Merge remote-tracking branch 'upstream/master'

platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp

@@ -48,10 +48,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testSingleBond() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(2.0);
     system.addParticle(2.0);
@@ -89,7 +90,6 @@ void testSingleBond() {
 void testConstraints() {
     const int numParticles = 8;
     const double temp = 500.0;
-    ReferencePlatform platform;
     System system;
     VariableVerletIntegrator integrator(1e-5);
     integrator.setConstraintTolerance(1e-5);
@@ -148,7 +148,6 @@ void testConstraints() {
 void testConstrainedClusters() {
     const int numParticles = 7;
     const double temp = 500.0;
-    ReferencePlatform platform;
     System system;
     VariableVerletIntegrator integrator(1e-5);
     integrator.setConstraintTolerance(1e-5);
@@ -211,7 +210,6 @@ void testConstrainedClusters() {
 }
 
 void testConstrainedMasslessParticles() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(0.0);
     system.addParticle(1.0);
@@ -255,7 +253,6 @@ void testArgonBox() {
 
     // Create a box of argon atoms.
     
-    ReferencePlatform platform;
     System system;
     NonbondedForce* nonbonded = new NonbondedForce();
     vector<Vec3> positions;

platforms/reference/tests/TestReferenceVerletIntegrator.cpp

@@ -48,10 +48,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testSingleBond() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(2.0);
     system.addParticle(2.0);
@@ -88,7 +89,6 @@ void testSingleBond() {
 void testConstraints() {
     const int numParticles = 8;
     const double temp = 500.0;
-    ReferencePlatform platform;
     System system;
     VerletIntegrator integrator(0.002);
     integrator.setConstraintTolerance(1e-5);
@@ -139,7 +139,6 @@ void testConstraints() {
 void testConstrainedClusters() {
     const int numParticles = 7;
     const double temp = 500.0;
-    ReferencePlatform platform;
     System system;
     VerletIntegrator integrator(0.001);
     integrator.setConstraintTolerance(1e-5);
@@ -201,7 +200,6 @@ void testConstrainedClusters() {
 }
 
 void testConstrainedMasslessParticles() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(0.0);
     system.addParticle(1.0);

platforms/reference/tests/TestReferenceVirtualSites.cpp

@@ -50,11 +50,12 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 /**
  * Check that massless particles are handled correctly.
  */
 void testMasslessParticle() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(0.0);
     system.addParticle(1.0);
@@ -91,7 +92,6 @@ void testMasslessParticle() {
  * Test a TwoParticleAverageSite virtual site.
  */
 void testTwoParticleAverage() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -128,7 +128,6 @@ void testTwoParticleAverage() {
  * Test a ThreeParticleAverageSite virtual site.
  */
 void testThreeParticleAverage() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -170,7 +169,6 @@ void testThreeParticleAverage() {
  * Test an OutOfPlaneSite virtual site.
  */
 void testOutOfPlane() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -223,7 +221,6 @@ void testLocalCoordinates() {
     const Vec3 xWeights(-1.0, 0.5, 0.5);
     const Vec3 yWeights(0.0, -1.0, 1.0);
     const Vec3 localPosition(0.4, 0.3, 0.2);
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -299,7 +296,6 @@ void testLocalCoordinates() {
  * when using virtual sites.
  */
 void testConservationLaws() {
-    ReferencePlatform platform;
     System system;
     NonbondedForce* forceField = new NonbondedForce();
     system.addForce(forceField);

plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h

@@ -159,7 +159,7 @@ public:
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-angle parameters.  The set of particles involved

plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h

@@ -131,7 +131,7 @@ public:
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-bond parameters.  The set of particles involved

plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h

@@ -156,7 +156,7 @@ public:
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-particle parameters.  All other aspects of the Force

plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h

@@ -164,7 +164,7 @@ public:
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-angle parameters.  The set of particles involved

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -340,7 +340,7 @@ public:
     /**
      * Update the multipole parameters in a Context to match those stored in this Force object.  This method
      * provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setMultipoleParameters() to modify this object's parameters, then call updateParametersInState() to
+     * Simply call setMultipoleParameters() to modify this object's parameters, then call updateParametersInContext() to
      * copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the parameters of multipoles.

plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h

@@ -156,7 +156,7 @@ public:
     /**
      * Update the per-bend term parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setOutOfPlaneBendParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setOutOfPlaneBendParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-bend term parameters.  The set of particles involved

plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h

@@ -106,7 +106,7 @@ public:
     /**
      * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setPiTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setPiTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-torsion parameters.  The set of particles involved

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -112,7 +112,7 @@ public:
     /**
      * Update the per-stretch-bend term parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setStretchBendParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setStretchBendParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-stretch-bend term parameters.  The set of particles involved

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -205,7 +205,7 @@ public:
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-particle parameters.  All other aspects of the Force

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -92,7 +92,7 @@ public:
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-particle parameters.  All other aspects of the Force

tests/TestVectorize.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) 2014 Stanford University and the Authors.           *
+ * Portions copyright (c) 2014-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -148,6 +148,7 @@ void testMathFunctions() {
     ASSERT_VEC4_EQUAL(min(f1, f2), 0.4, 1.2, -1.2, -5.0);
     ASSERT_VEC4_EQUAL(max(f1, f2), 1.1, 1.9, 1.3, -3.8);
     ASSERT_VEC4_EQUAL(sqrt(fvec4(1.5, 3.1, 4.0, 15.0)), sqrt(1.5), sqrt(3.1), sqrt(4.0), sqrt(15.0));
+    ASSERT_VEC4_EQUAL(rsqrt(fvec4(1.5, 3.1, 4.0, 15.0)), 1.0/sqrt(1.5), 1.0/sqrt(3.1), 1.0/sqrt(4.0), 1.0/sqrt(15.0));
     ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2], dot3(f1, f2), 1e-6);
     ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2]+f1[3]*f2[3], dot4(f1, f2), 1e-6);
     ASSERT(any(f1 > 0.5));

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

@@ -73,9 +73,8 @@ class AmberPrmtopFile(object):
 
     def __init__(self, file):
         """Load a prmtop file."""
-        top = Topology()
         ## The Topology read from the prmtop file
-        self.topology = top
+        self.topology = top = Topology()
         self.elements = []
 
         # Load the prmtop file
@@ -229,7 +228,7 @@ class AmberPrmtopFile(object):
         elif implicitSolvent is None:
             implicitSolventKappa = 0.0
 
-        sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString,
+        sys = amber_file_parser.readAmberSystem(self.topology, prmtop_loader=self._prmtop, shake=constraintString,
                         nonbondedCutoff=nonbondedCutoff, nonbondedMethod=methodMap[nonbondedMethod],
                         flexibleConstraints=False, gbmodel=implicitString, soluteDielectric=soluteDielectric,
                         solventDielectric=solventDielectric, implicitSolventKappa=implicitSolventKappa,

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

@@ -37,6 +37,7 @@ from __future__ import division
 from functools import wraps
 from math import pi, cos, sin, sqrt
 import os
+import re
 import simtk.openmm as mm
 from simtk.openmm.vec3 import Vec3
 import simtk.unit as u
@@ -99,6 +100,8 @@ class _ZeroDict(dict):
 
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
+_resre = re.compile(r'(\d+)([a-zA-Z]*)')
+
 class CharmmPsfFile(object):
     """
     A chemical structure instantiated from CHARMM files.
@@ -192,11 +195,13 @@ class CharmmPsfFile(object):
         atom_list = AtomList()
         for i in xrange(natom):
             words = psfsections['NATOM'][1][i].split()
-            atid = int(words[0])
-            if atid != i + 1:
-                raise CharmmPSFError('Nonsequential atoms detected!')
             system = words[1]
-            resid = conv(words[2], int, 'residue number')
+            rematch = _resre.match(words[2])
+            if not rematch:
+                raise RuntimeError('Could not parse residue number %s' %
+                                   words[2])
+            resid, inscode = rematch.groups()
+            resid = int(resid)
             resname = words[3]
             name = words[4]
             attype = words[5]
@@ -209,7 +214,7 @@ class CharmmPsfFile(object):
             mass = conv(words[7], float, 'atomic mass')
             props = words[8:]
             atom = residue_list.add_atom(system, resid, resname, name,
-                                         attype, charge, mass, props)
+                            attype, charge, mass, inscode, props)
             atom_list.append(atom)
         atom_list.assign_indexes()
         atom_list.changed = False
@@ -443,175 +448,6 @@ class CharmmPsfFile(object):
                 line = psf.readline().strip()
         return title, pointers, data
 
