Merge branch 'master' into amber-switching

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

In fixing the merge conflict, I went ahead and fixed up the switchDistance logic
to match what I did in CharmmPsfFile.

serialization/CMakeLists.txt

@@ -6,6 +6,8 @@ INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/in
 INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/SerializationProxy.h)
 INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/XmlSerializer.h)
 
-IF(BUILD_TESTING)
+SET(OPENMM_BUILD_SERIALIZATION_TESTS TRUE CACHE BOOL "Whether to build serialization test cases")
+MARK_AS_ADVANCED(OPENMM_BUILD_SERIALIZATION_TESTS)
+IF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)
     ADD_SUBDIRECTORY(tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)

serialization/include/openmm/serialization/CompoundIntegratorProxy.h

+#ifndef OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
+#define OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
+
+#include "openmm/serialization/XmlSerializer.h"
+
+namespace OpenMM {
+
+class CompoundIntegratorProxy : public SerializationProxy {
+public:
+    CompoundIntegratorProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+}
+
+#endif /*OPENMM_COMPOUND_INTEGRATOR_PROXY_H_*/
\ No newline at end of file

serialization/include/openmm/serialization/SerializationNode.h

@@ -105,7 +105,7 @@ public:
     /**
      * Determine whether this node has a property with a particular node.
      *
-     * @param the name of the property to check for
+     * @param name  the name of the property to check for
      */
     bool hasProperty(const std::string& name) const;
     /**

openmmapi/include/openmm/internal/GBVIForceImpl.h → serialization/src/CompoundIntegratorProxy.cpp

-#ifndef OPENMM_GBVIFORCEFIELDIMPL_H_
-#define OPENMM_GBVIFORCEFIELDIMPL_H_
-
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
  * -------------------------------------------------------------------------- *
@@ -9,7 +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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -32,46 +29,29 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "ForceImpl.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/Kernel.h"
-#include <string>
-
-namespace OpenMM {
-
-/**
- * This is the internal implementation of GBVIForce.
- */
-
-class GBVIForceImpl : public ForceImpl {
-public:
-    GBVIForceImpl(const GBVIForce& owner);
-    void initialize(ContextImpl& context);
-    const GBVIForce& getOwner() const {
-        return owner;
-    }
-    
-    // calculate scaled radii (Eq. 5 of Labute paper [JCC 29 1693-1698 2008])
-
-    void findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
-                          const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const;
-
-    // if bond info not set, then use bond forces/constraints
-    int getBondsFromForces(ContextImpl& context);
-
-    void updateContextState(ContextImpl& context) {
-        // This force field doesn't update the state directly.
-    }
-    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
-    std::map<std::string, double> getDefaultParameters() {
-        return std::map<std::string, double>(); // This force field doesn't define any parameters.
-    }
-    std::vector<std::string> getKernelNames();
-private:
-    const GBVIForce& owner;
-    Kernel kernel;
-};
-
-} // namespace OpenMM
-
-#endif /*OPENMM_GBVIFORCEFIELDIMPL_H_*/
+#include "openmm/serialization/CompoundIntegratorProxy.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+CompoundIntegratorProxy::CompoundIntegratorProxy() : SerializationProxy("CompoundIntegrator") {
+}
+
+void CompoundIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const CompoundIntegrator& integrator = *reinterpret_cast<const CompoundIntegrator*>(object);
+    node.setIntProperty("currentIntegrator", integrator.getCurrentIntegrator());
+    for (int i = 0; i < integrator.getNumIntegrators(); i++)
+        node.createChildNode("Integrator", &integrator.getIntegrator(i));
+}
+
+void* CompoundIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    CompoundIntegrator *integrator = new CompoundIntegrator();
+    for (int i = 0; i < node.getChildren().size(); i++)
+        integrator->addIntegrator(node.getChildren()[i].decodeObject<Integrator>());
+    integrator->setCurrentIntegrator(node.getIntProperty("currentIntegrator"));
+    return integrator;
+}
\ No newline at end of file

serialization/src/GBVIForceProxy.cpp

-/* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * 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) 2010-2014 Stanford University and the Authors.      *
- * Authors: Peter Eastman                                                     *
- * Contributors:                                                              *
- *                                                                            *
- * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation  *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
- * and/or sell copies of the Software, and to permit persons to whom the      *
- * Software is furnished to do so, subject to the following conditions:       *
- *                                                                            *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software.                        *
- *                                                                            *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
- * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
- * -------------------------------------------------------------------------- */
-
-#include "openmm/serialization/GBVIForceProxy.h"
-#include "openmm/serialization/SerializationNode.h"
-#include "openmm/Force.h"
-#include "openmm/GBVIForce.h"
-#include <sstream>
-
-using namespace OpenMM;
-using namespace std;
-
-GBVIForceProxy::GBVIForceProxy() : SerializationProxy("GBVIForce") {
-}
-
-void GBVIForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
-    const GBVIForce& force = *reinterpret_cast<const GBVIForce*>(object);
-    node.setIntProperty("forceGroup", force.getForceGroup());
-    node.setIntProperty("method", (int) force.getNonbondedMethod());
-    node.setIntProperty("scalingMethod", (int) force.getBornRadiusScalingMethod());
-    node.setDoubleProperty("quinticLowerLimitFactor", force.getQuinticLowerLimitFactor());
-    node.setDoubleProperty("quinticUpperBornRadiusLimit", force.getQuinticUpperBornRadiusLimit());
-    node.setDoubleProperty("cutoff", force.getCutoffDistance());
-    node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric());
-    node.setDoubleProperty("solventDielectric", force.getSolventDielectric());
-    SerializationNode& particles = node.createChildNode("Particles");
-    for (int i = 0; i < force.getNumParticles(); i++) {
-        double charge, radius, gamma;
-        force.getParticleParameters(i, charge, radius, gamma);
-        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("r", radius).setDoubleProperty("gamma", gamma);
-    }
-    SerializationNode& bonds = node.createChildNode("Bonds");
-    for (int i = 0; i < force.getNumBonds(); i++) {
-        int particle1, particle2;
-        double distance;
-        force.getBondParameters(i, particle1, particle2, distance);
-        bonds.createChildNode("Bond").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("d", distance);
-    }
-}
-
-void* GBVIForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
-        throw OpenMMException("Unsupported version number");
-    GBVIForce* force = new GBVIForce();
-    try {
-        force->setForceGroup(node.getIntProperty("forceGroup", 0));
-        force->setNonbondedMethod((GBVIForce::NonbondedMethod) node.getIntProperty("method"));
-        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
-        force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));
-        force->setSolventDielectric(node.getDoubleProperty("solventDielectric"));
-
-        if( node.getIntProperty("version") >= 2 ){
-            force->setBornRadiusScalingMethod( (GBVIForce::BornRadiusScalingMethod) node.getIntProperty( "scalingMethod"));
-            force->setQuinticLowerLimitFactor(node.getDoubleProperty("quinticLowerLimitFactor"));
-            force->setQuinticUpperBornRadiusLimit(node.getDoubleProperty("quinticUpperBornRadiusLimit"));
-        }
-
-        const SerializationNode& particles = node.getChildNode("Particles");
-        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
-            const SerializationNode& particle = particles.getChildren()[i];
-            force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("r"), particle.getDoubleProperty("gamma"));
-        }
-        const SerializationNode& bonds = node.getChildNode("Bonds");
-        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& bond = bonds.getChildren()[i];
-            force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"));
-        }
-    }
-    catch (...) {
-        delete force;
-        throw;
-    }
-    return force;
-}

