setForceGroup(3);
     force1.addStretchBend(0, 1, 3, 1.0, 1.2, 150.1, 83.2, 100.);
     force1.addStretchBend(2, 4, 4, 1.1, 2.2, 180.1, 89.2, 100.);
     force1.addStretchBend(5, 0, 1, 3.1, 8.2, 140.1, 98.2, 100.);
@@ -57,6 +58,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaStretchBendForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getNumStretchBends(), force2.getNumStretchBends());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumStretchBends()); ii++) {
         int p11, p12, p13;

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -81,6 +81,7 @@ void testSerialization() {
 
     AmoebaTorsionTorsionForce force1;
 
+    force1.setForceGroup(3);
     for (unsigned int ii = 0; ii < 5; ii++) {
         std::vector< std::vector< std::vector<double> > > gridVector;
         loadTorsionTorsionGrid(gridVector);
@@ -99,6 +100,7 @@ void testSerialization() {
     // Compare the two force1s to see if they are identical.  
 
     AmoebaTorsionTorsionForce & force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getNumTorsionTorsions(), force2.getNumTorsionTorsions());
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsions()); ii++) {
 

plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaVdwForce force1;
+    force1.setForceGroup(3);
     force1.setSigmaCombiningRule("GEOMETRIC");
     force1.setEpsilonCombiningRule("GEOMETRIC");
     force1.setCutoff(0.9);
@@ -70,6 +71,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaVdwForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getSigmaCombiningRule(),    force2.getSigmaCombiningRule());
     ASSERT_EQUAL(force1.getEpsilonCombiningRule(),  force2.getEpsilonCombiningRule());
     ASSERT_EQUAL(force1.getCutoff(),                force2.getCutoff());

plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaWcaDispersionForce force1;
+    force1.setForceGroup(3);
     force1.setEpso(   1.0);
     force1.setEpsh(   1.1);
     force1.setRmino(  1.2);
@@ -68,6 +69,7 @@ void testSerialization() {
 
     AmoebaWcaDispersionForce& force2 = *copy;
 
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getEpso(),    force2.getEpso());
     ASSERT_EQUAL(force1.getEpsh(),    force2.getEpsh());
     ASSERT_EQUAL(force1.getRmino(),   force2.getRmino());

serialization/src/CustomCentroidBondForceProxy.cpp

@@ -64,7 +64,8 @@ void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNo
         for (int j = 0; j < (int) particles.size(); j++) {
             SerializationNode& node = group.createChildNode("Particle");
             node.setIntProperty("p", particles[j]);
-            node.setDoubleProperty("weight", weights[j]);
+            if (j < weights.size())
+                node.setDoubleProperty("weight", weights[j]);
         }
     }
     SerializationNode& bonds = node.createChildNode("Bonds");
@@ -115,7 +116,8 @@ void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) c
             vector<double> weights;
             for (int j = 0; j < (int) group.getChildren().size(); j++) {
                 particles.push_back(group.getChildren()[j].getIntProperty("p"));
-                weights.push_back(group.getChildren()[j].getDoubleProperty("weight"));
+                if (group.getChildren()[j].hasProperty("weight"))
+                    weights.push_back(group.getChildren()[j].getDoubleProperty("weight"));
             }
             force->addGroup(particles, weights);
         }

serialization/tests/TestSerializeCustomCentroidBondForce.cpp

@@ -51,7 +51,8 @@ void testSerialization() {
         vector<double> weights;
         for (int j = 0; j < i+1; j++) {
             particles.push_back(i+j);
-            weights.push_back(1.0/(i+1));
+            if (i < 2)
+                weights.push_back(1.0/(i+1));
         }
         force.addGroup(particles, weights);
     }

wrappers/python/simtk/openmm/app/data/hydrogens.xml

@@ -220,6 +220,7 @@
   <Variant name="HID"/>
   <Variant name="HIE"/>
   <Variant name="HIP"/>
+  <Variant name="HIN"/>
   <H name="H" parent="N"/>
   <H name="H2" parent="N" terminal="N"/>
   <H name="H3" parent="N" terminal="N"/>

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

@@ -3760,6 +3760,8 @@ class AmoebaMultipoleGenerator:
                 polarizationType = args['polarization']
                 if (polarizationType.lower() == 'direct'):
                     force.setPolarizationType(mm.AmoebaMultipoleForce.Direct)
+                elif (polarizationType.lower() == 'extrapolated'):
+                    force.setPolarizationType(mm.AmoebaMultipoleForce.Extrapolated)
                 else:
                     force.setPolarizationType(mm.AmoebaMultipoleForce.Mutual)
 

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

@@ -123,7 +123,7 @@ class PdbStructure(object):
     """
 
 
-    def __init__(self, input_stream, load_all_models=False):
+    def __init__(self, input_stream, load_all_models=False, extraParticleIdentifier='EP'):
         """Create a PDB model from a PDB file stream.
 
