Merge remote-tracking branch 'origin/master' into qc

platforms/opencl/tests/TestOpenCLVirtualSites.cpp

@@ -524,6 +524,47 @@ void testReordering() {
     }
 }
 
+/**
+ * Test a System where multiple virtual sites are all calculated from the same particles.
+ */
+void testOverlappingSites() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    NonbondedForce* nonbonded = new NonbondedForce();
+    system.addForce(nonbonded);
+    nonbonded->addParticle(1.0, 0.0, 0.0);
+    nonbonded->addParticle(-0.5, 0.0, 0.0);
+    nonbonded->addParticle(-0.5, 0.0, 0.0);
+    vector<Vec3> positions;
+    positions.push_back(Vec3(0, 0, 0));
+    positions.push_back(Vec3(10, 0, 0));
+    positions.push_back(Vec3(0, 10, 0));
+    for (int i = 0; i < 20; i++) {
+        system.addParticle(0.0);
+        double u = 0.1*((i+1)%4);
+        double v = 0.05*i;
+        system.setVirtualSite(3+i, new ThreeParticleAverageSite(0, 1, 2, u, v, 1-u-v));
+        nonbonded->addParticle(i%2 == 0 ? -1.0 : 1.0, 0.0, 0.0);
+        positions.push_back(Vec3());
+    }
+    VerletIntegrator i1(0.002);
+    VerletIntegrator i2(0.002);
+    Context c1(system, i1, Platform::getPlatformByName("Reference"));
+    Context c2(system, i2, platform);
+    c1.setPositions(positions);
+    c2.setPositions(positions);
+    c1.applyConstraints(0.0001);
+    c2.applyConstraints(0.0001);
+    State s1 = c1.getState(State::Positions | State::Forces);
+    State s2 = c2.getState(State::Positions | State::Forces);
+    for (int i = 0; i < system.getNumParticles(); i++)
+        ASSERT_EQUAL_VEC(s1.getPositions()[i], s2.getPositions()[i], 1e-5);
+    for (int i = 0; i < 3; i++)
+        ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 1e-5);
+}
+
 int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
@@ -535,6 +576,7 @@ int main(int argc, char* argv[]) {
         testLocalCoordinates();
         testConservationLaws();
         testReordering();
+        testOverlappingSites();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

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

@@ -126,13 +126,15 @@ public:
      * Set the torsion-torsion grid at the specified index
      *
      * @param index         the index of the torsion-torsion for which to get parameters
-     * @param grid          grid
+     * @param grid          either 3 or 6 values may be specified per grid point.  If the derivatives
+     *                      are omitted, they are calculated automatically by fitting a 2D spline to
+     *                      the energies.
      *                         grid[x][y][0] = x value
      *                         grid[x][y][1] = y value
-     *                         grid[x][y][2] = function value
-     *                         grid[x][y][3] = dfdx value
-     *                         grid[x][y][4] = dfdy value
-     *                         grid[x][y][5] = dfd(xy) value
+     *                         grid[x][y][2] = energy
+     *                         grid[x][y][3] = dEdx value
+     *                         grid[x][y][4] = dEdy value
+     *                         grid[x][y][5] = dEd(xy) value
      */
     void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
 
@@ -181,29 +183,7 @@ public:
         _spacing[0]     = _spacing[1]     = 1.0;
     }
 
-    TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
-
-        _grid.resize(grid.size());
-        for(unsigned int kk = 0; kk < grid.size(); kk++){
-            _grid[kk].resize(grid[kk].size());
-            for(unsigned int jj = 0; jj < grid[kk].size(); jj++){
-                _grid[kk][jj].resize(grid[kk][jj].size());
-                for(unsigned int ii = 0; ii < grid[kk][jj].size(); ii++){
-                    _grid[kk][jj][ii] = grid[kk][jj][ii];
-                }
-            }
-        }
-
-        _startValues[0] =  _grid[0][0][0];
-        _startValues[1] =  _grid[0][0][1];
-
-        _spacing[0]     = static_cast<double>(_grid.size()-1)/360.0;
-        _spacing[1]     = static_cast<double>(grid.size()-1)/360.0;
-
-        _size[0]        = static_cast<int>(grid.size());
-        _size[1]        = static_cast<int>(grid[0].size());
-
-    }
+    TorsionTorsionGridInfo(const TorsionTorsionGrid& grid);
 
     const TorsionTorsionGrid& getTorsionTorsionGrid(void) const {
         return _grid;

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,8 +33,10 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/AmoebaTorsionTorsionForce.h"
 #include "openmm/internal/AmoebaTorsionTorsionForceImpl.h"
+#include "openmm/internal/SplineFitter.h"
 
 using namespace OpenMM;
+using namespace std;
 
 AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() {
 }
@@ -82,3 +84,102 @@ void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTo
 ForceImpl* AmoebaTorsionTorsionForce::createImpl() const {
     return new AmoebaTorsionTorsionForceImpl(*this);
 }
+
+AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
+    if (grid[0][0][0] != grid[1][0][0])
+        _grid = grid;
+    else {
+        // We need to transpose the grid.
+        
+        int xsize = grid[0].size();
+        int ysize = grid.size();
+        _grid.resize(xsize);
+        for (int i = 0; i < xsize; i++) {
+            _grid[i].resize(ysize);
+            for (int j = 0; j < ysize; j++)
+                _grid[i][j] = grid[j][i];
+        }
+    }
+
+    _startValues[0] =  _grid[0][0][0];
+    _startValues[1] =  _grid[0][0][1];
+
+    _spacing[0]     = static_cast<double>(_grid.size()-1)/360.0;
+    _spacing[1]     = static_cast<double>(_grid.size()-1)/360.0;
+
+    _size[0]        = static_cast<int>(_grid.size());
+    _size[1]        = static_cast<int>(_grid[0].size());
+    
+    if (_grid[0][0].size() == 3) {
+        // We need to compute the derivatives ourselves.  First determine if the grid is periodic.
+        
+        int xsize = _size[0];
+        int ysize = _size[1];
+        bool periodic = true;
+        for (int i = 0; i < xsize; i++)
+            if (_grid[i][0][2] != _grid[i][ysize-1][2])
+                periodic = false;
+        for (int i = 0; i < ysize; i++)
+            if (_grid[0][i][2] != _grid[xsize-1][i][2])
+                periodic = false;
+        
+        // Compute derivatives with respect to the first angle.
+
+        vector<double> x(xsize), y(ysize);
+        for (int i = 0; i < xsize; i++)
+            x[i] = _grid[i][0][0];
+        for (int i = 0; i < ysize; i++)
+            y[i] = _grid[0][i][1];
+        vector<double> d1(xsize*ysize), d2(xsize*ysize), d12(xsize*ysize);
+        vector<double> t(xsize), deriv(xsize);
+        for (int i = 0; i < ysize; i++) {
+            for (int j = 0; j < xsize; j++)
+                t[j] = _grid[j][i][2];
+            if (periodic)
+                SplineFitter::createPeriodicSpline(x, t, deriv);
+            else
+                SplineFitter::createNaturalSpline(x, t, deriv);
+            for (int j = 0; j < xsize; j++)
+                d1[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
+        }
+
+        // Compute derivatives with respect to the second angle.
+
+        t.resize(ysize);
+        deriv.resize(ysize);
+        for (int i = 0; i < xsize; i++) {
+            for (int j = 0; j < ysize; j++)
+                t[j] = _grid[i][j][2];
+            if (periodic)
+                SplineFitter::createPeriodicSpline(y, t, deriv);
+            else
+                SplineFitter::createNaturalSpline(y, t, deriv);
+            for (int j = 0; j < ysize; j++)
+                d2[i+xsize*j] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[j]);
+        }
+
+        // Compute cross derivatives.
+
+        t.resize(xsize);
+        deriv.resize(xsize);
+        for (int i = 0; i < ysize; i++) {
+            for (int j = 0; j < xsize; j++)
+                t[j] = d2[j+xsize*i];
+            if (periodic)
+                SplineFitter::createPeriodicSpline(x, t, deriv);
+            else
+                SplineFitter::createNaturalSpline(x, t, deriv);
+            for (int j = 0; j < xsize; j++)
+                d12[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
+        }
+        
+        // Add the derivatives to the grid.
+        
+        for (int i = 0; i < xsize; i++)
+            for (int j = 0; j < ysize; j++) {
+                _grid[i][j].push_back(d1[i+xsize*j]);
+                _grid[i][j].push_back(d2[i+xsize*j]);
+                _grid[i][j].push_back(d12[i+xsize*j]);
+            }
+    }
+}

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp

@@ -49,7 +49,7 @@ extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
 
 const double TOL = 1e-4;
 
-TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {
+TorsionTorsionGrid getTorsionGrid(int gridIndex, bool includeDerivs) {
 
 static double grid[4][625][6] = { 
     {
@@ -2557,35 +2557,32 @@ static double grid[4][625][6] = {
 {     165.0000,     180.0000, -0.182999000E+01,  0.377952854E-01,  0.233583295E-01, -0.109828932E-02 }, 
 {     180.0000,     180.0000, -0.146854000E+01,  0.491175487E-02,  0.195601580E-02, -0.163177030E-02 }  } };
 