-    def writePsf(self, dest, vmd=False):
-        """
-        Writes a PSF file from the stored molecule
-
-        Parameters:
-            - dest (str or file-like) : The place to write the output PSF file.
-                    If it has a "write" attribute, it will be used to print the
-                    PSF file. Otherwise, it will be treated like a string and a
-                    file will be opened, printed, then closed
-            - vmd (bool) : If True, it will write out a PSF in the format that
-                    VMD prints it in (i.e., no NUMLP/NUMLPH or MOLNT sections)
-        Example:
-            >>> cs = CharmmPsfFile('testfiles/test.psf')
-            >>> cs.writePsf('testfiles/test2.psf')
-        """
-        # See if this is an extended format
-        ext = 'EXT' in self.flags
-        own_handle = False
-        # Index the atoms and residues
-        self.residue_list.assign_indexes()
-        self.atom_list.assign_indexes()
-        if not hasattr(dest, 'write'):
-            own_handle = True
-            dest = open(dest, 'w')
-
-        # Assign the formats we need to write with
-        if ext:
-            atmfmt1 = ('%10d %-8s %-8i %-8s %-8s %4d %10.6f %13.4f' + 11*' ')
-            atmfmt2 = ('%10d %-8s %-8i %-8s %-8s %-4s %10.6f %13.4f' + 11*' ')
-            intfmt = '%10d' # For pointers
-        else:
-            atmfmt1 = ('%8d %-4s %-4i %-4s %-4s %4d %10.6f %13.4f' + 11*' ')
-            atmfmt2 = ('%8d %-4s %-4i %-4s %-4s %-4s %10.6f %13.4f' + 11*' ')
-            intfmt = '%8d' # For pointers
-
-        # Now print the header then the title
-        dest.write('PSF ' + ' '.join(self.flags) + '\n')
-        dest.write('\n')
-        dest.write(intfmt % len(self.title) + ' !NTITLE\n')
-        dest.write('\n'.join(self.title) + '\n\n')
-        # Now time for the atoms
-        dest.write(intfmt % len(self.atom_list) + ' !NATOM\n')
-        # atmfmt1 is for CHARMM format (i.e., atom types are integers)
-        # atmfmt is for XPLOR format (i.e., atom types are strings)
-        for i, atom in enumerate(self.atom_list):
-            if isinstance(atom.attype, str):
-                fmt = atmfmt2
-            else:
-                fmt = atmfmt1
-            atmstr = fmt % (i+1, atom.system, atom.residue.resnum,
-                            atom.residue.resname, atom.name, atom.attype,
-                            atom.charge, atom.mass)
-            dest.write(atmstr + '   '.join(atom.props) + '\n')
-        dest.write('\n')
-        # Bonds
-        dest.write(intfmt % len(self.bond_list) + ' !NBOND: bonds\n')
-        for i, bond in enumerate(self.bond_list):
-            dest.write((intfmt*2) % (bond.atom1.idx+1, bond.atom2.idx+1))
-            if i % 4 == 3: # Write 4 bonds per line
-                dest.write('\n')
-        # See if we need to terminate
-        if len(self.bond_list) % 4 != 0 or len(self.bond_list) == 0:
-            dest.write('\n')
-        dest.write('\n')
-        # Angles
-        dest.write(intfmt % len(self.angle_list) + ' !NTHETA: angles\n')
-        for i, angle in enumerate(self.angle_list):
-            dest.write((intfmt*3) % (angle.atom1.idx+1, angle.atom2.idx+1,
-                                     angle.atom3.idx+1)
-            )
-            if i % 3 == 2: # Write 3 angles per line
-                dest.write('\n')
-        # See if we need to terminate
-        if len(self.angle_list) % 3 != 0 or len(self.angle_list) == 0:
-            dest.write('\n')
-        dest.write('\n')
-        # Dihedrals
-        dest.write(intfmt % len(self.dihedral_list) + ' !NPHI: dihedrals\n')
-        for i, dih in enumerate(self.dihedral_list):
-            dest.write((intfmt*4) % (dih.atom1.idx+1, dih.atom2.idx+1,
-                                     dih.atom3.idx+1, dih.atom4.idx+1)
-            )
-            if i % 2 == 1: # Write 2 dihedrals per line
-                dest.write('\n')
-        # See if we need to terminate
-        if len(self.dihedral_list) % 2 != 0 or len(self.dihedral_list) == 0:
-            dest.write('\n')
-        dest.write('\n')
-        # Impropers
-        dest.write(intfmt % len(self.improper_list) + ' !NIMPHI: impropers\n')
-        for i, imp in enumerate(self.improper_list):
-            dest.write((intfmt*4) % (imp.atom1.idx+1, imp.atom2.idx+1,
-                                     imp.atom3.idx+1, imp.atom4.idx+1)
-            )
-            if i % 2 == 1: # Write 2 dihedrals per line