         Parameters
@@ -135,9 +135,12 @@ class PdbStructure(object):
         load_all_models : bool
             Whether to load every model of an NMR structure or trajectory, or
             just load the first model, to save memory.
+        extraParticleIdentifier : string='EP'
+            if this value appears in the element column for an ATOM record, the Atom's element will be set to 'EP' to mark it as an extra particle
         """
         # initialize models
         self.load_all_models = load_all_models
+        self.extraParticleIdentifier = extraParticleIdentifier
         self.models = []
         self._current_model = None
         self.default_model = None
@@ -157,7 +160,7 @@ class PdbStructure(object):
                 pdb_line = pdb_line.decode('utf-8')
             # Look for atoms
             if (pdb_line.find("ATOM  ") == 0) or (pdb_line.find("HETATM") == 0):
-                self._add_atom(Atom(pdb_line, self))
+                self._add_atom(Atom(pdb_line, self, self.extraParticleIdentifier))
             # Notice MODEL punctuation, for the next level of detail
             # in the structure->model->chain->residue->atom->position hierarchy
             elif (pdb_line.find("MODEL") == 0):
@@ -682,7 +685,7 @@ class Residue(object):
 class Atom(object):
     """Atom represents one atom in a PDB structure.
     """
-    def __init__(self, pdb_line, pdbstructure=None):
+    def __init__(self, pdb_line, pdbstructure=None, extraParticleIdentifier='EP'):
         """Create a new pdb.Atom from an ATOM or HETATM line.
 
         Example line:
@@ -795,11 +798,14 @@ class Atom(object):
         try: self.formal_charge = int(pdb_line[78:80])
         except ValueError: self.formal_charge = None
         # figure out atom element
-        try:
-            # Try to find a sensible element symbol from columns 76-77
-            self.element = element.get_by_symbol(self.element_symbol)
-        except KeyError:
-            self.element = None
+        if self.element_symbol == extraParticleIdentifier:
+            self.element = 'EP'
+        else:
+            try:
+                # Try to find a sensible element symbol from columns 76-77
+                self.element = element.get_by_symbol(self.element_symbol)
+            except KeyError:    
+                self.element = None
         if pdbstructure is not None:
             pdbstructure._next_atom_number = self.serial_number+1
             pdbstructure._next_residue_number = self.residue_number+1

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

@@ -6,7 +6,7 @@ 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) 2012-2015 Stanford University and the Authors.
+Portions copyright (c) 2012-2016 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -614,6 +614,7 @@ class Modeller(object):
             HID: Neutral form with a hydrogen on the ND1 atom
             HIE: Neutral form with a hydrogen on the NE2 atom
             HIP: Positively charged form with hydrogens on both ND1 and NE2
+            HIN: Negatively charged form without a hydrogen on either ND1 or NE2
 
         Lysine:
             LYN: Neutral form with two hydrogens on the zeta nitrogen
@@ -625,9 +626,14 @@ class Modeller(object):
         2. Any Cysteine that participates in a disulfide bond uses the CYX variant regardless of pH.
         3. For a neutral Histidine residue, the HID or HIE variant is selected based on which one forms a better hydrogen bond.
 
-        You can override these rules by explicitly specifying a variant for any residue.  Also keep in mind that this
-        function will only add hydrogens.  It will never remove ones that are already present in the model, regardless
-        of the specified pH.
+        You can override these rules by explicitly specifying a variant for any residue.  To do that, provide a list for the
+        'variants' parameter, and set the corresponding element to the name of the variant to use.
+
+        A special case is when the model already contains a hydrogen that should not be present in the desired variant.
+        If you explicitly specify a variant using the 'variants' parameter, the residue will be modified to match the
+        desired variant, removing hydrogens if necessary.  On the other hand, for residues whose variant is selected
+        automatically, this function will only add hydrogens.  It will never remove ones that are already present in the
+        model, regardless of the specified pH.
 