-    // static std::vector< std::vector< std::vector<double> > > TorsionTorsionGrid
-    static std::vector<TorsionTorsionGrid> grids;
-    if( grids.size() == 0 ){
-        grids.resize(4);
-        for( int ii = 0; ii < 4; ii++ ){
-            grids[ii].resize( 25 );
-            for( int jj = 0; jj < 25; jj++ ){
-                grids[ii][jj].resize(25);
-                for( int kk = 0; kk < 25; kk++ ){
-                    grids[ii][jj][kk].resize(6);
-                }
+    int elementCount = (includeDerivs ? 6 : 3);
+    std::vector<TorsionTorsionGrid> grids(4);
+    for( int ii = 0; ii < 4; ii++ ){
+        grids[ii].resize( 25 );
+        for( int jj = 0; jj < 25; jj++ ){
+            grids[ii][jj].resize(25);
+            for( int kk = 0; kk < 25; kk++ ){
+                grids[ii][jj][kk].resize(elementCount);
             }
-            int index = 0;
-            for( int jj = 0; jj < 25; jj++ ){
-                for( int kk = 0; kk < 25; kk++ ){
-                    int jjIndex = static_cast<int>(((grid[ii][index][0] + 180.0)/15.0)+1.0e-05);
-                    int kkIndex = static_cast<int>(((grid[ii][index][1] + 180.0)/15.0)+1.0e-05);
-                    for( int ll = 0; ll < 6; ll++ ){
-                        grids[ii][kk][jj][ll] = grid[ii][index][ll];
-                    }
-                    index++;
+        }
+        int index = 0;
+        for( int jj = 0; jj < 25; jj++ ){
+            for( int kk = 0; kk < 25; kk++ ){
+                int jjIndex = static_cast<int>(((grid[ii][index][0] + 180.0)/15.0)+1.0e-05);
+                int kkIndex = static_cast<int>(((grid[ii][index][1] + 180.0)/15.0)+1.0e-05);
+                for( int ll = 0; ll < elementCount; ll++ ){
+                    grids[ii][kk][jj][ll] = grid[ii][index][ll];
                 }
+                index++;
             }
         }
     }
     return grids[gridIndex];
 }
 
-void testTorsionTorsion( FILE* log, int systemId ) {
+void testTorsionTorsion(int systemId, bool includeDerivs) {
 
     System system;
     int numberOfParticles = 6;
@@ -2645,11 +2642,11 @@ void testTorsionTorsion( FILE* log, int systemId ) {
 
         expectedEnergy        = -3.372536909E+00;
     }
-    amoebaTorsionTorsionForce->addTorsionTorsion( 0, 1, 2, 3, 4, chiralCheckAtomIndex, 0 );
-    amoebaTorsionTorsionForce->setTorsionTorsionGrid( 0, getTorsionGrid( gridIndex ) );
+    amoebaTorsionTorsionForce->addTorsionTorsion(0, 1, 2, 3, 4, chiralCheckAtomIndex, 0);
+    amoebaTorsionTorsionForce->setTorsionTorsionGrid(0, getTorsionGrid(gridIndex, includeDerivs));
     
     system.addForce(amoebaTorsionTorsionForce);
-    Context context(system, integrator, Platform::getPlatformByName( "Reference"));
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
 
     context.setPositions(positions);
     State state                      = context.getState(State::Forces | State::Energy);
@@ -2662,18 +2659,6 @@ void testTorsionTorsion( FILE* log, int systemId ) {
         forces[ii][2] *= conversion;
     }
 
-#ifdef AMOEBA_DEBUG
-    if( log ){
-        (void) fprintf( log, "computeAmoebaTorsionTorsionForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
-        for( unsigned int ii = 0; ii < forces.size(); ii++ ){
-            (void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]   [%14.7e %14.7e %14.7e]\n", ii,
-                            expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2],
-                            forces[ii][0], forces[ii][1], forces[ii][2] );
-        }
-        (void) fflush( log );
-    }
-#endif
-
     double tolerance = 1.0e-03;
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -2687,10 +2672,8 @@ int main( int numberOfArguments, char* argv[] ) {
     try {
         std::cout << "TestReferenceAmoebaTorsionTorsionForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
-        //registerAmoebaCudaKernelFactories();
-
-        FILE* log = NULL;
-        testTorsionTorsion( log, 1 );
+        testTorsionTorsion(1, true);
+        testTorsionTorsion(1, false);
     } catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;
         std::cout << "FAIL - ERROR.  Test failed." << std::endl;

plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp

@@ -33,8 +33,8 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/DrudeKernels.h"
-#include <cmath>
 #include <ctime>
 #include <string>
 
@@ -49,7 +49,7 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
     setDrudeFriction(drudeFrictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -33,10 +33,10 @@
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
 #include "openmm/RpmdKernels.h"
 #include "SimTKOpenMMRealType.h"
 #include <cmath>
-#include <ctime>
 #include <string>
 
 using namespace OpenMM;
@@ -48,7 +48,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
@@ -57,7 +57,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
     setFriction(frictionCoeff);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
-    setRandomNumberSeed((int) time(NULL));
+    setRandomNumberSeed(osrngseed());
 }
 
 void RPMDIntegrator::initialize(ContextImpl& contextRef) {

tests/TestFindExclusions.cpp

@@ -30,6 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/internal/AssertionUtilities.h"
+#include "openmm/CustomNonbondedForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/OpenMMException.h"
 #include <iostream>
@@ -166,10 +167,62 @@ void testReplaceExceptions() {
     ASSERT(charge == 5.0);
 }
 
+/**
+ * This is the same as testFindExceptions(), except it tests adding exclusions to a CustomNonbondedForce.
+ */
+
+void testFindCustomExclusions() {
+    CustomNonbondedForce nonbonded("r");
+    vector<pair<int, int> > bonds;
+    vector<double> params;
+    for (int i = 0; i < NUM_ATOMS; i++)
+        nonbonded.addParticle(params);
+    // loop over all main-chain atoms (even numbered atoms)
+    for (int i = 0; i < NUM_ATOMS-1; i += 2)
+    {
+        // side-chain bonds
+        bonds.push_back(pair<int, int>(i, i+1));
+        // main-chain bonds
+        if (i < NUM_ATOMS-2) // penultimate atom (NUM_ATOMS-2) has no subsequent main-chain atom
+            bonds.push_back(pair<int, int>(i, i+2));
+    }
+    nonbonded.createExclusionsFromBonds(bonds, 3);
+
+    // Build lists of the expected exclusions.
+
+    vector<set<int> > expectedExclusions(NUM_ATOMS);
+    int totalExclusions = 0;
+    for (int i = 0; i < NUM_ATOMS; i += 2) {
+        addAtomsToExclusions(i, i+1, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+2, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+3, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+4, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i+1, i+2, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+5, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+6, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i+1, i+3, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i+1, i+4, expectedExclusions, totalExclusions);
+    }
+    for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
+        int particle1, particle2;
+        nonbonded.getExclusionParticles(i, particle1, particle2);
+    }
+
+    // Compare them to the exceptions that were generated.
+
+    ASSERT_EQUAL(totalExclusions, nonbonded.getNumExclusions());
+    for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
+        int particle1, particle2;
+        nonbonded.getExclusionParticles(i, particle1, particle2);
+        ASSERT(expectedExclusions[particle1].find(particle2) != expectedExclusions[particle1].end());
+    }
+}
+
 int main() {
     try {
         testFindExceptions();
         testReplaceExceptions();
+        testFindCustomExclusions();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

wrappers/python/CMakeLists.txt

@@ -55,8 +55,12 @@ foreach(SUBDIR ${SUBDIRS})
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.parm7"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rst7"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.ncrst"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
+        "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.par"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
         "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
     )

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

@@ -6,9 +6,9 @@ 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) 2012-2014 Stanford University and the Authors.
 Authors: Peter Eastman
-Contributors:
+Contributors: Jason Swails
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -31,87 +31,97 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
+from functools import wraps
 from simtk.openmm.app.internal import amber_file_parser
 from simtk.unit import Quantity, nanometers, picoseconds
+import warnings
 try:
-    import numpy
+    import numpy as np
 except:
-    pass
+    np = None
+
+def numpy_protector(func):
+    """
+    Decorator to emit useful error messages if users try to request numpy
+    processing if numpy is not available. Raises ImportError if numpy could not
+    be found
+    """
+    @wraps(func)
+    def wrapper(self, asNumpy=False):
+        if asNumpy and np is None:
+            raise ImportError('Could not import numpy. Cannot set asNumpy=True')
+        return func(self, asNumpy=asNumpy)
+    return wrapper
 
 class AmberInpcrdFile(object):
     """AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it."""
 
-    def __init__(self, file, loadVelocities=False, loadBoxVectors=False):
+    def __init__(self, file, loadVelocities=None, loadBoxVectors=None):
         """Load an inpcrd file.
 
         An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
-        Unfortunately, it is sometimes impossible to determine from the file itself exactly what data
-        it contains.  You therefore must specify in advance what data to load.  It is stored into this
-        object's "positions", "velocities", and "boxVectors" fields.
 