-                dest.write('\n')
-        # See if we need to terminate
-        if len(self.improper_list) % 2 != 0 or len(self.improper_list) == 0:
-            dest.write('\n')
-        dest.write('\n')
-        # Donor section
-        dest.write(intfmt % len(self.donor_list) + ' !NDON: donors\n')
-        for i, don in enumerate(self.donor_list):
-            dest.write((intfmt*2) % (don.atom1.idx+1, don.atom2.idx+1))
-            if i % 4 == 3: # 4 donors per line
-                dest.write('\n')
-        if len(self.donor_list) % 4 != 0 or len(self.donor_list) == 0:
-            dest.write('\n')
-        dest.write('\n')
-        # Acceptor section
-        dest.write(intfmt % len(self.acceptor_list) + ' !NACC: acceptors\n')
-        for i, acc in enumerate(self.acceptor_list):
-            dest.write((intfmt*2) % (acc.atom1.idx+1, acc.atom2.idx+1))
-            if i % 4 == 3: # 4 donors per line
-                dest.write('\n')
-        if len(self.acceptor_list) % 4 != 0 or len(self.acceptor_list) == 0:
-            dest.write('\n')
-        dest.write('\n')
-        # NNB section ??
-        dest.write(intfmt % 0 + ' !NNB\n\n')
-        for i in range(len(self.atom_list)):
-            dest.write(intfmt % 0)
-            if i % 8 == 7: # Write 8 0's per line
-                dest.write('\n')
-        if len(self.atom_list) % 8 != 0: dest.write('\n')
-        dest.write('\n')
-        # Group section
-        dest.write((intfmt*2) % (len(self.group_list), self.group_list.nst2))
-        dest.write(' !NGRP NST2\n')
-        for i, gp in enumerate(self.group_list):
-            dest.write((intfmt*3) % (gp.bs, gp.type, gp.move))
-            if i % 3 == 2: dest.write('\n')
-        if len(self.group_list) % 3 != 0 or len(self.group_list) == 0:
-            dest.write('\n')
-        dest.write('\n')
-        # The next two sections are never found in VMD prmtops...
-        if not vmd:
-            # Molecule section; first set molecularity
-            set_molecules(self.atom_list)
-            mollist = [a.marked for a in self.atom_list]
-            dest.write(intfmt % max(mollist) + ' !MOLNT\n')
-            for i, atom in enumerate(self.atom_list):
-                dest.write(intfmt % atom.marked)
-                if i % 8 == 7: dest.write('\n')
-            if len(self.atom_list) % 8 != 0: dest.write('\n')
-            dest.write('\n')
-            # NUMLP/NUMLPH section
-            dest.write((intfmt*2) % (0, 0) + ' !NUMLP NUMLPH\n')
-            dest.write('\n')
-        # CMAP section
-        dest.write(intfmt % len(self.cmap_list) + ' !NCRTERM: cross-terms\n')
-        for i, cmap in enumerate(self.cmap_list):
-            dest.write((intfmt*4) % (cmap.atom1.idx+1, cmap.atom2.idx+1,
-                                     cmap.atom3.idx+1, cmap.atom4.idx+1)
-            )
-            if cmap.consecutive:
-                dest.write((intfmt*4) % (cmap.atom2.idx+1, cmap.atom3.idx+1,
-                                         cmap.atom4.idx+1, cmap.atom5.idx+1)
-                )
-            else:
-                dest.write((intfmt*4) % (cmap.atom5.idx+1, cmap.atom6.idx+1,
-                                         cmap.atom7.idx+1, cmap.atom8.idx+1)
-                )
-            dest.write('\n')
-        # Done!
-        # If we opened our own handle, close it
-        if own_handle:
-            dest.close()
-        
     def loadParameters(self, parmset):
         """
         Loads parameters from a parameter set that was loaded via CHARMM RTF,
@@ -776,13 +612,13 @@ class CharmmPsfFile(object):
         last_residue = None
         # Add each chain (separate 'system's) and residue
         for atom in self.atom_list:
+            resid = '%d%s' % (atom.residue.idx, atom.residue.inscode)
             if atom.system != last_chain:
                 chain = topology.addChain(atom.system)
                 last_chain = atom.system
-            if atom.residue.idx != last_residue:
-                last_residue = atom.residue.idx
-                residue = topology.addResidue(atom.residue.resname, chain,
-                                              str(atom.residue.idx))
+            if resid != last_residue:
+                last_residue = resid
+                residue = topology.addResidue(atom.residue.resname, chain, resid)
             if atom.type is not None:
                 # This is the most reliable way of determining the element
                 atomic_num = atom.type.atomic_number