serialization/src/SerializationProxyRegistration.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,6 +33,7 @@
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomAngleForce.h"
 #include "openmm/CustomBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
@@ -44,7 +45,6 @@
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/CustomTorsionForce.h"
 #include "openmm/GBSAOBCForce.h"
-#include "openmm/GBVIForce.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/LangevinIntegrator.h"
@@ -65,6 +65,7 @@
 #include "openmm/serialization/AndersenThermostatProxy.h"
 #include "openmm/serialization/CMAPTorsionForceProxy.h"
 #include "openmm/serialization/CMMotionRemoverProxy.h"
+#include "openmm/serialization/CompoundIntegratorProxy.h"
 #include "openmm/serialization/CustomAngleForceProxy.h"
 #include "openmm/serialization/CustomBondForceProxy.h"
 #include "openmm/serialization/CustomCompoundBondForceProxy.h"
@@ -76,7 +77,6 @@
 #include "openmm/serialization/CustomNonbondedForceProxy.h"
 #include "openmm/serialization/CustomTorsionForceProxy.h"
 #include "openmm/serialization/GBSAOBCForceProxy.h"
-#include "openmm/serialization/GBVIForceProxy.h"
 #include "openmm/serialization/HarmonicAngleForceProxy.h"
 #include "openmm/serialization/HarmonicBondForceProxy.h"
 #include "openmm/serialization/LangevinIntegratorProxy.h"
@@ -112,6 +112,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
     SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy());
+    SerializationProxy::registerProxy(typeid(CompoundIntegrator), new CompoundIntegratorProxy());
     SerializationProxy::registerProxy(typeid(Continuous1DFunction), new Continuous1DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Continuous2DFunction), new Continuous2DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy());
@@ -129,7 +130,6 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(Discrete2DFunction), new Discrete2DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Discrete3DFunction), new Discrete3DFunctionProxy());
     SerializationProxy::registerProxy(typeid(GBSAOBCForce), new GBSAOBCForceProxy());
-    SerializationProxy::registerProxy(typeid(GBVIForce), new GBVIForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicBondForce), new HarmonicBondForceProxy());
     SerializationProxy::registerProxy(typeid(LangevinIntegrator), new LangevinIntegratorProxy());

serialization/tests/TestSerializeIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Yutong Zhao                                        *
  * Contributors:                                                              *
  *                                                                            *
@@ -32,6 +32,7 @@
 #include "openmm/internal/AssertionUtilities.h"
 
 #include "openmm/BrownianIntegrator.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomIntegrator.h"
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/VariableLangevinIntegrator.h"
@@ -185,6 +186,29 @@ void testSerializeCustomIntegrator() {
     delete intg2;
 }
 
+void testSerializeCompoundIntegrator() {
+    CompoundIntegrator integ;
+    integ.addIntegrator(new LangevinIntegrator(372.4, 1.234, 0.0018));
+    integ.addIntegrator(new VerletIntegrator(0.002));
+    integ.setCurrentIntegrator(1);
+    stringstream ss;
+    XmlSerializer::serialize<Integrator>(&integ, "CompoundIntegrator", ss);
+    CompoundIntegrator *integ2 = dynamic_cast<CompoundIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
+    ASSERT_EQUAL(integ.getCurrentIntegrator(), integ2->getCurrentIntegrator());
+    LangevinIntegrator& langevin1 = dynamic_cast<LangevinIntegrator&>(integ.getIntegrator(0));
+    LangevinIntegrator& langevin2 = dynamic_cast<LangevinIntegrator&>(integ2->getIntegrator(0));
+    ASSERT_EQUAL(langevin1.getConstraintTolerance(), langevin2.getConstraintTolerance());
+    ASSERT_EQUAL(langevin1.getStepSize(), langevin2.getStepSize());
+    ASSERT_EQUAL(langevin1.getTemperature(), langevin2.getTemperature());
+    ASSERT_EQUAL(langevin1.getFriction(), langevin2.getFriction());
+    ASSERT_EQUAL(langevin1.getRandomNumberSeed(), langevin2.getRandomNumberSeed());
+    VerletIntegrator& verlet1 = dynamic_cast<VerletIntegrator&>(integ.getIntegrator(1));
+    VerletIntegrator& verlet2 = dynamic_cast<VerletIntegrator&>(integ2->getIntegrator(1));
+    ASSERT_EQUAL(verlet1.getConstraintTolerance(), verlet2.getConstraintTolerance());
+    ASSERT_EQUAL(verlet1.getStepSize(), verlet2.getStepSize());
+    delete integ2;
+}
+
 int main() {
     try {
         testSerializeBrownianIntegrator();
@@ -193,6 +217,7 @@ int main() {
         testSerializeVariableLangevinIntegrator();
         testSerializeVariableVerletIntegrator();
         testSerializeLangevinIntegrator(); 
+        testSerializeCompoundIntegrator();
     }
     catch(const exception& e) {
 		return 1;

platforms/reference/tests/TestReferenceGBVIForce.cpp → tests/TestCompoundIntegrator.h

@@ -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) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,214 +29,194 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the reference implementation of GBVIForce.
- */
-
 #include "openmm/internal/AssertionUtilities.h"
+#include "openmm/BrownianIntegrator.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/Context.h"
-#include "ReferencePlatform.h"
 #include "openmm/HarmonicBondForce.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
-#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
 #include "SimTKOpenMMRealType.h"
-#include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>
 
 using namespace OpenMM;
 using namespace std;
 
-ReferencePlatform platform;
-
 const double TOL = 1e-5;
 
-void testSingleParticle() {
+void testChangingIntegrator() {
     System system;
     system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-
-    GBVIForce* forceField = new GBVIForce();
-
-    double charge         = -1.0;
-    double radius         =  0.15;
-    double gamma          =  1.0;
-    forceField->addParticle(charge, radius, gamma);
-    system.addForce(forceField);
-    ASSERT(!forceField->usesPeriodicBoundaryConditions());
-    ASSERT(!system.usesPeriodicBoundaryConditions());
-
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-
-    double bornRadius     = radius; 
-    double eps0           = EPSILON0;
-    double tau            = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
-
-    double bornEnergy     = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
-    double nonpolarEnergy = -gamma*tau*std::pow(radius/bornRadius, 3.0);
-
-    double expectedE      = (bornEnergy+nonpolarEnergy); 
-    double obtainedE      = state.getPotentialEnergy(); 
-    double diff           = fabs((obtainedE - expectedE)/expectedE);
-
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-}
-
-void testEnergyEthane(int applyBornRadiiScaling) {
-    const int numParticles = 8;
-    System system;
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-
-    // harmonic bond
-
-    double C_HBondDistance   = 0.1097;
-    double C_CBondDistance   = 0.1504;
+    system.addParticle(2.0);
     HarmonicBondForce* bonds = new HarmonicBondForce();
-    bonds->addBond(0, 1, C_HBondDistance, 0.0);
-    bonds->addBond(2, 1, C_HBondDistance, 0.0);
-    bonds->addBond(3, 1, C_HBondDistance, 0.0);
-
-    bonds->addBond(1, 4, C_CBondDistance, 0.0);
-
-    bonds->addBond(5, 4, C_HBondDistance, 0.0);
-    bonds->addBond(6, 4, C_HBondDistance, 0.0);
-    bonds->addBond(7, 4, C_HBondDistance, 0.0);
-
+    bonds->addBond(0, 1, 1.5, 1);
     system.addForce(bonds);
-
-    double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
-
-    int AM1_BCC = 1;
-    H_charge    = -0.053;
-    C_charge    = -3.0*H_charge;
-    if (AM1_BCC) {
-       C_radius =  0.180;
-       C_gamma  = -0.2863;
-       H_radius =  0.125;
-       H_gamma  =  0.2437;
-    }
-    else {
-       C_radius =  0.215;
-       C_gamma  = -1.1087;
-       H_radius =  0.150;
-       H_gamma  =  0.1237;
+    CompoundIntegrator integrator;
+    integrator.addIntegrator(new VerletIntegrator(0.01));
+    integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.011));
+    integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.012));
+    Context context(system, integrator, platform);
+    ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    for (int iteration = 0; iteration < 2; ++iteration) {
+        context.setPositions(positions);
+
+        // First integrate with the Verlet integrator and compare it to the analytical solution.
+
+        const double freq = 1.0;
+        State state = context.getState(State::Energy);
+        const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+        for (int i = 0; i < 100; ++i) {
+            state = context.getState(State::Positions | State::Velocities | State::Energy);
+            double time = state.getTime();
+            double expectedDist = 1.5+0.5*std::cos(freq*time);
+            ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+            ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+            double expectedSpeed = -0.5*freq*std::sin(freq*time);
+            ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
+            ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
+            double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+            integrator.step(1);
+        }
+        ASSERT_EQUAL_TOL(100*0.01, context.getState(0).getTime(), 1e-5);
+
+        // Switch to the Langevin integrator and make sure that it heats up.
+
+        integrator.setCurrentIntegrator(1);
+        integrator.step(100);
+        double ke = 0.0;
+        for (int i = 0; i < 1000; ++i) {
+            integrator.step(10);
+            state = context.getState(State::Energy);
+            ke += state.getKineticEnergy();
+        }
+        double expectedKE = 0.5*2*3*BOLTZ*300.0;
+        ASSERT_USUALLY_EQUAL_TOL(expectedKE, ke/1000, 0.1);
+        ASSERT_EQUAL_TOL(100*0.01+10100*0.011, context.getState(0).getTime(), 1e-5);
+        
+        // Now reinitialize the context and repeat all of these tests to make sure that works correctly.
+        
+        context.reinitialize();
+        integrator.setCurrentIntegrator(0);
     }
+}
 