         Parameters:
          - file (string) the name of the file to load
-         - loadVelocities (boolean=False) whether to load velocities from the file
-         - loadBoxVectors (boolean=False) whether to load the periodic box vectors
+         - loadVelocities (boolean=None) deprecated. Velocities are loaded automatically if present
+         - loadBoxVectors (boolean=None) deprecated. Box vectors are loaded automatically if present
         """
-        results = amber_file_parser.readAmberCoordinates(file, read_velocities=loadVelocities, read_box=loadBoxVectors)
-        if loadVelocities:
-            ## The atom positions read from the inpcrd file
-            self.positions = results[0]
-            if loadBoxVectors:
-                ## The periodic box vectors read from the inpcrd file
-                self.boxVectors = results[1]
-                ## The atom velocities read from the inpcrd file
-                self.velocities = results[2]
-            else:
-                self.velocities = results[1]
-        elif loadBoxVectors:
-            self.positions = results[0]
-            self.boxVectors = results[1]
-        else:
-            self.positions = results
+        self.file = file
+        if loadVelocities is not None or loadBoxVectors is not None:
+            warnings.warn('loadVelocities and loadBoxVectors have been '
+                          'deprecated. velocities and box information '
+                          'is loaded automatically if the inpcrd file contains '
+                          'them.', DeprecationWarning)
+        results = amber_file_parser.readAmberCoordinates(file)
+        self.positions, self.velocities, self.boxVectors = results
+        # Cached numpy arrays
         self._numpyPositions = None
-        if loadVelocities:
-            self._numpyVelocities = None
-        if loadBoxVectors:
-            self._numpyBoxVectors = None
+        self._numpyVelocities = None
+        self._numpyBoxVectors = None
 
+    @numpy_protector
     def getPositions(self, asNumpy=False):
         """Get the atomic positions.
 
         Parameters:
          - asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
-         """
+        """
         if asNumpy:
             if self._numpyPositions is None:
-                self._numpyPositions = Quantity(numpy.array(self.positions.value_in_unit(nanometers)), nanometers)
+                self._numpyPositions = Quantity(np.array(self.positions.value_in_unit(nanometers)), nanometers)
             return self._numpyPositions
         return self.positions
 
+    @numpy_protector
     def getVelocities(self, asNumpy=False):
         """Get the atomic velocities.
 
         Parameters:
          - asNumpy (boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s
-         """
+        """
+        if self.velocities is None:
+            raise AttributeError('velocities not found in %s' % self.file)
         if asNumpy:
             if self._numpyVelocities is None:
-                self._numpyVelocities = Quantity(numpy.array(self.velocities.value_in_unit(nanometers/picoseconds)), nanometers/picoseconds)
+                self._numpyVelocities = Quantity(np.array(self.velocities.value_in_unit(nanometers/picoseconds)), nanometers/picoseconds)
             return self._numpyVelocities
         return self.velocities
 
+    @numpy_protector
     def getBoxVectors(self, asNumpy=False):
         """Get the periodic box vectors.
 
         Parameters:
          - asNumpy (boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
-         """
+        """
+        if self.boxVectors is None:
+            raise AttributeError('Box information not found in %s' % self.file)
         if asNumpy:
             if self._numpyBoxVectors is None:
                 self._numpyBoxVectors = []
-                self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[0].value_in_unit(nanometers)), nanometers))
-                self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[1].value_in_unit(nanometers)), nanometers))
-                self._numpyBoxVectors.append(Quantity(numpy.array(self.boxVectors[2].value_in_unit(nanometers)), nanometers))
+                self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[0].value_in_unit(nanometers)), nanometers))
+                self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[1].value_in_unit(nanometers)), nanometers))
+                self._numpyBoxVectors.append(Quantity(np.array(self.boxVectors[2].value_in_unit(nanometers)), nanometers))
             return self._numpyBoxVectors
         return self.boxVectors
 

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

@@ -13,7 +13,7 @@ Copyright (c) 2014 the Authors
 
 Author: Jason Deckman
 Contributors: Jason M. Swails
-Date: April 19, 2014
+Date: June 6, 2014
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -105,7 +105,7 @@ class CharmmCrdFile(object):
                 self.resname.append(line[2])
                 self.attype.append(line[3])
                 pos = Vec3(float(line[4]), float(line[5]), float(line[6]))
-                self.positions.append(pos * u.angstroms)
+                self.positions.append(pos)
                 self.segid.append(line[7])
                 self.resid.append(int(line[8]))
                 self.weighting.append(float(line[9]))
@@ -120,6 +120,10 @@ class CharmmCrdFile(object):
         except (ValueError, IndexError), e:
             raise CharmmFileError('Error parsing CHARMM coordinate file')
 
+        # Apply units to the positions now. Do it this way to allow for
+        # (possible) numpy functionality in the future.
+        self.positions = u.Quantity(self.positions, u.angstroms)
+
 class CharmmRstFile(object):
     """
     Reads and parses data, velocities and coordinates from a CHARMM restart
@@ -209,8 +213,9 @@ class CharmmRstFile(object):
         self.velocities = [v * ONE_TIMESCALE for v in self.velocities]
 
         # Add units to positions and velocities
-        self.positions *= u.angstroms
-        self.velocities *= u.angstroms / u.picoseconds
+        self.positions = u.Quantity(self.positions, u.angstroms)
+        self.positionsold = u.Quantity(self.positionsold, u.angstroms)
+        self.velocities = u.Quantity(self.velocities, u.angstroms/u.picoseconds)
 
     def _scan(self, handle, str, r=0): # read lines in file until str is found
         scanning = True

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

@@ -241,6 +241,10 @@ class CharmmParameterSet(object):
             if line.startswith('HBOND'):
                 section = None
                 continue
+            # It seems like files? sections? can be terminated with 'END'
+            if line.startswith('END'): # should this be case-insensitive?
+                section = None
+                continue
             # If we have no section, skip
             if section is None: continue
             # Now handle each section specifically

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

@@ -90,6 +90,7 @@ class CharmmPsfFile(object):
         - bond_list
         - angle_list
         - dihedral_list
+        - dihedral_parameter_list
         - improper_list
         - cmap_list
         - donor_list    # hbonds donors?
@@ -349,6 +350,7 @@ class CharmmPsfFile(object):
         self.bond_list = bond_list
         self.angle_list = angle_list
         self.dihedral_list = dihedral_list
+        self.dihedral_parameter_list = TrackedList()
         self.improper_list = improper_list
         self.cmap_list = cmap_list
         self.donor_list = donor_list
@@ -599,9 +601,9 @@ class CharmmPsfFile(object):
               central atoms in impropers) and see if that matches.  Wild-cards
               will apply ONLY if specific parameters cannot be found.
 
-            - This method will expand the dihedral_list attribute by adding a
-              separate Dihedral object for each term for types that have a
-              multi-term expansion
+            - This method will expand the dihedral_parameter_list attribute by
+              adding a separate Dihedral object for each term for types that
+              have a multi-term expansion
         """
         # First load the atom types
         types_are_int = False
@@ -643,12 +645,9 @@ class CharmmPsfFile(object):
                     self.urey_bradley_list.append(ub)
             except KeyError:
                 raise MissingParameter('Missing angle type for %r' % ang)
-        # Next load all of the dihedrals. This is a little trickier since we
-        # need to back up the existing dihedral list and replace it with a
-        # longer one that has only one Fourier term per Dihedral instance.
-        dihedral_list = self.dihedral_list
-        self.dihedral_list = TrackedList()
-        for dih in dihedral_list:
+        # Next load all of the dihedrals.
+        self.dihedral_parameter_list = TrackedList()
+        for dih in self.dihedral_list:
             # Store the atoms
             a1, a2, a3, a4 = dih.atom1, dih.atom2, dih.atom3, dih.atom4
             at1, at2, at3, at4 = a1.attype, a2.attype, a3.attype, a4.attype
@@ -662,14 +661,14 @@ class CharmmPsfFile(object):
                                            '%r' % dih)
             dtlist = parmset.dihedral_types[key]
             for i, dt in enumerate(dtlist):
-                self.dihedral_list.append(Dihedral(a1, a2, a3, a4, dt))
+                self.dihedral_parameter_list.append(Dihedral(a1,a2,a3,a4,dt))
                 # See if we include the end-group interactions for this
                 # dihedral. We do IFF it is the last or only dihedral term and
                 # it is NOT in the angle/bond partners
                 if i != len(dtlist) - 1:
-                    self.dihedral_list[-1].end_groups_active = False
+                    self.dihedral_parameter_list[-1].end_groups_active = False
                 elif a1 in a4.bond_partners or a1 in a4.angle_partners:
-                    self.dihedral_list[-1].end_groups_active = False
+                    self.dihedral_parameter_list[-1].end_groups_active = False
         # Now do the impropers
         for imp in self.improper_list:
             # Store the atoms
@@ -755,6 +754,12 @@ class CharmmPsfFile(object):
             - alpha, beta, gamma (floats, optional) : Angles between the
                 periodic cells.
         """
+        try:
+            # Since we are setting the box, delete the cached box lengths if we
+            # have them to make sure they are recomputed if desired.
+            del self._boxLengths
+        except AttributeError:
+            pass
         self.box_vectors = _box_vectors_from_lengths_angles(a, b, c,
                                                             alpha, beta, gamma)
         # If we already have a _topology instance, then we have possibly changed
@@ -952,8 +957,6 @@ class CharmmPsfFile(object):
          -  flexibleConstraints (bool=True) Are our constraints flexible or not?
          -  verbose (bool=False) Optionally prints out a running progress report
         """
-        # back up the dihedral list
-        dihedral_list = self.dihedral_list
         # Load the parameter set
         self.loadParameters(params.condense())
         hasbox = self.topology.getUnitCellDimensions() is not None
@@ -1103,7 +1106,7 @@ class CharmmPsfFile(object):
         if verbose: print('Adding torsions...')
         force = mm.PeriodicTorsionForce()
         force.setForceGroup(self.DIHEDRAL_FORCE_GROUP)
-        for tor in self.dihedral_list:
+        for tor in self.dihedral_parameter_list:
             force.addTorsion(tor.atom1.idx, tor.atom2.idx, tor.atom3.idx,
                              tor.atom4.idx, tor.dihedral_type.per,
                              tor.dihedral_type.phase*pi/180,
@@ -1235,7 +1238,7 @@ class CharmmPsfFile(object):
         # Add 1-4 interactions
         excluded_atom_pairs = set() # save these pairs so we don't zero them out
         sigma_scale = 2**(-1/6)
-        for tor in self.dihedral_list:
+        for tor in self.dihedral_parameter_list:
             # First check to see if atoms 1 and 4 are already excluded because
             # they are 1-2 or 1-3 pairs (would happen in 6-member rings or
             # fewer). Then check that they're not already added as exclusions
@@ -1355,9 +1358,6 @@ class CharmmPsfFile(object):
         # Cache our system for easy access
         self._system = system
 