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

@@ -37,6 +37,8 @@ import time
 import struct
 import math
 from simtk.unit import picoseconds, nanometers, angstroms, is_quantity, norm
+from simtk.openmm import Vec3
+from simtk.openmm.app.internal.unitcell import computeLengthsAndAngles
 
 class DCDFile(object):
     """DCDFile provides methods for creating DCD files.
@@ -112,16 +114,16 @@ class DCDFile(object):
         file.seek(0, os.SEEK_END)
         boxVectors = self._topology.getPeriodicBoxVectors()
         if boxVectors is not None:
-            if getPeriodicBoxVectors is not None:
-                boxVectors = getPeriodicBoxVectors
+            if periodicBoxVectors is not None:
+                boxVectors = periodicBoxVectors
             elif unitCellDimensions is not None:
                 if is_quantity(unitCellDimensions):
                     unitCellDimensions = unitCellDimensions.value_in_unit(nanometers)
                 boxVectors = (Vec3(unitCellDimensions[0], 0, 0), Vec3(0, unitCellDimensions[1], 0), Vec3(0, 0, unitCellDimensions[2]))*nanometers
             (a_length, b_length, c_length, alpha, beta, gamma) = computeLengthsAndAngles(boxVectors)
-            a_length = a_length.value_in_unit(angstroms)
-            b_length = b_length.value_in_unit(angstroms)
-            c_length = c_length.value_in_unit(angstroms)
+            a_length = a_length * 10.  # computeLengthsAndAngles returns unitless nanometers, but need angstroms here.
+            b_length = b_length * 10.  # computeLengthsAndAngles returns unitless nanometers, but need angstroms here.
+            c_length = c_length * 10.  # computeLengthsAndAngles returns unitless nanometers, but need angstroms here.
             angle1 = math.sin(math.pi/2-gamma)
             angle2 = math.sin(math.pi/2-beta)
             angle3 = math.sin(math.pi/2-alpha)

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

@@ -31,7 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 __author__ = "Christopher M. Bruns"
 __version__ = "1.0"
 
-
+from collections import OrderedDict
 from simtk.unit import daltons, is_quantity
 import copy_reg
 
@@ -47,6 +47,7 @@ class Element(object):
 
     _elements_by_symbol = {}
     _elements_by_atomic_number = {}
+    _elements_by_mass = None
 
     def __init__(self, number, name, symbol, mass):
         """Create a new element
@@ -67,8 +68,11 @@ class Element(object):
         self._mass = mass
         # Index this element in a global table
         s = symbol.strip().upper()
+        ## If we add a new element, we need to re-hash elements by mass
+        Element._elements_by_mass = None
 