-    NonbondedForce* nonbonded = new NonbondedForce();
-    nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
-
-    GBVIForce* forceField = new GBVIForce();
-    if (applyBornRadiiScaling) {
-        forceField->setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
+void testChangingParameters() {
+    System system;
+    system.addParticle(1.0);
+    CompoundIntegrator integrator;
+    integrator.addIntegrator(new VerletIntegrator(0.01));
+    integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.02));
+    integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.03));
+    
+    // Try getting and setting the step size for different component integrators.
+    
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(0.01*(i+1), integrator.getStepSize(), 1e-7);
     }
-    else {
-        forceField->setBornRadiusScalingMethod(GBVIForce::NoScaling);
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        integrator.setStepSize(0.02*(i+1));
+        ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
     }
-    for (int i = 0; i < numParticles; i++) {
-       system.addParticle(1.0);
-       forceField->addParticle(H_charge, H_radius, H_gamma);
-       nonbonded->addParticle( H_charge, H_radius, 0.0);
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
     }
- 
-    forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
-    forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
- 
-    nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
-    nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
- 
-    forceField->addBond(0, 1, C_HBondDistance);
-    forceField->addBond(2, 1, C_HBondDistance);
-    forceField->addBond(3, 1, C_HBondDistance);
-    forceField->addBond(1, 4, C_CBondDistance);
-    forceField->addBond(5, 4, C_HBondDistance);
-    forceField->addBond(6, 4, C_HBondDistance);
-    forceField->addBond(7, 4, C_HBondDistance);
-    
-    std::vector<pair<int, int> > bondExceptions;
-    std::vector<double> bondDistances;
-    
-    bondExceptions.push_back(pair<int, int>(0, 1)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(2, 1)); 
-    bondDistances.push_back(C_HBondDistance);
     
-    bondExceptions.push_back(pair<int, int>(3, 1)); 
-    bondDistances.push_back(C_HBondDistance);
+    // Try getting and setting the constraint tolerance for different component integrators.
     
-    bondExceptions.push_back(pair<int, int>(1, 4)); 
-    bondDistances.push_back(C_CBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(5, 4)); 
-    bondDistances.push_back(C_HBondDistance);
-    
-    bondExceptions.push_back(pair<int, int>(6, 4)); 
-    bondDistances.push_back(C_HBondDistance);
- 
-    bondExceptions.push_back(pair<int, int>(7, 4));
-    bondDistances.push_back(C_HBondDistance);
- 
-    nonbonded->createExceptionsFromBonds(bondExceptions, 0.0, 0.0);
- 
-    system.addForce(forceField);
-    system.addForce(nonbonded);
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(1e-5, integrator.getConstraintTolerance(), 1e-7);
+    }
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        integrator.setConstraintTolerance(1e-4*(i+1));
+        ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
+    }
+    for (int i = 0; i < 3; i++) {
+        integrator.setCurrentIntegrator(i);
+        ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
+    }
+}
 
+void testDifferentStepSizes() {
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(0, 1, 1.5, 1);
+    system.addForce(bonds);
+    CompoundIntegrator integrator;
+    integrator.addIntegrator(new VerletIntegrator(0.005));
+    integrator.addIntegrator(new VerletIntegrator(0.01));
     Context context(system, integrator, platform);
-    
-    vector<Vec3> positions(numParticles);
-    positions[0] = Vec3(0.5480,    1.7661,    0.0000);
-    positions[1] = Vec3(0.7286,    0.8978,    0.6468);
-    positions[2] = Vec3(0.4974,    0.0000,    0.0588);
-    positions[3] = Vec3(0.0000,    0.9459,    1.4666);
-    positions[4] = Vec3(2.1421,    0.8746,    1.1615);
-    positions[5] = Vec3(2.3239,    0.0050,    1.8065);
-    positions[6] = Vec3(2.8705,    0.8295,    0.3416);
-    positions[7] = Vec3(2.3722,    1.7711,    1.7518);
+    ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
     context.setPositions(positions);
 
-    State state = context.getState(State::Forces | State::Energy);
-    
-    // Take a small step in the direction of the energy gradient.
-    
-    double norm        = 0.0;
-    double forceSum[3] = { 0.0, 0.0, 0.0 };
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 f  = state.getForces()[i];
-        norm        += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
-        forceSum[0] += f[0];
-        forceSum[1] += f[1];
-        forceSum[2] += f[2];
+    // Integrate with the first Verlet integrator and compare it to the analytical solution.
+
+    const double freq = 1.0;
+    double expectedTime = 0;
+    for (int i = 0; i < 100; ++i) {
+        State state = context.getState(State::Positions);
+        double time = state.getTime();
+        ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        integrator.step(1);
+        expectedTime += 0.005;
     }
-    norm               = std::sqrt(norm);
-
-    const double delta = 1e-4;
-    double step = delta/norm;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = state.getForces()[i];
-        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-    }
-    context.setPositions(positions);
     
-    State state2 = context.getState(State::Energy);
-
-    // See whether the potential energy changed by the expected amount.
+    // Now switch to the second Verlet integrator which has a different step size.
+
+    integrator.setCurrentIntegrator(1);
+    for (int i = 0; i < 100; ++i) {
+        State state = context.getState(State::Positions);
+        double time = state.getTime();
+        ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        integrator.step(1);
+        expectedTime += 0.01;
+    }
     
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
+    // Finally, switch back to the first one again.
+
+    integrator.setCurrentIntegrator(0);
+    for (int i = 0; i < 100; ++i) {
+        State state = context.getState(State::Positions);
+        double time = state.getTime();
+        ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        integrator.step(1);
+        expectedTime += 0.005;
+    }
 }
 
-int main() {
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
     try {
-        testSingleParticle();
-        testEnergyEthane(0);
-        testEnergyEthane(1);
+        initializeTests(argc, argv);
+        testChangingIntegrator();
+        testChangingParameters();
+        testDifferentStepSizes();
+        runPlatformTests();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

tests/TestCustomExternalForce.h

@@ -167,6 +167,38 @@ void testPeriodic() {
     }
 }
 
+void testZeroPeriodicDistance() {
+    Vec3 vx(5, 0, 0);
+    Vec3 vy(0, 6, 0);
+    Vec3 vz(1, 2, 7);
+    double x0 = 51, y0 = -17, z0 = 11.2;
+    System system;
+    system.setDefaultPeriodicBoxVectors(vx, vy, vz);
+    system.addParticle(1.0);
+    CustomExternalForce* force = new CustomExternalForce("periodicdistance(x, y, z, x0, y0, z0)^2");
+    force->addPerParticleParameter("x0");
+    force->addPerParticleParameter("y0");
+    force->addPerParticleParameter("z0");
+    vector<double> params(3);
+    params[0] = x0;
+    params[1] = y0;
+    params[2] = z0;
+    force->addParticle(0, params);
+    system.addForce(force);
+    ASSERT(force->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(1);
+    positions[0] = Vec3(x0, y0, z0);
+    context.setPositions(positions);
+
+    State state = context.getState(State::Positions | State::Forces | State::Energy);
+    vector<Vec3> forces = state.getForces();
+    for (int i = 0; i < 3; i++)
+        ASSERT_EQUAL(forces[0][i], forces[0][i]);
+}
+
 void testIllegalVariable() {
     System system;
     system.addParticle(1.0);
@@ -192,6 +224,7 @@ int main(int argc, char* argv[]) {
         testForce();
         testManyParameters();
         testPeriodic();
+        testZeroPeriodicDistance();
         testIllegalVariable();
         runPlatformTests();
     }

serialization/tests/TestSerializeGBVIForce.cpp → tests/TestEnforcePeriodicBox.cpp