-        # Restore the dihedral list to allow reparametrization later
-        self.dihedral_list = dihedral_list
-
         return system
 
     @property
@@ -1422,9 +1422,30 @@ class CharmmPsfFile(object):
     @property
     def boxLengths(self):
         """ Return tuple of 3 units """
+        try:
+            # See if we have a cached version
+            return self._boxLengths
+        except AttributeError:
+            pass
         if self.box_vectors is not None:
-            return (self.box_vectors[0][0], self.box_vectors[0][1],
-                    self.box_vectors[0][2])
+            # Get the lengths of each vector
+            if u.is_quantity(self.box_vectors):
+                # Unlikely -- each vector is like a quantity
+                vecs = self.box_vectors.value_in_unit(u.nanometers)
+            elif u.is_quantity(self.box_vectors[0]):
+                # Assume all box vectors are quantities
+                vecs = [x.value_in_unit(u.nanometers) for x in self.box_vectors]
+            else:
+                # Assume nanometers
+                vecs = self.box_vectors
+            a = sqrt(vecs[0][0]*vecs[0][0] + vecs[0][1]*vecs[0][1] +
+                     vecs[0][2]*vecs[0][2])
+            b = sqrt(vecs[1][0]*vecs[1][0] + vecs[1][1]*vecs[1][1] +
+                     vecs[1][2]*vecs[1][2])
+            c = sqrt(vecs[2][0]*vecs[2][0] + vecs[2][1]*vecs[2][1] +
+                     vecs[2][2]*vecs[2][2])
+            self._boxLengths = (a, b, c) * u.nanometers
+            return self._boxLengths
         return None
 
     @boxLengths.setter
@@ -1440,6 +1461,12 @@ class CharmmPsfFile(object):
     @boxVectors.setter
     def boxVectors(self, stuff):
         """ Sets the box vectors """
+        try:
+            # We may be changing the box, so delete the cached box lengths to
+            # make sure they are recomputed if desired
+            del self._boxLengths
+        except AttributeError:
+            pass
         self.box_vectors = stuff
 
     def deleteCmap(self):

wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml

+<ForceField>
+ <Info>
+  <Source>amoebapro13_5-2014.prm</Source>
+  <DateGenerated>2014-05-08</DateGenerated>
+  <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
+ </Info>
+ <AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">
+  <GeneralizedKirkwood type="1" charge="-0.22483" shct="0.79"  /> 
+  <GeneralizedKirkwood type="2" charge="-0.09722" shct="0.72"  /> 
+  <GeneralizedKirkwood type="2" charge="-0.31113" shct="0.72"  /> 
+  <GeneralizedKirkwood type="2" charge="-0.18217" shct="0.72"  /> 
+  <GeneralizedKirkwood type="2" charge="-0.06142" shct="0.72"  /> 
+  <GeneralizedKirkwood type="3" charge="0.79586" shct="0.72"  /> 
+  <GeneralizedKirkwood type="4" charge="0.13964" shct="0.85"  /> 
+  <GeneralizedKirkwood type="5" charge="-0.76219" shct="0.85"  /> 
+  <GeneralizedKirkwood type="6" charge="0.07437" shct="0.85"  /> 
+  <GeneralizedKirkwood type="7" charge="-0.15418" shct="0.79"  /> 
+  <GeneralizedKirkwood type="7" charge="-0.14115" shct="0.79"  /> 
+  <GeneralizedKirkwood type="8" charge="-0.17302" shct="0.72"  /> 
+  <GeneralizedKirkwood type="8" charge="-0.36199" shct="0.72"  /> 
+  <GeneralizedKirkwood type="8" charge="-0.11441" shct="0.72"  /> 
+  <GeneralizedKirkwood type="8" charge="0.04440" shct="0.72"  /> 
+  <GeneralizedKirkwood type="9" charge="0.81010" shct="0.72"  /> 
+  <GeneralizedKirkwood type="9" charge="0.85003" shct="0.72"  /> 
+  <GeneralizedKirkwood type="10" charge="0.12044" shct="0.85"  /> 
+  <GeneralizedKirkwood type="10" charge="0.12637" shct="0.85"  /> 
+  <GeneralizedKirkwood type="11" charge="-0.75149" shct="0.85"  /> 
+  <GeneralizedKirkwood type="11" charge="-0.77014" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.08514" shct="0.85"  /> 
+  <GeneralizedKirkwood type="12" charge="0.07834" shct="0.85"  /> 
+  <GeneralizedKirkwood type="13" charge="-0.15959" shct="0.72"  /> 
+  <GeneralizedKirkwood type="14" charge="0.07420" shct="0.85"  /> 
+  <GeneralizedKirkwood type="15" charge="-0.06548" shct="0.72"  /> 
+  <GeneralizedKirkwood type="16" charge="0.07117" shct="0.85"  /> 
+  <GeneralizedKirkwood type="17" charge="-0.16832" shct="0.72"  /> 
+  <GeneralizedKirkwood type="18" charge="0.06566" shct="0.85"  /> 
+  <GeneralizedKirkwood type="19" charge="-0.13173" shct="0.72"  /> 
+  <GeneralizedKirkwood type="20" charge="0.06916" shct="0.85"  /> 
+  <GeneralizedKirkwood type="21" charge="-0.02887" shct="0.72"  /> 
+  <GeneralizedKirkwood type="22" charge="0.08767" shct="0.85"  /> 
+  <GeneralizedKirkwood type="23" charge="-0.17741" shct="0.72"  /> 
+  <GeneralizedKirkwood type="24" charge="0.05874" shct="0.85"  /> 
+  <GeneralizedKirkwood type="25" charge="-0.08555" shct="0.72"  /> 
+  <GeneralizedKirkwood type="26" charge="0.08230" shct="0.85"  /> 
+  <GeneralizedKirkwood type="27" charge="-0.11939" shct="0.72"  /> 
+  <GeneralizedKirkwood type="28" charge="0.07096" shct="0.85"  /> 
+  <GeneralizedKirkwood type="29" charge="-0.17217" shct="0.72"  /> 
+  <GeneralizedKirkwood type="30" charge="0.06823" shct="0.85"  /> 
+  <GeneralizedKirkwood type="31" charge="-0.16882" shct="0.72"  /> 
+  <GeneralizedKirkwood type="32" charge="0.06001" shct="0.85"  /> 
+  <GeneralizedKirkwood type="33" charge="0.16229" shct="0.72"  /> 
+  <GeneralizedKirkwood type="34" charge="0.05600" shct="0.85"  /> 
+  <GeneralizedKirkwood type="35" charge="-0.44145" shct="0.85"  /> 
+  <GeneralizedKirkwood type="36" charge="0.23017" shct="0.85"  /> 
+  <GeneralizedKirkwood type="37" charge="0.10834" shct="0.72"  /> 
+  <GeneralizedKirkwood type="38" charge="0.06805" shct="0.85"  /> 
+  <GeneralizedKirkwood type="39" charge="-0.40177" shct="0.85"  /> 
+  <GeneralizedKirkwood type="40" charge="0.24568" shct="0.85"  /> 
+  <GeneralizedKirkwood type="41" charge="-0.16081" shct="0.72"  /> 
+  <GeneralizedKirkwood type="42" charge="0.06784" shct="0.85"  /> 
+  <GeneralizedKirkwood type="43" charge="-0.30144" shct="0.72"  /> 
+  <GeneralizedKirkwood type="43" charge="-0.30144" shct="0.72"  /> 
+  <GeneralizedKirkwood type="43" charge="-0.08027" shct="0.72"  /> 
+  <GeneralizedKirkwood type="44" charge="0.14381" shct="0.85"  /> 
+  <GeneralizedKirkwood type="44" charge="0.00975" shct="0.85"  /> 
+  <GeneralizedKirkwood type="45" charge="-0.03264" shct="0.96"  /> 
+  <GeneralizedKirkwood type="46" charge="0.10947" shct="0.85"  /> 
+  <GeneralizedKirkwood type="47" charge="0.07683" shct="0.96"  /> 
+  <GeneralizedKirkwood type="48" charge="-0.23113" shct="0.72"  /> 
+  <GeneralizedKirkwood type="49" charge="-0.85155" shct="0.96"  /> 
+  <GeneralizedKirkwood type="50" charge="-0.13558" shct="0.79"  /> 
+  <GeneralizedKirkwood type="51" charge="-0.26070" shct="0.72"  /> 
+  <GeneralizedKirkwood type="52" charge="0.90470" shct="0.72"  /> 
+  <GeneralizedKirkwood type="53" charge="-0.76984" shct="0.85"  /> 
+  <GeneralizedKirkwood type="54" charge="0.09550" shct="0.85"  /> 
+  <GeneralizedKirkwood type="55" charge="-0.13205" shct="0.72"  /> 
+  <GeneralizedKirkwood type="55" charge="-0.12680" shct="0.72"  /> 
+  <GeneralizedKirkwood type="56" charge="0.09686" shct="0.85"  /> 
+  <GeneralizedKirkwood type="56" charge="0.11510" shct="0.85"  /> 
+  <GeneralizedKirkwood type="57" charge="-0.16591" shct="0.72"  /> 
+  <GeneralizedKirkwood type="57" charge="-0.14420" shct="0.72"  /> 
+  <GeneralizedKirkwood type="58" charge="0.08886" shct="0.85"  /> 
+  <GeneralizedKirkwood type="58" charge="0.12121" shct="0.85"  /> 
+  <GeneralizedKirkwood type="59" charge="-0.03932" shct="0.72"  /> 
+  <GeneralizedKirkwood type="60" charge="0.06588" shct="0.85"  /> 
+  <GeneralizedKirkwood type="61" charge="-0.11216" shct="0.72"  /> 
+  <GeneralizedKirkwood type="62" charge="0.09205" shct="0.85"  /> 
+  <GeneralizedKirkwood type="63" charge="-0.04246" shct="0.72"  /> 
+  <GeneralizedKirkwood type="64" charge="0.04681" shct="0.72"  /> 
+  <GeneralizedKirkwood type="65" charge="0.00023" shct="0.85"  /> 
+  <GeneralizedKirkwood type="66" charge="-0.02656" shct="0.72"  /> 
+  <GeneralizedKirkwood type="67" charge="0.00719" shct="0.85"  /> 
+  <GeneralizedKirkwood type="68" charge="-0.02866" shct="0.72"  /> 
+  <GeneralizedKirkwood type="69" charge="0.00685" shct="0.85"  /> 
+  <GeneralizedKirkwood type="70" charge="-0.10731" shct="0.72"  /> 
+  <GeneralizedKirkwood type="71" charge="0.09011" shct="0.85"  /> 
+  <GeneralizedKirkwood type="72" charge="-0.05309" shct="0.72"  /> 
+  <GeneralizedKirkwood type="73" charge="0.07134" shct="0.72"  /> 
+  <GeneralizedKirkwood type="74" charge="0.00345" shct="0.85"  /> 
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+ </AmoebaWcaDispersionForce>
+</ForceField>