         Definitions for standard amino acids and nucleotides are built in.  You can call loadHydrogenDefinitions() to load
         additional definitions for other residue types.
@@ -771,6 +777,7 @@ class Modeller(object):
                     if variant is not None and variant not in spec.variants:
                         raise ValueError('Illegal variant for %s residue: %s' % (residue.name, variant))
                     actualVariants[residue.index] = variant
+                    removeExtraHydrogens = (variants[residue.index] is not None)
 
                     # Make a list of hydrogens that should be present in the residue.
 
@@ -783,6 +790,11 @@ class Modeller(object):
                     # Loop over atoms in the residue, adding them to the new topology along with required hydrogens.
 
                     for parent in residue.atoms():
+                        # Check whether this is a hydrogen that should be removed.
+
+                        if removeExtraHydrogens and parent.element == elem.hydrogen and not any(parent.name == h.name for h in hydrogens):
+                            continue
+
                         # Add the atom.
 
                         newAtom = newTopology.addAtom(parent.name, parent.element, newResidue)

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

@@ -59,7 +59,7 @@ class PDBFile(object):
     _residueNameReplacements = {}
     _atomNameReplacements = {}
 
-    def __init__(self, file):
+    def __init__(self, file, extraParticleIdentifier='EP'):
         """Load a PDB file.
 
         The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
@@ -68,6 +68,8 @@ class PDBFile(object):
         ----------
         file : string
             the name of the file to load
+        extraParticleIdentifier : string='EP'
+            if this value appears in the element column for an ATOM record, the Atom's element will be set to None to mark it as an extra particle
         """
         
         metalElements = ['Al','As','Ba','Ca','Cd','Ce','Co','Cs','Cu','Dy','Fe','Gd','Hg','Ho','In','Ir','K','Li','Mg',
@@ -91,7 +93,7 @@ class PDBFile(object):
             if isinstance(file, str):
                 inputfile = open(file)
                 own_handle = True
-            pdb = PdbStructure(inputfile, load_all_models=True)
+            pdb = PdbStructure(inputfile, load_all_models=True, extraParticleIdentifier=extraParticleIdentifier)
             if own_handle:
                 inputfile.close()
         PDBFile._loadNameReplacementTables()
@@ -116,7 +118,9 @@ class PDBFile(object):
                         atomName = atomReplacements[atomName]
                     atomName = atomName.strip()
                     element = atom.element
-                    if element is None:
+                    if element == 'EP':
+                        element = None
+                    elif element is None:
                         # Try to guess the element.
 
                         upper = atomName.upper()
@@ -253,7 +257,7 @@ class PDBFile(object):
                 map[atom.attrib[id]] = name
 
     @staticmethod
-    def writeFile(topology, positions, file=sys.stdout, keepIds=False):
+    def writeFile(topology, positions, file=sys.stdout, keepIds=False, extraParticleIdentifier=' '):
         """Write a PDB file containing a single model.
 
         Parameters
@@ -269,9 +273,11 @@ class PDBFile(object):
             rather than generating new ones.  Warning: It is up to the caller to
             make sure these are valid IDs that satisfy the requirements of the
             PDB format.  Otherwise, the output file will be invalid.
+        extraParticleIdentifier : string=' '
+            String to write in the element column of the ATOM records for atoms whose element is None (extra particles)
         """
         PDBFile.writeHeader(topology, file)
-        PDBFile.writeModel(topology, positions, file, keepIds=keepIds)
+        PDBFile.writeModel(topology, positions, file, keepIds=keepIds, extraParticleIdentifier=extraParticleIdentifier)
         PDBFile.writeFooter(topology, file)
 
     @staticmethod
@@ -294,7 +300,7 @@ class PDBFile(object):
                     a*10, b*10, c*10, alpha*RAD_TO_DEG, beta*RAD_TO_DEG, gamma*RAD_TO_DEG), file=file)
 
     @staticmethod
-    def writeModel(topology, positions, file=sys.stdout, modelIndex=None, keepIds=False):
+    def writeModel(topology, positions, file=sys.stdout, modelIndex=None, keepIds=False, extraParticleIdentifier=' '):
         """Write out a model to a PDB file.
 