@@ -6,8 +6,8 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
- * Authors: Peter Eastman                                                     *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
+ * Authors: Robert McGibbon                                                   *
  * Contributors:                                                              *
  *                                                                            *
  * Permission is hereby granted, free of charge, to any person obtaining a    *
@@ -30,74 +30,61 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/serialization/XmlSerializer.h"
+#include "openmm/Context.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/Platform.h"
+#include "openmm/VerletIntegrator.h"
+#include "sfmt/SFMT.h"
 #include <iostream>
-#include <sstream>
 
 using namespace OpenMM;
 using namespace std;
 
-void testSerialization() {
-    // Create a Force.
-
-    GBVIForce force;
-    force.setForceGroup(3);
-    force.setNonbondedMethod(GBVIForce::CutoffPeriodic);
-    force.setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
-    force.setQuinticLowerLimitFactor(0.123);
-    force.setQuinticUpperBornRadiusLimit(5.123);
-    force.setCutoffDistance(2.0);
-    force.setSoluteDielectric(5.1);
-    force.setSolventDielectric(50.0);
-    force.addParticle(1, 0.1, 0.01);
-    force.addParticle(0.5, 0.2, 0.02);
-    force.addParticle(-0.5, 0.3, 0.03);
-    force.addBond(0, 1, 2.0);
-    force.addBond(3, 5, 1.2);
-
-    // Serialize and then deserialize it.
-
-    stringstream buffer;
-    XmlSerializer::serialize<GBVIForce>(&force, "Force", buffer);
-    GBVIForce* copy = XmlSerializer::deserialize<GBVIForce>(buffer);
+void testTruncatedOctahedron() {
+    const int numMolecules = 5;
+    const int numParticles = numMolecules*2;
+    const float cutoff = 2.0;
+    Vec3 a(6.7929, 0, 0);
+    Vec3 b(-2.264163559406279, 6.404455775962287, 0);
+    Vec3 c(-2.264163559406279, -3.2019384603140684, 5.54658849047036);
+        
+    System system;
+    system.setDefaultPeriodicBoxVectors(a, b, c);
+    NonbondedForce* force = new NonbondedForce();
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    
+    force->setCutoffDistance(cutoff);
+    force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    
+    for (int i = 0; i < numMolecules; i++) {
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        force->addParticle(-1, 0.2, 0.2);
+        force->addParticle(1, 0.2, 0.2);
+        positions[2*i] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
+        positions[2*i+1] = positions[2*i] + Vec3(1.0, 0.0, 0.0);
+        system.addConstraint(2*i, 2*i+1, 1.0);
+    }
+    system.addForce(force);
+    
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    context.setPositions(positions);
+    State initialState = context.getState(State::Positions | State::Energy, true);
+    double initialEnergy = initialState.getPotentialEnergy();
 
-    // Compare the two forces to see if they are identical.
+    context.setState(initialState);
+    State finalState = context.getState(State::Positions | State::Energy, true);
+    double finalEnergy = finalState.getPotentialEnergy();
 
-    GBVIForce& force2 = *copy;
-    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
-    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
-    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
-    ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
-    ASSERT_EQUAL(force.getSolventDielectric(), force2.getSolventDielectric());
-    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
-    ASSERT_EQUAL(force.getQuinticUpperBornRadiusLimit(), force2.getQuinticUpperBornRadiusLimit());
-    ASSERT_EQUAL(force.getQuinticLowerLimitFactor(), force2.getQuinticLowerLimitFactor());
-    ASSERT_EQUAL(force.getBornRadiusScalingMethod(), force2.getBornRadiusScalingMethod());
-    for (int i = 0; i < force.getNumParticles(); i++) {
-        double charge1, radius1, scale1;
-        double charge2, radius2, scale2;
-        force.getParticleParameters(i, charge1, radius1, scale1);
-        force2.getParticleParameters(i, charge2, radius2, scale2);
-        ASSERT_EQUAL(charge1, charge2);
-        ASSERT_EQUAL(radius1, radius2);
-        ASSERT_EQUAL(scale1, scale2);
-    }
-    ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
-    for (int i = 0; i < force.getNumBonds(); i++) {
-        int a1, a2, b1, b2;
-        double da, db;
-        force.getBondParameters(i, a1, a2, da);
-        force2.getBondParameters(i, b1, b2, db);
-        ASSERT_EQUAL(a1, b1);
-        ASSERT_EQUAL(a2, b2);
-        ASSERT_EQUAL(da, db);
-    }
+    ASSERT_EQUAL_TOL(initialEnergy, finalEnergy, 1e-4);
 }
 
-int main() {
+int main(int argc, char* argv[]) {
     try {
-        testSerialization();
+        testTruncatedOctahedron();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

tests/TestGBSAOBCForce.h

@@ -255,7 +255,7 @@ void testForce(int numParticles, NonbondedForce::NonbondedMethod method, GBSAOBC
         State state2 = context.getState(State::Energy);
         context.setPositions(positions3);
         State state3 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-2)
+        ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state3.getPotentialEnergy()+norm*delta, 1e-5)
     }
 }
 

tests/TestLocalEnergyMinimizer.h

@@ -78,7 +78,7 @@ void testLargeSystem() {
     const int numParticles = numMolecules*2;
     const double cutoff = 2.0;
     const double boxSize = 4.0;
-    const double tolerance = 10;
+    const double tolerance = 15;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nonbonded = new NonbondedForce();

wrappers/python/filterPythonFiles.py

+
 from __future__ import print_function
+import re
 import sys
+import textwrap
+from inspect import cleandoc
+from numpydoc.docscrape import NumpyDocString
+
 
-# Doxygen does a bad job of generating documentation based on docstrings.  This script is run as a filter
-# on each file, and converts the docstrings into Doxygen style comments so we get better documentation.
+# Doxygen does a bad job of generating documentation based on docstrings.
+# This script is run as a filter
+# on each file, and converts the docstrings into Doxygen style comments
+# so we get better documentation.
 