wrappers/python/simtk/openmm/app/data/tip3pfb.xml

+<ForceField>
+ <Info>
+  <DateGenerated>2014-05-28</DateGenerated>
+  <Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. Building force fields - an automatic, systematic and reproducible approach.  Journal of Physical Chemistry Letters, 2014, 5, pp 1885-1891.  DOI:10.1021/jz500737m</Reference>
+ </Info>
+ <AtomTypes>
+  <Type name="tip3p-fb-O" class="OW" element="O" mass="15.99943"/>
+  <Type name="tip3p-fb-H" class="HW" element="H" mass="1.007947"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="HOH">
+   <Atom name="O" type="tip3p-fb-O"/>
+   <Atom name="H1" type="tip3p-fb-H"/>
+   <Atom name="H2" type="tip3p-fb-H"/>
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+  </Residue>
+ </Residues>
+ <HarmonicBondForce>
+  <Bond class1="OW" class2="HW" length="0.101181082494" k="462750.4"/>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
+  <Angle class1="HW" class2="OW" class3="HW" angle="1.88754640288" k="836.8"/>
+ </HarmonicAngleForce>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <Atom type="tip3p-fb-O" charge="-0.848448690103" sigma="0.317796456355" epsilon="0.652143528104" />
+  <Atom type="tip3p-fb-H" charge="0.4242243450515" sigma="1" epsilon="0" />
+ </NonbondedForce>
+</ForceField>
+

wrappers/python/simtk/openmm/app/data/tip4pfb.xml

+<ForceField>
+ <Info>
+  <DateGenerated>2014-05-28</DateGenerated>
+  <Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. Building force fields - an automatic, systematic and reproducible approach.  Journal of Physical Chemistry Letters, 2014, 5, pp 1885-1891.  DOI:10.1021/jz500737m</Reference>
+ </Info>
+ <AtomTypes>
+  <Type name="tip4p-fb-O" class="OW" element="O" mass="15.99943"/>
+  <Type name="tip4p-fb-H" class="HW" element="H" mass="1.007947"/>
+  <Type name="tip4p-fb-M" class="MW" mass="0"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="HOH">
+   <Atom name="O" type="tip4p-fb-O"/>
+   <Atom name="H1" type="tip4p-fb-H"/>
+   <Atom name="H2" type="tip4p-fb-H"/>
+   <Atom name="M" type="tip4p-fb-M"/>
+   <VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="8.203146574531e-01" weight2="8.984267127345e-02" weight3="8.984267127345e-02" />
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+  </Residue>
+ </Residues>
+ <HarmonicBondForce>
+  <Bond class1="OW" class2="HW" length="0.09572" k="462750.4"/>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
+  <Angle class1="HW" class2="OW" class3="HW" angle="1.82421813418" k="836.8"/>
+ </HarmonicAngleForce>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <Atom type="tip4p-fb-O" charge="0" sigma="3.165552430462e-01" epsilon="7.492790213533e-01" />
+  <Atom type="tip4p-fb-H" charge="5.258681106763e-01" sigma="1" epsilon="0" />
+  <Atom type="tip4p-fb-M" charge="-1.0517362213526e+00" sigma="1" epsilon="0" />
+ </NonbondedForce>
+</ForceField>

wrappers/python/simtk/openmm/app/forcefield.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) 2012-2013 Stanford University and the Authors.
+Portions copyright (c) 2012-2014 Stanford University and the Authors.
 Authors: Peter Eastman, Mark Friedrichs
 Contributors:
 
@@ -1485,6 +1485,104 @@ class CustomTorsionGenerator:
 parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement
 
 
+## @private
+class CustomNonbondedGenerator:
+    """A CustomNonbondedGenerator constructs a CustomNonbondedForce."""
+
+    def __init__(self, energy, bondCutoff):
+        self.energy = energy
+        self.bondCutoff = bondCutoff
+        self.typeMap = {}
+        self.globalParams = {}
+        self.perParticleParams = []
+        self.functions = []
+
+    @staticmethod
+    def parseElement(element, ff):
+        generator = CustomNonbondedGenerator(element.attrib['energy'], int(element.attrib['bondCutoff']))
+        ff._forces.append(generator)
+        for param in element.findall('GlobalParameter'):
+            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
+        for param in element.findall('PerParticleParameter'):
+            generator.perParticleParams.append(param.attrib['name'])
+        for atom in element.findall('Atom'):
+            types = ff._findAtomTypes(atom, 1)
+            if None not in types:
+                values = [float(atom.attrib[param]) for param in generator.perParticleParams]
+                for t in types[0]:
+                    generator.typeMap[t] = values
+
+    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
+        methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
+                     CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic,
+                     CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic}
+        if nonbondedMethod not in methodMap:
+            raise ValueError('Illegal nonbonded method for CustomNonbondedForce')
+        force = mm.CustomNonbondedForce(self.energy)
+        for param in self.globalParams:
+            force.addGlobalParameter(param, self.globalParams[param])
+        for param in self.perParticleParams:
+            force.addPerParticleParameter(param)
+        for (name, type, values, params) in self.functions:
+            if type == 'Continuous1D':
+                force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
+            elif type == 'Continuous2D':
+                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
+            elif type == 'Continuous3D':
+                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
+            elif type == 'Discrete1D':
+                force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
+            elif type == 'Discrete2D':
+                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
+            elif type == 'Discrete3D':
+                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
+        for atom in data.atoms:
+            t = data.atomType[atom]
+            if t in self.typeMap:
+                values = self.typeMap[t]
+                force.addParticle(self.typeMap[t])
+            else:
+                raise ValueError('No CustomNonbonded parameters defined for atom type '+t)
+        force.setNonbondedMethod(methodMap[nonbondedMethod])
+        force.setCutoffDistance(nonbondedCutoff)
+        sys.addForce(force)
+
+    def postprocessSystem(self, sys, data, args):
+        # Create exceptions based on bonds, virtual sites, and Drude particles.
+        if self.bondCutoff == 0:
+            return
+        bondIndices = []
+        for bond in data.bonds:
+            bondIndices.append((bond.atom1, bond.atom2))
+        for i in range(sys.getNumParticles()):
+            if sys.isVirtualSite(i):
+                site = sys.getVirtualSite(i)
+                for j in range(site.getNumParticles()):
+                    bondIndices.append((i, site.getParticle(j)))
+        drude = [f for f in sys.getForces() if isinstance(f, mm.DrudeForce)]
+        if len(drude) > 0:
+            drude = drude[0]
+            # For purposes of creating exceptions, a Drude particle is "bonded" to anything
+            # its parent atom is bonded to.
+            drudeMap = {}
+            for i in range(drude.getNumParticles()):
+                params = drude.getParticleParameters(i)
+                drudeMap[params[1]] = params[0]
+            for atom1, atom2 in bondIndices:
+                drude1 = drudeMap[atom1] if atom1 in drudeMap else None
+                drude2 = drudeMap[atom2] if atom2 in drudeMap else None
+                if drude1 is not None:
+                    bondIndices.append((drude1, atom2))
+                    if drude2 is not None:
+                        bondIndices.append((drude1, drude2))
+                if drude2 is not None:
+                    bondIndices.append((atom1, drude2))
+        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
+        nonbonded.createExclusionsFromBonds(bondIndices, self.bondCutoff)
+
+parsers["CustomNonbondedForce"] = CustomNonbondedGenerator.parseElement
+
+
 ## @private
 class CustomGBGenerator:
     """A CustomGBGenerator constructs a CustomGBForce."""
@@ -1493,7 +1591,6 @@ class CustomGBGenerator:
         self.typeMap = {}
         self.globalParams = {}
         self.perParticleParams = []
-        self.paramValues = []
         self.computedValues = []
         self.energyTerms = []
         self.functions = []
@@ -2517,9 +2614,10 @@ class AmoebaTorsionTorsionGenerator:
                 gridRow.append(float(gridEntry.attrib['angle1']))
                 gridRow.append(float(gridEntry.attrib['angle2']))
                 gridRow.append(float(gridEntry.attrib['f']))
-                gridRow.append(float(gridEntry.attrib['fx']))
-                gridRow.append(float(gridEntry.attrib['fy']))
-                gridRow.append(float(gridEntry.attrib['fxy']))
+                if 'fx' in gridEntry.attrib:
+                    gridRow.append(float(gridEntry.attrib['fx']))
+                    gridRow.append(float(gridEntry.attrib['fy']))
+                    gridRow.append(float(gridEntry.attrib['fxy']))
                 gridCol.append(gridRow)
 