         Parameters
@@ -313,6 +319,8 @@ class PDBFile(object):
             rather than generating new ones.  Warning: It is up to the caller to
             make sure these are valid IDs that satisfy the requirements of the
             PDB format.  Otherwise, the output file will be invalid.
+        extraParticleIdentifier : string=' '
+            String to write in the element column of the ATOM records for atoms whose element is None (extra particles)
         """
 
         if len(list(topology.atoms())) != len(positions):
@@ -343,17 +351,17 @@ class PDBFile(object):
                 else:
                     resId = "%4d" % ((resIndex+1)%10000)
                 for atom in res.atoms():
-                    if len(atom.name) < 4 and atom.name[:1].isalpha() and (atom.element is None or len(atom.element.symbol) < 2):
+                    if atom.element is not None:
+                        symbol = atom.element.symbol
+                    else:
+                        symbol = extraParticleIdentifier
+                    if len(atom.name) < 4 and atom.name[:1].isalpha() and len(symbol) < 2:
                         atomName = ' '+atom.name
                     elif len(atom.name) > 4:
                         atomName = atom.name[:4]
                     else:
                         atomName = atom.name
                     coords = positions[posIndex]
-                    if atom.element is not None:
-                        symbol = atom.element.symbol
-                    else:
-                        symbol = ' '
                     line = "ATOM  %5d %-4s %3s %s%4s    %s%s%s  1.00  0.00          %2s  " % (
                         atomIndex%100000, atomName, resName, chainName, resId, _format_83(coords[0]),
                         _format_83(coords[1]), _format_83(coords[2]), symbol)

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -247,6 +247,7 @@ UNITS = {
 ("AmoebaMultipoleForce",                 "getPmeBSplineOrder")                            :  ( None,()),
 ("AmoebaMultipoleForce",                 "getMutualInducedMaxIterations")                 :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getMutualInducedTargetEpsilon")                 :  ( None, ()),
+("AmoebaMultipoleForce",                 "getExtrapolationCoefficients")                            :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getEwaldErrorTolerance")                        :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getPmeGridDimensions")                          :  ( None,()),
 

wrappers/python/tests/TestModeller.py

@@ -903,6 +903,29 @@ class TestModeller(unittest.TestCase):
         validate_equivalence(self, topology_LYN, topology_after)
 
 
+    def test_removeExtraHydrogens(self):
+        """Test that addHydrogens() can remove hydrogens that shouldn't be there. """
+
+        topology_start = self.topology_start3
+        positions = self.positions3
+        modeller = Modeller(topology_start, positions)
+
+        # Add hydrogens, forcing residue 1 to be ASH.
+
+        variants = [None]*25
+        variants[1] = 'ASH'
+        modeller.addHydrogens(self.forcefield, variants=variants)
+        residue = list(modeller.topology.residues())[1]
+        self.assertTrue(any(a.name == 'HD2' for a in residue.atoms()))
+
+        # Now force it to be ASP and see if HD2 gets removed.
+
+        variants[1] = 'ASP'
+        modeller.addHydrogens(self.forcefield, variants=variants)
+        residue = list(modeller.topology.residues())[1]
+        self.assertFalse(any(a.name == 'HD2' for a in residue.atoms()))
+
+
     def test_addExtraParticles(self):
         """Test addExtraParticles()."""
 

wrappers/python/tests/TestPdbFile.py

@@ -70,6 +70,20 @@ class TestPdbFile(unittest.TestCase):
         pdb = PDBFile(open('systems/triclinic.pdb', 'rb'))
         self.assertEqual(len(pdb.positions), 8)
 
+    def test_ExtraParticles(self):
+        """Test reading, and writing and re-reading of a file containing extra particle atoms."""
+        pdb = PDBFile('systems/tip5p.pdb')  
+        for atom in pdb.topology.atoms():
+            if atom.index > 2:
+                self.assertEqual(None, atom.element)
+        output = StringIO()
+        PDBFile.writeFile(pdb.topology, pdb.positions, output)
+        input = StringIO(output.getvalue())
+        pdb = PDBFile(input, extraParticleIdentifier = '')
+        for atom in pdb.topology.atoms():
+            if atom.index > 2:
+                self.assertEqual(None, atom.element)
+
 
     def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
         unit = p1.unit