 input = open(sys.argv[1])
+
 while True:
     line = input.readline()
     if len(line) == 0:
@@ -15,46 +24,57 @@ while True:
         split = stripped.split()
         if split[0] == 'class' and split[1][0].islower():
             # Classes that start with a lowercase letter were defined by SWIG.  We want to hide them.
-            print("%s## @private" % prefix)
+            print("%s## @private" % prefix, end='')
         if split[1][0] == '_' and split[1][1] != '_':
             # Names starting with a single _ are assumed to be private.
-            print("%s## @private" % prefix)
-        
+            print("%s## @private" % prefix, end='')
+
         # We're at the start of a class or function definition.  Find all lines that contain the declaration.
-        
+
         declaration = line
         while len(line) > 0 and line.find(':') == -1:
             line = input.readline()
             declaration += line
-        
+
         # Now look for a docstring.
-        
-        docstrings = []
+        docstringlines = []
         line = input.readline()
-        stripped = line.lstrip()
-        if stripped.startswith('"""'):
-            line = stripped[3:]
-            readingParameters = False
-            while line.find('"""') == -1:
-                docstrings.append(line)
+        l = line.strip()
+        if l.startswith('"""') or l.startswith("'''"):
+            if l.count('"""') == 2 or l.count("'''") == 2:
+                docstringlines.append(l[3:-3])
+            else:
+                docstringlines.append(l[3:])
                 line = input.readline()
-                if line.strip() == 'Parameters:':
-                    readingParameters = True
+                l = line.strip()
+                while l.find('"""') == -1 and l.find("'''") == -1:
+                    docstringlines.append(line.rstrip())
                     line = input.readline()
-                stripped = line.lstrip()
-                if readingParameters and stripped.startswith('- '):
-                    line = "@param %s" % stripped[2:]
-                elif stripped.startswith('Returns:'):
-                    line = "@return %s" % stripped[8:]
-            line = line[:line.find('"""')]
-            docstrings.append(line)            
-        
+                    l = line.strip()
+                if line.rstrip().endswith('"""') or line.rstrip().endswith("'''"):
+                    # last line
+                    docstringlines.append(line.rstrip()[:-3])
+
+        docstring = NumpyDocString(cleandoc('\n'.join(docstringlines)))
+        # print(docstringlines)
+
         # Print out the docstring in Doxygen syntax, followed by the declaration.
-        
-        for s in docstrings:
-            print("%s##%s" % (prefix, s.strip()))
-        print(declaration)
-        if len(docstrings) == 0:
-            print(line)
+        for line in docstring['Summary']:
+            print('{prefix}## {line}'.format(prefix=prefix, line=line))
+        if len(docstring['Extended Summary']) > 0:
+            print('{prefix}##'.format(prefix=prefix))
+            for line in docstring['Extended Summary']:
+                print('{prefix}## {line}'.format(prefix=prefix, line=line.strip()))
+        print('{prefix}##'.format(prefix=prefix))
+        for name, type, descr in docstring['Parameters']:
+            print('{prefix}## @param {name} ({type}) {descr}'.format(prefix=prefix, type=type, name=name, descr=' '.join(descr)))
+        for name, type, descr in docstring['Returns']:
+            if type == '':
+                type = name
+            print('{prefix}## @return ({type}) {descr}'.format(prefix=prefix, type=type, name=name, descr=' '.join(descr)))
+
+        print(declaration, end='')
+        if len(docstringlines) == 0:
+            print(line, end='')
     else:
-        print(line)
\ No newline at end of file
+        print(line, end='')

wrappers/python/simtk/openmm/amd.py

@@ -10,7 +10,7 @@ Portions copyright (c) 2012 Stanford University and the Authors.
 Authors: Peter Eastman, Steffen Lindert
 Contributors:
 
-Permission is hereby granted, free of charge, to any person obtaining a 
+Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
 to deal in the Software without restriction, including without limitation
 the rights to use, copy, modify, merge, publish, distribute, sublicense,
@@ -37,22 +37,26 @@ from simtk.unit import kilojoules_per_mole, is_quantity
 
 class AMDIntegrator(CustomIntegrator):
     """AMDIntegrator implements the aMD integration algorithm.
-    
+
     The system is integrated based on a modified potential.  Whenever the energy V(r) is less than a
     cutoff value E, the following effective potential is used:
-    
+
     V*(r) = V(r) + (E-V(r))^2 / (alpha+E-V(r))
-    
+
     For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
     """
-    
+
     def __init__(self, dt, alpha, E):
         """Create an AMDIntegrator.
-        
-        Parameters:
-         - dt (time) The integration time step to use
-         - alpha (energy) The alpha parameter to use
-         - E (energy) The energy cutoff to use
+
+        Parameters
+        ----------
+        dt : time
+            The integration time step to use
+        alpha : energy
+            The alpha parameter to use
+        E : energy
+            The energy cutoff to use
         """
         CustomIntegrator.__init__(self, dt)
         self.addGlobalVariable("alpha", alpha)
@@ -64,23 +68,23 @@ class AMDIntegrator(CustomIntegrator):
         self.addComputePerDof("x", "x+dt*v")
         self.addConstrainPositions()
         self.addComputePerDof("v", "(x-oldx)/dt")
-    
+
     def getAlpha(self):
         """Get the value of alpha for the integrator."""
         return self.getGlobalVariable(0)*kilojoules_per_mole
-    
+
     def setAlpha(self, alpha):
         """Set the value of alpha for the integrator."""
         self.setGlobalVariable(0, alpha)
-    
+
     def getE(self):
         """Get the energy threshold E for the integrator."""
         return self.getGlobalVariable(1)*kilojoules_per_mole
-    
+
     def setE(self, E):
         """Set the energy threshold E for the integrator."""
         self.setGlobalVariable(1, E)
-    
+
     def getEffectiveEnergy(self, energy):
         """Given the actual potential energy of the system, return the value of the effective potential."""
         alpha = self.getAlpha()
@@ -94,21 +98,26 @@ class AMDIntegrator(CustomIntegrator):
 
 class AMDForceGroupIntegrator(CustomIntegrator):
     """AMDForceGroupIntegrator implements a single boost aMD integration algorithm.
-    
+
     This is similar to AMDIntegrator, but is applied based on the energy of a single force group
     (typically representing torsions).
-    
+
     For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
     """
-    
+
     def __init__(self, dt, group, alphaGroup, EGroup):
         """Create a AMDForceGroupIntegrator.
-        
-        Parameters:
-         - dt (time) The integration time step to use
-         - group (int) The force group to apply the boost to
-         - alphaGroup (energy) The alpha parameter to use for the boosted force group
-         - EGroup (energy) The energy cutoff to use for the boosted force group
+
+        Parameters
+        ----------
+        dt : time
+            The integration time step to use
+        group : int
+            The force group to apply the boost to
+        alphaGroup : energy
+            The alpha parameter to use for the boosted force group
+        EGroup : energy
+            The energy cutoff to use for the boosted force group
         """
         CustomIntegrator.__init__(self, dt)
         self.addGlobalVariable("alphaGroup", alphaGroup)
@@ -124,29 +133,35 @@ class AMDForceGroupIntegrator(CustomIntegrator):
         self.addComputePerDof("x", "x+dt*v")
         self.addConstrainPositions()
         self.addComputePerDof("v", "(x-oldx)/dt")
-    
+
     def getAlphaGroup(self):
         """Get the value of alpha for the boosted force group."""
         return self.getGlobalVariable(0)*kilojoules_per_mole
-    
+
     def setAlphaGroup(self, alpha):
         """Set the value of alpha for the boosted force group."""
         self.setGlobalVariable(0, alpha)
-    
+
     def getEGroup(self):
         """Get the energy threshold E for the boosted force group."""
         return self.getGlobalVariable(1)*kilojoules_per_mole
-    
+
     def setEGroup(self, E):
         """Set the energy threshold E for the boosted force group."""
         self.setGlobalVariable(1, E)
-    
+
     def getEffectiveEnergy(self, groupEnergy):
         """Given the actual group energy of the system, return the value of the effective potential.
-        
-        Parameters:
-          - groupEnergy (energy): the actual potential energy of the boosted force group
-        Returns: the value of the effective potential
+
+        Parameters
+        ----------
+        groupEnergy : energy
+            the actual potential energy of the boosted force group
+
+        Returns
+        -------
+        energy
+            the value of the effective potential
         """
         alphaGroup = self.getAlphaGroup()
         EGroup = self.getEGroup()
@@ -161,24 +176,31 @@ class AMDForceGroupIntegrator(CustomIntegrator):
 
 class DualAMDIntegrator(CustomIntegrator):
     """DualAMDIntegrator implements a dual boost aMD integration algorithm.
-    
+
     This is similar to AMDIntegrator, but two different boosts are applied to the potential:
     one based on the total energy, and one based on the energy of a single force group
     (typically representing torsions).
 
     For details, see Hamelberg et al., J. Chem. Phys. 127, 155102 (2007).
     """
-    
+
     def __init__(self, dt, group, alphaTotal, ETotal, alphaGroup, EGroup):
         """Create a DualAMDIntegrator.
 