                 gridColIndex  += 1

wrappers/python/simtk/openmm/app/gromacstopfile.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) 2012-2013 Stanford University and the Authors.
+Portions copyright (c) 2012-2014 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -745,6 +745,12 @@ class GromacsTopFile(object):
                     atom1params = nb.getParticleParameters(baseAtomIndex+atoms[0])
                     atom2params = nb.getParticleParameters(baseAtomIndex+atoms[1])
                     exceptions.append((baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], atom1params[0]*atom2params[0]*fudgeQQ, params[0], params[1]))
+                for fields in moleculeType.exclusions:
+                    atoms = [int(x)-1 for x in fields]
+                    for atom in atoms[1:]:
+                        if atom > atoms[0]:
+                            exceptions.append((baseAtomIndex+atoms[0], baseAtomIndex+atom, 0, 0, 0))
+                    
 
         # Create nonbonded exceptions.
 

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

@@ -40,15 +40,14 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 #=============================================================================================
 
 import os
-import os.path
 import re
-import math
+from math import ceil, cos, sin, asin, sqrt, pi
 import warnings
 
 try:
-    import numpy
+    import numpy as np
 except:
-    pass
+    np = None
 
 import simtk.unit as units
 import simtk.openmm
@@ -74,6 +73,9 @@ POINTER_LABELS  = """
 # Pointer labels (above) as a list, not string.
 POINTER_LABEL_LIST = POINTER_LABELS.replace(',', '').split()
 
+VELSCALE = 20.455 # velocity conversion factor to angstroms/picosecond
+TINY = 1.0e-8
+
 class PrmtopLoader(object):
     """Parsed AMBER prmtop file.
 
@@ -83,14 +85,14 @@ class PrmtopLoader(object):
 
     Parse a prmtop file of alanine dipeptide in implicit solvent.
 
-    >>> import os, os.path
+    >>> import os
     >>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-gbsa')
     >>> prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop')
     >>> prmtop = PrmtopLoader(prmtop_filename)
 
     Parse a prmtop file of alanine dipeptide in explicit solvent.
 
-    >>> import os, os.path
+    >>> import os
     >>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit')
     >>> prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop')
     >>> prmtop = PrmtopLoader(prmtop_filename)
@@ -437,7 +439,7 @@ class PrmtopLoader(object):
                 (rVdwI, epsilonI) = nonbondTerms[iAtom]
                 (rVdwL, epsilonL) = nonbondTerms[lAtom]
                 rMin = (rVdwI+rVdwL)
-                epsilon = math.sqrt(epsilonI*epsilonL)
+                epsilon = sqrt(epsilonI*epsilonL)
                 try:
                     iScee = float(self._raw_data["SCEE_SCALE_FACTOR"][iidx])
                 except KeyError:
@@ -708,7 +710,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
                     l2 = bond[1]
 
             # Compute the distance between atoms and add a constraint
-            length = math.sqrt(l1*l1 + l2*l2 - 2*l1*l2*math.cos(aMin))
+            length = sqrt(l1*l1 + l2*l2 - 2*l1*l2*cos(aMin))
             system.addConstraint(iAtom, kAtom, length)
         if flexibleConstraints or not constrained:
             force.addAngle(iAtom, jAtom, kAtom, aMin, 2*k)
@@ -739,10 +741,17 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
         # System is periodic.
         # Set periodic box vectors for periodic system
         (boxBeta, boxX, boxY, boxZ) = prmtop.getBoxBetaAndDimensions()
-        d0 = units.Quantity(0.0, units.angstroms)
-        xVec = units.Quantity((boxX, d0,   d0))
-        yVec = units.Quantity((d0,   boxY, d0))
-        zVec = units.Quantity((d0,   d0,   boxZ))
+        boxBeta = boxBeta.value_in_unit(units.degrees)
+        boxX = boxX.value_in_unit(units.angstroms)
+        boxY = boxY.value_in_unit(units.angstroms)
+        boxZ = boxZ.value_in_unit(units.angstroms)
+        tmp = [[0.0, 0.0, 0.0],[0.0, 0.0, 0.0],[0.0, 0.0, 0.0]]
+        _box_vectors_from_lengths_angles([boxX, boxY, boxZ],
+                                         [boxBeta, boxBeta, boxBeta],
+                                         tmp)
+        xVec = units.Quantity(tmp[0], units.angstroms)
+        yVec = units.Quantity(tmp[1], units.angstroms)
+        zVec = units.Quantity(tmp[2], units.angstroms)
         system.setDefaultPeriodicBoxVectors(xVec, yVec, zVec)
 
         # Set cutoff.
@@ -848,13 +857,13 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
             if len(waterO[res]) == 1 and len(waterH[res]) == 2:
                 if len(waterEP[res]) == 1:
                     # Four point water
-                    weightH = distOE[res]/math.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
+                    weightH = distOE[res]/sqrt(distOH[res]**2-(0.5*distHH[res])**2)
                     system.setVirtualSite(waterEP[res][0], mm.ThreeParticleAverageSite(waterO[res][0], waterH[res][0], waterH[res][1], 1-weightH, weightH/2, weightH/2))
                 elif len(waterEP[res]) == 2:
                     # Five point water
-                    weightH = cosOOP*distOE[res]/math.sqrt(distOH[res]**2-(0.5*distHH[res])**2)
-                    angleHOH = 2*math.asin(0.5*distHH[res]/distOH[res])
-                    lenCross = (distOH[res]**2)*math.sin(angleHOH)
+                    weightH = cosOOP*distOE[res]/sqrt(distOH[res]**2-(0.5*distHH[res])**2)
+                    angleHOH = 2*asin(0.5*distHH[res]/distOH[res])
+                    lenCross = (distOH[res]**2)*sin(angleHOH)
                     weightCross = sinOOP*distOE[res]/lenCross
                     system.setVirtualSite(waterEP[res][0], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, weightCross))
                     system.setVirtualSite(waterEP[res][1], mm.OutOfPlaneSite(waterO[res][0], waterH[res][0], waterH[res][1], weightH/2, weightH/2, -weightCross))
@@ -917,134 +926,395 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     return system
 
 #=============================================================================================
-# AMBER INPCRD loader
+# AMBER INPCRD loader classes
 #=============================================================================================
 