-        assert s not in Element._elements_by_symbol
+        if s in Element._elements_by_symbol:
+            raise ValueError('Duplicate element symbol %s' % s)
         Element._elements_by_symbol[s] = self
         if number in Element._elements_by_atomic_number:
             other_element = Element._elements_by_atomic_number[number]
@@ -96,20 +100,45 @@ class Element(object):
         """
         Get the element whose mass is CLOSEST to the requested mass. This method
         should not be used for repartitioned masses
+
+        Parameters
+        ----------
+        mass : float or Quantity
+            Mass of the atom to find the element for. Units assumed to be
+            daltons if not specified
+
+        Returns
+        -------
+        element : Element
+            The element whose atomic mass is closest to the input mass
         """
         # Assume masses are in daltons if they are not units
-        if not is_quantity(mass):
-            mass = mass * daltons
+        if is_quantity(mass):
+            mass = mass.value_in_unit(daltons)
+        if mass < 0:
+            raise ValueError('Invalid Higgs field')
+        # If this is our first time calling getByMass (or we added an element
+        # since the last call), re-generate the ordered by-mass dict cache
+        if Element._elements_by_mass is None:
+            Element._elements_by_mass = OrderedDict()
+            for elem in sorted(Element._elements_by_symbol.values(),
+                               key=lambda x: x.mass):
+                Element._elements_by_mass[elem.mass] = elem
+
         diff = mass
         best_guess = None
 
-        for key in Element._elements_by_atomic_number:
-            element = Element._elements_by_atomic_number[key]
-            massdiff = abs(element.mass - mass)
+        for elemmass, element in Element._elements_by_mass.iteritems():
+            massdiff = abs(elemmass._value - mass)
             if massdiff < diff:
                 best_guess = element
                 diff = massdiff
+            if elemmass._value > mass:
+                # Elements are only getting heavier, so bail out early
+                return best_guess
 
+        # This really should only happen if we wanted ununoctium or something
+        # bigger... won't really happen but still make sure we return an Element
         return best_guess
 
     @property
@@ -145,6 +174,9 @@ def _pickle_element(element):
 
 copy_reg.pickle(Element, _pickle_element)
 
+# NOTE: getElementByMass assumes all masses are Quantity instances with unit
+# "daltons". All elements need to obey this assumption, or that method will
+# fail. No checking is done in getElementByMass for performance reasons
 hydrogen =       Element(  1, "hydrogen", "H", 1.007947*daltons)
 deuterium =      Element(  1, "deuterium", "D", 2.01355321270*daltons)
 helium =         Element(  2, "helium", "He", 4.003*daltons)

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

@@ -122,21 +122,22 @@ class PrmtopLoader(object):
 