-        Parameters:
-         - dt (time) The integration time step to use
-         - group (int) The force group to apply the second boost to
-         - alphaTotal (energy) The alpha parameter to use for the total energy
-         - ETotal (energy) The energy cutoff to use for the total energy
-         - alphaGroup (energy) The alpha parameter to use for the boosted force group
-         - EGroup (energy) The energy cutoff to use for the boosted force group
+        Parameters
+        ----------
+        dt : time
+            The integration time step to use
+        group : int
+            The force group to apply the second boost to
+        alphaTotal : energy
+            The alpha parameter to use for the total energy
+        ETotal : energy
+            The energy cutoff to use for the total energy
+        alphaGroup : energy
+            The alpha parameter to use for the boosted force group
+        EGroup : energy
+            The energy cutoff to use for the boosted force group
         """
         CustomIntegrator.__init__(self, dt)
         self.addGlobalVariable("alphaTotal", alphaTotal)
@@ -201,46 +223,53 @@ class DualAMDIntegrator(CustomIntegrator):
         self.addComputePerDof("x", "x+dt*v")
         self.addConstrainPositions()
         self.addComputePerDof("v", "(x-oldx)/dt")
-    
+
     def getAlphaTotal(self):
         """Get the value of alpha for the total energy."""
         return self.getGlobalVariable(0)*kilojoules_per_mole
-    
+
     def setAlphaTotal(self, alpha):
         """Set the value of alpha for the total energy."""
         self.setGlobalVariable(0, alpha)
-    
+
     def getETotal(self):
         """Get the energy threshold E for the total energy."""
         return self.getGlobalVariable(1)*kilojoules_per_mole
-    
+
     def setETotal(self, E):
         """Set the energy threshold E for the total energy."""
         self.setGlobalVariable(1, E)
-    
+
     def getAlphaGroup(self):
         """Get the value of alpha for the boosted force group."""
         return self.getGlobalVariable(2)*kilojoules_per_mole
-    
+
     def setAlphaGroup(self, alpha):
         """Set the value of alpha for the boosted force group."""
         self.setGlobalVariable(2, alpha)
-    
+
     def getEGroup(self):
         """Get the energy threshold E for the boosted force group."""
         return self.getGlobalVariable(3)*kilojoules_per_mole
-    
+
     def setEGroup(self, E):
         """Set the energy threshold E for the boosted force group."""
         self.setGlobalVariable(3, E)
-    
+
     def getEffectiveEnergy(self, totalEnergy, groupEnergy):
         """Given the actual potential energy of the system, return the value of the effective potential.
-        
-        Parameters:
-         - totalEnergy (energy): the actual potential energy of the whole system
-         - groupEnergy (energy): the actual potential energy of the boosted force group
-        Returns: the value of the effective potential
+
+        Parameters
+        ----------
+        totalEnergy : energy
+            the actual potential energy of the whole system
+        groupEnergy : energy
+            the actual potential energy of the boosted force group
+
+        Returns
+        -------
+        energy
+            the value of the effective potential
         """
         alphaTotal = self.getAlphaTotal()
         ETotal = self.getETotal()

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

@@ -60,12 +60,17 @@ class AmberInpcrdFile(object):
     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.
-
-        Parameters:
-         - file (string) the name of the file to load
-         - loadVelocities (boolean=None) deprecated. Velocities are loaded automatically if present
-         - loadBoxVectors (boolean=None) deprecated. Box vectors are loaded automatically if present
+        An inpcrd file contains atom positions and, optionally, velocities and
+        periodic box dimensions.
+
+        Parameters
+        ----------
+        file : str
+             The name of the file to load
+        loadVelocities : bool
+             Deprecated. Velocities are loaded automatically if present
+        loadBoxVectors : bool
+            Deprecated. Box vectors are loaded automatically if present
         """
         self.file = file
         if loadVelocities is not None or loadBoxVectors is not None:
@@ -84,8 +89,11 @@ class AmberInpcrdFile(object):
     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
+        Parameters
+        ----------
+        asNumpy : bool=False
+            if true, the values are returned as a numpy array instead of a list
+            of Vec3s
         """
         if asNumpy:
             if self._numpyPositions is None:
@@ -97,8 +105,10 @@ class AmberInpcrdFile(object):
     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
+        Parameters
+        ----------
+        asNumpy : bool=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)
@@ -112,8 +122,11 @@ class AmberInpcrdFile(object):
     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
+        Parameters
+        ----------
+        asNumpy : bool=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)

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

@@ -69,6 +69,15 @@ class GBn2(object):
         return 'GBn2'
 GBn2 = GBn2()
 
+def _strip_optunit(thing, unit):
+    """
+    Strips optional units, converting to specified unit type. If no unit
+    present, it just returns the number
+    """
+    if u.is_quantity(thing):
+        return thing.value_in_unit(unit)
+    return thing
+
 class AmberPrmtopFile(object):
     """AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it."""
 
@@ -150,36 +159,59 @@ class AmberPrmtopFile(object):
                      implicitSolventSaltConc=0.0*(unit.moles/unit.liter),
                      implicitSolventKappa=None, temperature=298.15*unit.kelvin,
                      soluteDielectric=1.0, solventDielectric=78.5,
-                     removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005, switchDistance=0.0*unit.nanometer):
-        """Construct an OpenMM System representing the topology described by this prmtop file.
-
-        Parameters:
-         - nonbondedMethod (object=NoCutoff) The method to use for nonbonded interactions.  Allowed values are
-           NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
-         - nonbondedCutoff (distance=1*nanometer) The cutoff distance to use for nonbonded interactions
-         - constraints (object=None) Specifies which bonds angles should be implemented with constraints.
-           Allowed values are None, HBonds, AllBonds, or HAngles.
-         - rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
-         - implicitSolvent (object=None) If not None, the implicit solvent model to use.  Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
-         - implicitSolventSaltConc (float=0.0*unit.moles/unit.liter) The salt concentration for GB 
-                    calculations (modelled as a debye screening parameter). It is converted to the debye length (kappa)
-                    using the provided temperature and solventDielectric
-         - temperature (float=300*kelvin) Temperature of the system. Only used to compute the Debye length from
-                    implicitSolventSoltConc
-         - implicitSolventKappa (float units of 1/length) If this value is set, implicitSolventSaltConc will be ignored.
-         - soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
-         - solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
-         - removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
-         - hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to heavy atoms.  Any mass added to a hydrogen is
-           subtracted from the heavy atom to keep their total mass the same.
-         - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
-         -  switchDistance (distance=0*nanometer) The distance at which the
-            switching function is active for nonbonded interactions. If the
-            switchDistance evaluates to boolean False (if it is 0), no
-            switching function will be used. Illegal values will raise a
-            ValueError
-
-        Returns: the newly created System
+                     removeCMMotion=True, hydrogenMass=None, ewaldErrorTolerance=0.0005,
+                     switchDistance=0.0*unit.nanometer):
+        """Construct an OpenMM System representing the topology described by this
+        prmtop file.
+
+        Parameters
+        ----------
+        nonbondedMethod : object=NoCutoff
+            The method to use for nonbonded interactions.  Allowed values are
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+        nonbondedCutoff : distance=1*nanometer
+            The cutoff distance to use for nonbonded interactions
+        constraints : object=None
+            Specifies which bonds angles should be implemented with constraints.
+            Allowed values are None, HBonds, AllBonds, or HAngles.
+        rigidWater : boolean=True
+            If true, water molecules will be fully rigid regardless of the value
+            passed for the constraints argument
+        implicitSolvent : object=None
+            If not None, the implicit solvent model to use.  Allowed values are
+            HCT, OBC1, OBC2, GBn, or GBn2.
+        implicitSolventSaltConc : float=0.0*unit.moles/unit.liter
+            The salt concentration for GB calculations (modelled as a debye
+            screening parameter). It is converted to the debye length (kappa)
+            using the provided temperature and solventDielectric
+        temperature : float=300*kelvin
+            Temperature of the system. Only used to compute the Debye length
+            from implicitSolventSoltConc
+        implicitSolventKappa : float units of 1/length
+            If this value is set, implicitSolventSaltConc will be ignored.
+        soluteDielectric : float=1.0
+            The solute dielectric constant to use in the implicit solvent model.
+        solventDielectric : float=78.5
+            The solvent dielectric constant to use in the implicit solvent
+            model.
+        removeCMMotion : boolean=True
+            If true, a CMMotionRemover will be added to the System
+        hydrogenMass : mass=None
+            The mass to use for hydrogen atoms bound to heavy atoms.  Any mass
+            added to a hydrogen is subtracted from the heavy atom to keep their
+            total mass the same.
+        ewaldErrorTolerance : float=0.0005
+            The error tolerance to use if nonbondedMethod is Ewald or PME.
+        switchDistance : float=0*nanometers
+            A positive value turns on a potential energy switching function for
+            Lennard-Jones interactions. If the switchDistance is 0 or evaluates
+            to boolean False, no switching function will be used. Illegal values
+            (e.g., less than 0) will raise a ValueError
+
+        Returns
+        -------
+        System
+            the newly created System
         """
         if self._prmtop.chamber:
             raise ValueError("CHAMBER-style topology file detected. CHAMBER "
@@ -257,13 +289,14 @@ class AmberPrmtopFile(object):
 