-def readAmberCoordinates(filename, read_box=False, read_velocities=False, verbose=False, asNumpy=False):
+class AmberAsciiRestart(object):
+    """
+    Class responsible for parsing Amber coordinates in the ASCII format.
+    Automatically detects the presence of velocities or box parameters in the
+    file.
+
+    Parameters
+    ----------
+    filename : str
+        Name of the restart file
+    asNumpy : bool (False)
+        Load the coordinates, velocities, and box as numpy ndarray objects
+
+    Attributes
+    ----------
+    coordinates : natom x 3 array, Quantity
+        Particle positions with units of length
+    velocities : natom x 3 array, Quantity
+        Particle velocities with units of length per time (None if velocities
+        are not present in the inpcrd file)
+    boxVectors : 3 x 3 array, Quantity
+        Box vectors with units of length (None if no box is present in the
+        inpcrd file)
+    time : float, Quantity
+        Simulation time (None if not present) with units of time
+    title : str
+        Title of the inpcrd file
+    filename : str
+        Name of the file we are parsing
+    natom : int
+        Number of atoms in the inpcrd file
+
+    Raises
+    ------
+        `IOError' if the file does not exist
+        `TypeError' if the format of the file is not recognized
+        `ValueError' if not all fields are numbers (for example, if a field is
+                     filled with ****'s)
+        `IndexError' if the file is empty
+        `ImportError' if numpy is requested but could not be imported
+    Example
+    -------
+    >>> f = AmberAsciiRestart('alanine-dipeptide.inpcrd')
+    >>> coordinates = f.coordinates
+    """
+
+    def __init__(self, filename, asNumpy=False):
+        # Make sure numpy is available if requested
+        if asNumpy and np is None:
+            raise ImportError('asNumpy=True: numpy is not available')
+        self._asNumpy = asNumpy
+        self.filename = filename
+        with open(filename, 'r') as f:
+            lines = f.readlines()
+            # Get rid of trailing blank lines
+            while lines and not lines[-1].strip():
+                lines.pop()
+            self._parse(lines)
+
+    def __str__(self):
+        return self.filename
+
+    def _parse(self, lines):
+        """ Parses through the inpcrd file """
+        global VELSCALE
+        self.title = lines[0].strip()
+        self.time = None
+
+        try:
+            words = lines[1].split()
+            self.natom = int(words[0])
+        except (IndexError, ValueError):
+            raise TypeError('Unrecognized file type [%s]' % self.filename)
+        
+        if len(words) >= 2:
+            self.time = float(words[1]) * units.picoseconds
+
+        if len(lines) == int(ceil(self.natom / 2.0) + 2):
+            hasbox = hasvels = False
+            self.boxVectors = self.velocities = None
+        elif self.natom in (1, 2) and len(lines) == 4:
+            # This is the _only_ case where line counting does not work -- there
+            # is either 1 or 2 atoms and there are 4 lines. The 1st 3 lines are
+            # the title, natom/time, and coordinates. The 4th are almost always
+            # velocities since Amber does not make it easy to make a periodic
+            # system with only 2 atoms. If natom is 1, the 4th line is either a
+            # velocity (3 #'s) or a box (6 #'s). If natom is 2, it is a bit
+            # ambiguous. However, velocities (which are scaled by 20.445) have a
+            # ~0% chance of being 60+, so we can pretty easily tell if the last
+            # line has box dimensions and angles or velocities. I cannot
+            # envision a _plausible_ scenario where the detection here will fail
+            # in real life.
+            line = lines[3]
+            if self.natom == 1:
+                tmp = [line[i:i+12] for i in range(0, 72, 12) if line[i:i+12]]
+                if len(tmp) == 3:
+                    hasvels = True
+                    hasbox = False
+                    self.boxVectors = False
+                elif len(tmp) == 6:
+                    hasbox = True
+                    hasvels = False
+                    self.velocities = None
+                else:
+                    raise TypeError('Unrecognized line in restart file %s' %
+                                    self.filename)
+            else:
+                # Ambiguous case
+                tmp = [float(line[i:i+12]) >= 60.0 for i in range(0, 72, 12)]
+                if any(tmp):
+                    hasbox = True
+                    hasvels = False
+                    self.velocities = False
+                else:
+                    hasvels = True
+                    hasbox = False
+                    self.boxVectors = False
+        elif len(lines) == int(ceil(self.natom / 2.0) + 3):
+            hasbox = True
+            hasvels = False
+            self.velocities = None
+        elif len(lines) == int(2 * ceil(self.natom / 2.0) + 2):
+            hasbox = False
+            self.boxVectors = None
+            hasvels = True
+        elif len(lines) == int(2 * ceil(self.natom / 2.0) + 3):
+            hasbox = hasvels = True
+        else:
+            raise TypeError('Badly formatted restart file. Has %d lines '
+                            'for %d atoms.' % (len(self.lines), self.natom))
+
+        if self._asNumpy:
+            coordinates = np.zeros((self.natom, 3), np.float32)
+            if hasvels:
+                velocities = np.zeros((self.natom, 3), np.float32)
+            if hasbox:
+                boxVectors = np.zeros((3, 3), np.float32)
+        else:
+            coordinates = [[0.0, 0.0, 0.0] for i in range(self.natom)]
+            if hasvels:
+                velocities = [[0.0, 0.0, 0.0] for i in range(self.natom)]
+            if hasbox:
+                boxVectors = [[0.0, 0.0, 0.0] for i in range(3)]
+
+        # Now it's time to parse.  Coordinates first
+        startline = 2
+        endline = startline + int(ceil(self.natom / 2.0))
+        idx = 0
+        for i in range(startline, endline):
+            line = lines[i]
+            coordinates[idx][0] = float(line[ 0:12])
+            coordinates[idx][1] = float(line[12:24])
+            coordinates[idx][2] = float(line[24:36])
+            idx += 1
+            if idx < self.natom:
+                coordinates[idx][0] = float(line[36:48])
+                coordinates[idx][1] = float(line[48:60])
+                coordinates[idx][2] = float(line[60:72])
+                idx += 1
+        self.coordinates = units.Quantity(coordinates, units.angstroms)
+        startline = endline
+        # Now it's time to parse velocities if we have them
+        if hasvels:
+            endline = startline + int(ceil(self.natom / 2.0))
+            idx = 0
+            for i in range(startline, endline):
+                line = lines[i]
+                velocities[idx][0] = float(line[ 0:12]) * VELSCALE
+                velocities[idx][1] = float(line[12:24]) * VELSCALE
+                velocities[idx][2] = float(line[24:36]) * VELSCALE
+                idx += 1
+                if idx < self.natom:
+                    velocities[idx][0] = float(line[36:48]) * VELSCALE
+                    velocities[idx][1] = float(line[48:60]) * VELSCALE
+                    velocities[idx][2] = float(line[60:72]) * VELSCALE
+                    idx += 1
+            startline = endline
+            self.velocities = units.Quantity(velocities,
+                                             units.angstroms/units.picoseconds)
+        if hasbox:
+            line = lines[startline]
+            try:
+                tmp = [float(line[i:i+12]) for i in range(0, 72, 12)]
+            except (IndexError, ValueError):
+                raise ValueError('Could not parse box line in %s' %
+                                 self.filename)
+            lengths = tmp[:3]
+            angles = tmp[3:]
+            _box_vectors_from_lengths_angles(lengths, angles, boxVectors)
+            self.boxVectors = units.Quantity(boxVectors, units.angstroms)
+
+class AmberNetcdfRestart(object):
+    """
+    Amber restart/inpcrd file in the NetCDF format (full double-precision
+    coordinates, velocities, and unit cell parameters). Reads NetCDF restarts
+    written by LEaP and pmemd/sander. Requires scipy to parse NetCDF files.
+
+    Parameters
+    ----------
+    filename : str
+        Name of the restart file
+    asNumpy : bool (False)
+        Load the coordinates, velocities, and box as numpy ndarray objects
+
+    Attributes
+    ----------
+    coordinates : natom x 3 array, Quantity
+        Particle positions with units of length
+    velocities : natom x 3 array, Quantity
+        Particle velocities with units of length per time (None if velocities
+        are not present in the inpcrd file)
+    boxVectors : 3 x 3 array, Quantity
+        Box vectors with units of length (None if no box is present in the
+        inpcrd file)
+    time : float, Quantity
+        Simulation time (None if not present) with units of time
+    title : str
+        Title of the inpcrd file
+    filename : str
+        Name of the file we are parsing
+    natom : int
+        Number of atoms in the inpcrd file
+
+    Raises
+    ------
+        `IOError' if the file does not exist
+        `TypeError' if the file is not a NetCDF v3 file
+        `ImportError' if scipy is not available
+    Example
+    -------
+    >>> f = AmberNetcdfRestart('alanine-dipeptide.ncrst')
+    >>> coordinates = f.coordinates
+    """
+    def __init__(self, filename, asNumpy=False):
+        try:
+            from scipy.io.netcdf import NetCDFFile
+        except ImportError:
+            raise ImportError('scipy is necessary to parse NetCDF restarts')
+        
+        self.filename = filename
+        self.velocities = self.boxVectors = self.time = None
+
+        # Extract the information from the NetCDF file. We need to make copies
+        # here because the NetCDF variables are mem-mapped, but is only mapped
+        # to valid memory while the file handle is open. Since the context
+        # manager GCs the ncfile handle, the memory for the original variables
+        # is no longer valid. So copy those arrays while the handle is still
+        # open. This is unnecessary in scipy v.0.12 and lower because NetCDFFile
+        # accidentally leaks the file handle, but that was 'fixed' in 0.13. This
+        # fix taken from MDTraj
+        ncfile = NetCDFFile(filename, 'r')
+        try:
+            self.natom = ncfile.dimensions['atom']
+            self.coordinates = np.array(ncfile.variables['coordinates'][:])
+            if 'velocities' in ncfile.variables:
+                vels = ncfile.variables['velocities']
+                self.velocities = np.array(vels[:]) * vels.scale_factor
+            if ('cell_lengths' in ncfile.variables and
+                'cell_angles' in ncfile.variables):
+                self.boxVectors = np.zeros((3,3), np.float32)
+                _box_vectors_from_lengths_angles(
+                        ncfile.variables['cell_lengths'][:],
+                        ncfile.variables['cell_angles'][:],
+                        self.boxVectors,
+                )
+            if 'time' in ncfile.variables:
+                self.time = ncfile.variables['time'].getValue()
+        finally:
+            ncfile.close()
+
+        # They are already numpy -- convert to list if we don't want numpy
+        if not asNumpy:
+            self.coordinates = self.coordinates.tolist()
+            if self.velocities is not None:
+                self.velocities = self.velocities.tolist()
+            if self.boxVectors is not None:
+                self.boxVectors = self.boxVectors.tolist()
+
+        # Now add the units
+        self.coordinates = units.Quantity(self.coordinates, units.angstroms)
+        if self.velocities is not None:
+            self.velocities = units.Quantity(self.velocities,
+                                             units.angstroms/units.picoseconds)
+        if self.boxVectors is not None:
+            self.boxVectors = units.Quantity(self.boxVectors, units.angstroms)
+        self.time = units.Quantity(self.time, units.picosecond)
+
+def _box_vectors_from_lengths_angles(lengths, angles, boxVectors):
+    """
+    Converts lengths and angles into a series of box vectors and modifies
+    boxVectors in-place (it must be a mutable sequence)
+
+    Parameters
+    ----------
+    lengths : 3-element array of floats
+        Lengths of the 3 periodic box vectors
+    angles : 3-element array of floats
+        Angles (in degrees) between the 3 periodic box vectors
+    boxVectors : mutable 3x3 sequence
+    """
+    alpha = angles[0] * pi / 180.0
+    beta = angles[1] * pi / 180.0
+    gamma = angles[2] * pi / 180.0
+
+    boxVectors[0][0] = lengths[0]
+
+    boxVectors[1][0] = lengths[1] * cos(gamma)
+    boxVectors[1][1] = lengths[1] * sin(gamma)
+
+    boxVectors[2][0] = cx = lengths[2] * cos(beta)
+    boxVectors[2][1] = cy = lengths[2] * (cos(alpha) - cos(beta) * cos(gamma))
+    boxVectors[2][2] = sqrt(lengths[2]*lengths[2] - cx*cx - cy*cy)
+
+    boxVectors[0][1] = boxVectors[0][2] = boxVectors[1][2] = 0.0
+
+    # Now make sure any vector close to zero is zero exactly
+    for i in range(3):
+        for j in range(3):
+            if abs(boxVectors[i][j]) < TINY:
+                boxVectors[i][j] = 0.0
+
+def readAmberCoordinates(filename, asNumpy=False):
     """
     Read atomic coordinates (and optionally, box vectors) from Amber formatted coordinate file.
 