         with open(inFilename, 'r') as fIn:
             for line in fIn:
-                if line.startswith('%VERSION'):
-                    tag, self._prmtopVersion = line.rstrip().split(None, 1)
-                elif line.startswith('%FLAG'):
-                    tag, flag = line.rstrip().split(None, 1)
-                    self._flags.append(flag)
-                    self._raw_data[flag] = []
-                elif line.startswith('%FORMAT'):
-                    format = line.rstrip()
-                    index0=format.index('(')
-                    index1=format.index(')')
-                    format = format[index0+1:index1]
-                    m = FORMAT_RE_PATTERN.search(format)
-                    self._raw_format[self._flags[-1]] = (format, m.group(1), m.group(2), m.group(3), m.group(4))
-                elif line.startswith('%COMMENT'):
-                    continue
+                if line[0] == '%':
+                    if line.startswith('%VERSION'):
+                        tag, self._prmtopVersion = line.rstrip().split(None, 1)
+                    elif line.startswith('%FLAG'):
+                        tag, flag = line.rstrip().split(None, 1)
+                        self._flags.append(flag)
+                        self._raw_data[flag] = []
+                    elif line.startswith('%FORMAT'):
+                        format = line.rstrip()
+                        index0=format.index('(')
+                        index1=format.index(')')
+                        format = format[index0+1:index1]
+                        m = FORMAT_RE_PATTERN.search(format)
+                        self._raw_format[self._flags[-1]] = (format, m.group(1), m.group(2), int(m.group(3)), m.group(4))
+                    elif line.startswith('%COMMENT'):
+                        continue
                 elif self._flags \
                      and 'TITLE'==self._flags[-1] \
                      and not self._raw_data['TITLE']:
@@ -144,8 +145,7 @@ class PrmtopLoader(object):
                 else:
                     flag=self._flags[-1]
                     (format, numItems, itemType,
-                     itemLength, itemPrecision) = self._getFormat(flag)
-                    iLength=int(itemLength)
+                     iLength, itemPrecision) = self._getFormat(flag)
                     line = line.rstrip()
                     for index in range(0, len(line), iLength):
                         item = line[index:index+iLength]
@@ -305,6 +305,10 @@ class PrmtopLoader(object):
             return self._nonbondTerms
         except AttributeError:
             pass
+        # Check if there are any non-zero HBOND terms
+        for x, y in zip(self._raw_data['HBOND_ACOEF'], self._raw_data['HBOND_BCOEF']):
+            if float(x) or float(y):
+                raise Exception('10-12 interactions are not supported')
         self._nonbondTerms=[]
         lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
         energyConversionFactor = units.kilocalorie_per_mole.conversion_factor_to(units.kilojoule_per_mole)
@@ -333,6 +337,7 @@ class PrmtopLoader(object):
         for i in range(numTypes):
             for j in range(numTypes):
                 index = int(self._raw_data['NONBONDED_PARM_INDEX'][numTypes*i+j]) - 1
+                if index < 0: continue
                 rij = type_parameters[i][0] + type_parameters[j][0]
                 wdij = sqrt(type_parameters[i][1] * type_parameters[j][1])
                 a = float(self._raw_data['LENNARD_JONES_ACOEF'][index])
@@ -477,6 +482,7 @@ class PrmtopLoader(object):
                     typ1 = atomTypeIndexes[iAtom] - 1
                     typ2 = atomTypeIndexes[lAtom] - 1
                     idx = nbidx[numTypes*typ1+typ2] - 1
+                    if idx < 0: continue
                     a = parm_acoef[idx]
                     b = parm_bcoef[idx]
                     try:
@@ -645,7 +651,7 @@ class PrmtopLoader(object):
 # AMBER System builder (based on, but not identical to, systemManager from 'zander')
 #=============================================================================================
 
-def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None,
+def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=None, gbmodel=None,
           soluteDielectric=1.0, solventDielectric=78.5,
           implicitSolventKappa=0.0*(1/units.nanometer), nonbondedCutoff=None,
           nonbondedMethod='NoCutoff', scee=None, scnb=None, mm=None, verbose=False,
@@ -653,6 +659,9 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     """
     Create an OpenMM System from an Amber prmtop file.
 
+    REQUIRED ARGUMENT
+      topology (forcefield.Topology) The topology for the system that is about
+      to be created
     ARGUMENTS (specify  one or the other, but not both)
       prmtop_filename (String) - name of Amber prmtop file (new-style only)
       prmtop_loader (PrmtopLoader) - the loaded prmtop file
@@ -733,7 +742,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
         system.addParticle(mass)
 