         if switchDistance and nonbondedMethod is not ff.NoCutoff:
             # make sure it's legal
-            if switchDistance >= nonbondedCutoff:
+            if (_strip_optunit(switchDistance, u.nanometer) >=
+                    _strip_optunit(nonbondedCutoff, u.nanometer)):
                 raise ValueError('switchDistance is too large compared '
-                                     'to the cutoff!')
-                if abs(switchDistance) != switchDistance:
-                    # Detects negatives for both Quantity and float
-                    raise ValueError('switchDistance must be non-negative!')
-                force.setUseSwitchingFunction(True)
-                force.setSwitchingDistance(switchDistance)
+                                 'to the cutoff!')
+            if _strip_optunit(switchDistance, u.nanometer) < 0:
+                # Detects negatives for both Quantity and float
+                raise ValueError('switchDistance must be non-negative!')
+            force.setUseSwitchingFunction(True)
+            force.setSwitchingDistance(switchDistance)
 
         return sys

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

 """
 Provides a class for parsing CHARMM-style coordinate files, namely CHARMM .crd
 (coordinate) files and CHARMM .rst (restart) file. Uses CharmmFile class in
-_charmmfile.py for reading files 
+_charmmfile.py for reading files
 
 This file is part of the OpenMM molecular simulation toolkit originating from
 Simbios, the NIH National Center for Physics-Based Simulation of Biological
@@ -49,12 +49,17 @@ class CharmmCrdFile(object):
     Reads and parses a CHARMM coordinate file (.crd) into its components,
     namely the coordinates, CHARMM atom types, resid, resname, etc.
 
-    Main attributes:
-        - natom (int) : Number of atoms in the system
-        - resname (list) : Names of all residues
-        - positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...]
-
-    Example:
+    Attributes
+    ----------
+    natom : int
+        Number of atoms in the system
+    resname : list
+        Names of all residues
+    positions : list
+        All cartesian coordinates [x1, y1, z1, x2, ...]
+
+    Examples
+    --------
     >>> chm = CharmmCrdFile('testfiles/1tnm.crd')
     >>> print '%d atoms; %d coords' % (chm.natom, len(chm.positions))
     1414 atoms; 1414 coords
@@ -91,15 +96,15 @@ class CharmmCrdFile(object):
                 intitle = False
             elif line.strip()[0] != '*':
                 intitle = False
-            else: 
+            else:
                 intitle = True
 
         while len(line.strip()) == 0:      # Skip whitespace
             line = crdfile.readline()
-        
+
         try:
             self.natom = int(line.strip().split()[0])
-            
+
             for row in range(self.natom):
                 line = crdfile.readline().strip().split()
                 self.atomno.append(int(line[0]))
@@ -131,14 +136,21 @@ class CharmmRstFile(object):
     Reads and parses data, velocities and coordinates from a CHARMM restart
     file (.rst) of file name 'fname' into class attributes
 
-    Main attributes:
-        - natom (int) : Number of atoms in the system
-        - resname (list) : Names of all residues
-        - positions (list) : All cartesian coordinates [x1, y1, z1, x2, ...]
-        - positionsold (list) : Old cartesian coordinates
-        - velocities (list) : List of all cartesian velocities
-
-    Example:
+    Attributes
+    ----------
+    natom : int
+        Number of atoms in the system
+    resname : list
+        Names of all residues
+    positions : list
+        All cartesian coordinates [x1, y1, z1, x2, ...]
+    positionsold : list
+        Old cartesian coordinates
+    velocities : list
+        List of all cartesian velocities
+
+    Examples
+    --------
     >>> chm = CharmmRstFile('testfiles/sample-charmm.rst')
     >>> print chm.header[0]
     REST    37     1
@@ -155,7 +167,7 @@ class CharmmRstFile(object):
         self.positionsold = []
         self.positions = []
         self.velocities = []
-        
+
         self.ff_version = 0
         self.natom = 0
         self.npriv = 0
@@ -169,7 +181,7 @@ class CharmmRstFile(object):
     def _parse(self, fname):
 
         crdfile = open(fname, 'r')
-        readingHeader = True 
+        readingHeader = True
 
         while readingHeader:
             line = crdfile.readline()
@@ -177,7 +189,7 @@ class CharmmRstFile(object):
                 raise CharmmFileError('Premature end of file')
             line = line.strip()
             words = line.split()
-            if len(line) != 0:  
+            if len(line) != 0:
                 if words[0] == 'ENERGIES' or words[0] == '!ENERGIES':
                     readingHeader = False
                 else:
@@ -191,14 +203,14 @@ class CharmmRstFile(object):
                 if line[0][0:5] == 'NATOM' or line[0][0:6] == '!NATOM':
                     try:
                         line = self.header[row+1].strip().split()
-                        self.natom = int(line[0])     
+                        self.natom = int(line[0])
                         self.npriv = int(line[1])     # num. previous steps
-                        self.nstep = int(line[2])     # num. steps in file  
-                        self.nsavc = int(line[3])     # coord save frequency 
+                        self.nstep = int(line[2])     # num. steps in file
+                        self.nsavc = int(line[3])     # coord save frequency
                         self.nsavv = int(line[4])     # velocities "
                         self.jhstrt = int(line[5])    # Num total steps?
                         break
-                   
+
                     except (ValueError, IndexError) as e:
                         raise CharmmFileError('Problem parsing CHARMM restart')
 
@@ -244,7 +256,7 @@ class CharmmRstFile(object):
             if len(line) < 3*CHARMMLEN:
                 raise CharmmFileError("Less than 3 coordinates present in "
                                       "coordinate row or positions may be "
-                                      "truncated.") 
+                                      "truncated.")
 
             line = line.replace('D','E')     # CHARMM uses 'D' for exponentials
 

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

@@ -51,41 +51,43 @@ class CharmmParameterSet(object):
     the information found in the MASS section of the CHARMM topology file
     (TOP/RTF) and all of the information in the parameter files (PAR)
 
-    Parameters:
-        - filenames : List of topology, parameter, and stream files to load into
-          the parameter set. The following file type suffixes are recognized.
-          Unrecognized file types raise a TypeError
-            .rtf, .top -- Residue topology file
-            .par, .prm -- Parameter file
-            .str -- Stream file
-            .inp -- If "par" is in the file name, it is a parameter file. If
+    Parameters
+    ----------
+    filenames : List of topology, parameter, and stream files to load into the parameter set.
+        The following file type suffixes are recognized. Unrecognized file types raise a TypeError
+          * .rtf, .top -- Residue topology file
+          * .par, .prm -- Parameter file
+          * .str -- Stream file
+          * .inp -- If "par" is in the file name, it is a parameter file. If
                     "top" is in the file name, it is a topology file. Otherwise,
                     raise TypeError
 