     ARGUMENTS
 
     filename (string) - name of Amber coordinates file to be read in
-    system (simtk.openmm.System) - System object for which coordinates are to be read
 
     OPTIONAL ARGUMENTS
 
-    verbose (boolean) - if True, will print out verbose information about the file being read
     asNumpy (boolean) - if True, results will be returned as Numpy arrays instead of lists of Vec3s
 
+    RETURNS
+
+    coordinates, velocities, boxVectors
+        The velocities and boxVectors will be None if they are not found in the
+        restart file
+
     EXAMPLES
 
     Read coordinates in vacuum.
 
     >>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-gbsa')
     >>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
-    >>> coordinates = readAmberCoordinates(crd_filename)
+    >>> coordinates, velocities, box_vectors = readAmberCoordinates(crd_filename)
 
     Read coordinates in solvent.
 
     >>> directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit')
     >>> crd_filename = os.path.join(directory, 'alanine-dipeptide.inpcrd')
-    >>> [coordinates, box_vectors] = readAmberCoordinates(crd_filename, read_box=True)
-
+    >>> coordinates, velocities, box_vectors = readAmberCoordinates(crd_filename)
     """
 
-    # Open coordinate file for reading.
-    infile = open(filename, 'r')
-
-    # Read title
-    title = infile.readline().strip()
-    if verbose: print "title: '%s'" % title
-
-    # Read number of atoms
-    natoms = int(infile.readline().split()[0])
-    if verbose: print "%d atoms" % natoms
-
-    # Allocate storage for coordinates
-    coordinates = []
-
-    # Read coordinates
-    mm = simtk.openmm
-    natoms_read = 0
-    while (natoms_read < natoms):
-        line = infile.readline()
-        if len(line) == 0:
-            raise ValueError("Unexpected end of file while reading coordinates")
-        line = line.strip()
-        elements = line.split()
-        while (len(elements) > 0):
-            coordinates.append(mm.Vec3(float(elements.pop(0)), float(elements.pop(0)), float(elements.pop(0))))
-            natoms_read += 1
-    if asNumpy:
-        newcoords = numpy.zeros([natoms,3], numpy.float32)
-        for i in range(len(coordinates)):
-            for j in range(3):
-                newcoords[i,j] = coordinates[i][j]
-        coordinates = newcoords
-    # Assign units.
-    coordinates = units.Quantity(coordinates, units.angstroms)
-
-    # Read velocities if requested.
-    velocities = None
-    if (read_velocities):
-        # Read velocities
-        velocities = []
-        natoms_read = 0
-        while (natoms_read < natoms):
-            line = infile.readline()
-            if len(line) == 0:
-                raise ValueError("Unexpected end of file while reading velocities")
-            line = line.strip()
-            elements = line.split()
-            while (len(elements) > 0):
-                velocities.append(20.455*mm.Vec3(float(elements.pop(0)), float(elements.pop(0)), float(elements.pop(0))))
-                natoms_read += 1
-        if asNumpy:
-            newvel = numpy.zeros([natoms,3], numpy.float32)
-            for i in range(len(velocities)):
-                for j in range(3):
-                    newvel[i,j] = velocities[i][j]
-            velocities = newvel
-        # Assign units.
-        velocities = units.Quantity(velocities, units.angstroms/units.picoseconds)
-
-    # Read box size if present
-    box_vectors = None
-    if (read_box):
-        line = infile.readline()
-        if len(line) == 0:
-            raise ValueError("Unexpected end of file while reading box vectors")
-        line = line.strip()
-        elements = line.split()
-        nelements = len(elements)
-        box_dimensions = [0.0]*nelements
-        for i in range(nelements):
-            box_dimensions[i] = float(elements[i])
-        # TODO: Deal with non-standard box sizes.
-        if nelements == 6:
-            if asNumpy:
-                a = units.Quantity(numpy.array([box_dimensions[0], 0.0, 0.0]), units.angstroms)
-                b = units.Quantity(numpy.array([0.0, box_dimensions[1], 0.0]), units.angstroms)
-                c = units.Quantity(numpy.array([0.0, 0.0, box_dimensions[2]]), units.angstroms)
-            else:
-                a = units.Quantity(mm.Vec3(box_dimensions[0], 0.0, 0.0), units.angstroms)
-                b = units.Quantity(mm.Vec3(0.0, box_dimensions[1], 0.0), units.angstroms)
-                c = units.Quantity(mm.Vec3(0.0, 0.0, box_dimensions[2]), units.angstroms)
-            box_vectors = [a,b,c]
-        else:
-            raise Exception("Don't know what to do with box vectors: %s" % line)
-
-    # Close file
-    infile.close()
-
-    if box_vectors and velocities:
-        return (coordinates, box_vectors, velocities)
-    if box_vectors:
-        return (coordinates, box_vectors)
-    if velocities:
-        return (coordinates, velocities)
-    return coordinates
+    try:
+        crdfile = AmberNetcdfRestart(filename)
+    except ImportError:
+        # See if it's an ASCII file.  If so, no need to complain
+        try:
+            crdfile = AmberAsciiRestart(filename)
+        except TypeError:
+            raise TypeError('Problem parsing %s as an ASCII Amber restart file '
+                            'and scipy could not be imported to try reading as '
+                            'a NetCDF restart file.' % filename)
+        except (IndexError, ValueError):
+            raise TypeError('Could not parse Amber ASCII restart file %s' %
+                            filename)
+        except ImportError:
+            raise ImportError('Could not find numpy; cannot use asNumpy=True')
+    except TypeError:
+        # We had scipy, but this is not a NetCDF v3 file. Try as ASCII now
+        try:
+            crdfile = AmberAsciiRestart(filename)
+        except TypeError:
+            raise TypeError('Problem parsing %s as an ASCII Amber restart file'
+                            % filename)
+        except (IndexError, ValueError):
+            raise TypeError('Could not parse Amber ASCII restart file %s' %
+                            filename)
+        # Import error cannot happen, since we had scipy which has numpy as a
+        # prereq. Do not catch that exception (only catch what you intend to
+        # catch...)
+
+    # We got here... one of the file types worked. Return the coordinates,
+    # velocities, and boxVectors
+    return crdfile.coordinates, crdfile.velocities, crdfile.boxVectors
 
 #=============================================================================================
 # MAIN AND TESTS

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

@@ -421,8 +421,10 @@ class ResidueList(list):
         if self._last_residue is None:
             res = self._last_residue = Residue(resname, resnum)
             list.append(self, res)
-        elif self._last_residue != (resname, resnum):
-            if self._last_residue.idx == resnum:
+        elif (self._last_residue != (resname, resnum) or
+              system != self._last_residue.system):
+            if (self._last_residue.idx == resnum and
+                system == self._last_residue.system):
                 lresname = self._last_residue.resname
                 warnings.warn('Residue %d split into separate residues %s '
                               'and %s' % (resnum, lresname, resname),
@@ -1063,7 +1065,6 @@ class TrackedList(list):
     __delitem__ = _tracking(list.__delitem__)
     append = _tracking(list.append)
     extend = _tracking(list.extend)
-    __delslice__ = _tracking(list.__delslice__)
     __setitem__ = _tracking(list.__setitem__)
 
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++