     # Add constraints.
-    isWater = [prmtop.getResidueLabel(i) in ('WAT', 'TP4', 'TP5', 'T4E') for i in range(prmtop.getNumAtoms())]
+    isWater = [prmtop.getResidueLabel(i) in ('WAT', 'HOH', 'TP4', 'TP5', 'T4E') for i in range(prmtop.getNumAtoms())]
     if shake in ('h-bonds', 'all-bonds', 'h-angles'):
         for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
             system.addConstraint(iAtom, jAtom, rMin)
@@ -768,13 +777,14 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             distance = c[2].value_in_unit(units.nanometer)
             atomConstraints[c[0]].append((c[1], distance))
             atomConstraints[c[1]].append((c[0], distance))
+    topatoms = list(topology.atoms())
     for (iAtom, jAtom, kAtom, k, aMin) in prmtop.getAngles():
         if shake == 'h-angles':
-            type1 = prmtop.getAtomType(iAtom)
-            type2 = prmtop.getAtomType(jAtom)
-            type3 = prmtop.getAtomType(kAtom)
-            numH = len([type for type in (type1, type3) if type.startswith('H')])
-            constrained = (numH == 2 or (numH == 1 and type2.startswith('O')))
+            atomI = topatoms[iAtom]
+            atomJ = topatoms[jAtom]
+            atomK = topatoms[kAtom]
+            numH = ((atomI.element.atomic_number == 1) + (atomK.element.atomic_number == 1))
+            constrained = (numH == 2 or (numH == 1 and atomJ.element is elem.oxygen))
         else:
             constrained = False
         if constrained:
@@ -870,6 +880,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
         for i in range(numTypes):
             for j in range(numTypes):
                 idx = nbidx[numTypes*i+j] - 1
+                if idx < 0: continue
                 acoef[i+numTypes*j] = sqrt(parm_acoef[idx]) * afac
                 bcoef[i+numTypes*j] = parm_bcoef[idx] * bfac
         if has_1264:
@@ -878,6 +889,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             for i in range(numTypes):
                 for j in range(numTypes):
                     idx = nbidx[numTypes*i+j] - 1
+                    if idx < 0: continue
                     ccoef[i+numTypes*j] = parm_ccoef[idx] * cfac
             cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6-c/r^4; r6=r^6;'
                                              'a=acoef(type1, type2);'
@@ -911,6 +923,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             for i in range(numTypes):
                 for j in range(numTypes):
                     idx = nbidx[numTypes*i+j] - 1
+                    if idx < 0: continue
                     ccoef[i+numTypes*j] = parm_ccoef[idx] * cfac
             cforce = mm.CustomNonbondedForce('-c/r^4; c=ccoef(type1, type2)')
             cforce.addTabulatedFunction('ccoef',

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -375,12 +375,13 @@ class AtomList(TrackedList):
 class Residue(object):
     """ Residue class """
 
-    def __init__(self, resname, idx):
+    def __init__(self, resname, idx, inscode=''):
         self.resname = resname
         self.idx = idx
         self.atoms = []
         self.resnum = None # Numbered based on SYSTEM name
         self.system = None
+        self.inscode = inscode
 
     def add_atom(self, atom):
         if self.system is None:
@@ -416,7 +417,7 @@ class Residue(object):
             return self.resname == thing.resname and self.idx == thing.idx
         if isinstance(thing, tuple) or isinstance(thing, list):
             # Must be resnum, resname
-            return thing == (self.resname, self.idx)
+            return thing == (self.resname, self.idx, self.inscode)
         return False # No other type can be equal.
 
     def __ne__(self, thing):
@@ -447,7 +448,7 @@ class ResidueList(list):
             resnum += 1
 
     def add_atom(self, system, resnum, resname, name,
-                 attype, charge, mass, props=None):
+                 attype, charge, mass, inscode, props=None):
         """
         Adds an atom to the list of residues. If the residue is not the same as
         the last residue that was created, a new Residue is created and added
@@ -461,25 +462,22 @@ class ResidueList(list):
             - attype (int or str) : Type of the atom
             - charge (float) : Partial atomic charge of the atom
             - mass (float) : Mass (amu) of the atom
+            - inscode (str) : Insertion code, if it is specified
 
         Returns:
             The Atom instance created and added to the list of residues
         """
-        if self._last_residue is None:
-            res = self._last_residue = Residue(resname, resnum)
+        lr = self._last_residue
+        if lr is None:
+            res = self._last_residue = Residue(resname, resnum, inscode)
             list.append(self, res)
-        elif (self._last_residue != (resname, resnum) or
-              system != self._last_residue.system):
-            if (self._last_residue.idx == resnum and
-                self._last_residue.system == system):
-                lresname = self._last_residue.resname
-                warnings.warn('Residue %d split into separate residues %s '
-                              'and %s' % (resnum, lresname, resname),
-                              SplitResidueWarning)
-            res = self._last_residue = Residue(resname, resnum)
+        elif (lr.resname != resname or lr.idx != resname or
+                lr.inscode != inscode  or system != lr.system):
+            res = self._last_residue = Residue(resname, resnum, inscode)
+            res.system = system
             list.append(self, res)
         else:
-            res = self._last_residue
+            res = lr
         atom = Atom(system, name, attype, float(charge), float(mass), props)
         res.add_atom(atom)
         return atom