-    Attributes:
-        All type lists are dictionaries whose keys are tuples (with however
-        many elements are needed to define that type of parameter). The types
-        that can be in any order are SORTED.
-        
-        - atom_types_str
-        - atom_types_int
-        - atom_types_tuple
-        - bond_types
-        - angle_types
-        - urey_bradley_types
-        - dihedral_types
-        - improper_types
-        - cmap_types
-        - nbfix_types
-
-        The dihedral types can be multiterm, so the values for each dict key is
-        actually a list of DihedralType instances. The atom_types are dicts that
-        match the name (str), number (int), or (name, number) tuple (tuple) to
-        the atom type. The tuple is guaranteed to be the most robust, although
-        when only the integer or string is available the other dictionaries are
-        helpful
-
-    Example:
+    Attributes
+    ----------
+    All type lists are dictionaries whose keys are tuples (with however
+    many elements are needed to define that type of parameter). The types
+    that can be in any order are SORTED.
+
+    - atom_types_str
+    - atom_types_int
+    - atom_types_tuple
+    - bond_types
+    - angle_types
+    - urey_bradley_types
+    - dihedral_types
+    - improper_types
+    - cmap_types
+    - nbfix_types
+
+    The dihedral types can be multiterm, so the values for each dict key is
+    actually a list of DihedralType instances. The atom_types are dicts that
+    match the name (str), number (int), or (name, number) tuple (tuple) to
+    the atom type. The tuple is guaranteed to be the most robust, although
+    when only the integer or string is available the other dictionaries are
+    helpful
+
+    Examples
+    --------
     >>> params = CharmmParameterSet('charmm22.top', 'charmm22.par', 'file.str')
     """
 
@@ -113,7 +115,7 @@ class CharmmParameterSet(object):
         self.cmap_types = dict()
         self.nbfix_types = dict()
         self.parametersets = []
-        
+
         # Load all of the files
         tops, pars, strs = [], [], []
         for arg in args:
@@ -150,23 +152,30 @@ class CharmmParameterSet(object):
         Instantiates a CharmmParameterSet from a Topology file and a Parameter
         file (or just a Parameter file if it has all information)
 
-        Parameters:
-            - tfile (str) : Name of the Topology (RTF/TOP) file
-            - pfile (str) : Name of the Parameter (PAR) file
-            - sfiles (list of str) : List or tuple of stream (STR) file names.
-            - permissive (bool) : Accept non-bonbded parameters for undefined 
-                                  atom types (default False)
-
-        Returns:
+        Parameters
+        -----------
+        tfile : str
+            Name of the Topology (RTF/TOP) file
+        pfile : str
+            Name of the Parameter (PAR) file
+        sfiles : list of str
+            List or tuple of stream (STR) file names.
+        permissive : bool=False
+            Accept non-bonbded parameters for undefined atom types
+
+        Returns
+        -------
+        CharmmParameterSet
             New CharmmParameterSet populated with the parameters found in the
             provided files.
-            
-        Notes:
-            The RTF file is read first (if provided), followed by the PAR file,
-            followed by the list of stream files (in the order they are
-            provided). Parameters in each stream file will overwrite those that
-            came before (or simply append to the existing set if they are
-            different)
+
+        Notes
+        -----
+        The RTF file is read first (if provided), followed by the PAR file,
+        followed by the list of stream files (in the order they are
+        provided). Parameters in each stream file will overwrite those that
+        came before (or simply append to the existing set if they are
+        different)
         """
         inst = cls()
         if tfile is not None:
@@ -183,21 +192,24 @@ class CharmmParameterSet(object):
         return inst
 
     def readParameterFile(self, pfile, permissive=False):
-        """
-        Reads all of the parameters from a parameter file. Versions 36 and
-        later of the CHARMM force field files have an ATOMS section defining
-        all of the atom types.  Older versions need to load this information
-        from the RTF/TOP files.
-
-        Parameters:
-            - pfile (str) : Name of the CHARMM PARameter file to read
-            - permissive (bool) : Accept non-bonbded parameters for undefined 
-                                  atom types (default False)
-
-        Notes: The atom types must all be loaded by the end of this routine.
-        Either supply a PAR file with atom definitions in them or read in a
-        RTF/TOP file first. Failure to do so will result in a raised
-        RuntimeError.
+        """Reads all of the parameters from a parameter file. Versions 36 and later
+        of the CHARMM force field files have an ATOMS section defining all of
+        the atom types.  Older versions need to load this information from the
+        RTF/TOP files.
+
+        Parameters
+        ----------
+        pfile : str
+            Name of the CHARMM PARameter file to read
+        permissive : bool
+            Accept non-bonbded parameters for undefined atom types (default:
+            False).
+
+        Notes
+        -----
+        The atom types must all be loaded by the end of this routine. Either
+        supply a PAR file with atom definitions in them or read in a RTF/TOP
+        file first. Failure to do so will result in a raised RuntimeError.
         """
         conv = CharmmParameterSet._convert
         if isinstance(pfile, str):
@@ -353,7 +365,7 @@ class CharmmParameterSet(object):
                         if dtype.per == dihedral.per:
                             # Replace. Warn if they are different
                             if dtype != dihedral:
-                                warnings.warn('Replacing dihedral %r with %r' % 
+                                warnings.warn('Replacing dihedral %r with %r' %
                                               (dtype, dihedral))
                             self.dihedral_types[key]
                             replaced = True
@@ -487,7 +499,7 @@ class CharmmParameterSet(object):
             ty = CmapType(current_cmap_res, current_cmap_data)
             self.cmap_types[current_cmap] = ty
 
-        # If in permissive mode create an atomtype for every type used in  
+        # If in permissive mode create an atomtype for every type used in
         # the nonbonded parameters. This is a work-around for when all that's
         # available is a CHARMM22 inp file, which has no ATOM/MASS fields
 
@@ -499,7 +511,7 @@ class CharmmParameterSet(object):
             for key in nonbonded_types:
                 if not key in self.atom_types_str:
                     atype =AtomType(name=key, number=idx, mass= float('NaN'), atomic_number= 1 )
-                    self.atom_types_str[key] = atype 
+                    self.atom_types_str[key] = atype
                     self.atom_types_int[idx] = atype
                     idx=idx+1
 
@@ -518,14 +530,17 @@ class CharmmParameterSet(object):
         if own_handle: f.close()
 
     def readTopologyFile(self, tfile):
-        """
-        Reads _only_ the atom type definitions from a topology file. This is
+        """Reads _only_ the atom type definitions from a topology file. This is
         unnecessary for versions 36 and later of the CHARMM force field.
 
-        Parameters:
-            - tfile (str) : Name of the CHARMM TOPology file to read
+        Parameters
+        ----------
+        tfile : str
+            : Name of the CHARMM TOPology file to read
 
-        Note: The CHARMM TOPology file is also called a Residue Topology File
+        Notes
+        -----
+        The CHARMM TOPology file is also called a Residue Topology File
         """
         conv = CharmmParameterSet._convert
         if isinstance(tfile, str):
@@ -564,12 +579,13 @@ class CharmmParameterSet(object):
         if own_handle: f.close()
 
     def readStreamFile(self, sfile):
-        """
-        Reads RTF and PAR sections from a stream file and dispatches the
+        """Reads RTF and PAR sections from a stream file and dispatches the
         sections to readTopologyFile or readParameterFile
 
-        Parameters:
-            - sfile (str or CharmmStreamFile) : Stream file to parse
+        Parameters
+        ----------
+        sfile : str or CharmmStreamFile
+            Stream file to parse
         """
         if isinstance(sfile, CharmmStreamFile):
             f = sfile
@@ -594,14 +610,8 @@ class CharmmParameterSet(object):
         bond, angle, dihedral, improper, or cmap type will pair with EVERY key
         in the type mapping dictionaries that points to the equivalent type
 
-        Returns:
-            - Returns the instance that is being condensed.
-
-        Notes:
-            The return value allows you to condense the types at construction
-            time.
-
-        Example:
+        Example
+        -------
         >>> params = CharmmParameterSet('charmm.prm').condense()
         """
         # First scan through all of the bond types
@@ -631,8 +641,10 @@ class CharmmParameterSet(object):
         """
         Loops through the given dict and condenses all types.
 
-        Parameter:
-            - typedict : Type dictionary to condense
+        Parameters
+        ----------
+        typedict
+            Type dictionary to condense
         """
         keylist = list(typedict.keys())
         for i in range(len(keylist) - 1):

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

@@ -102,17 +102,22 @@ class _ZeroDict(dict):
                 return [0, 0], []
             return 0, []
 
+def _strip_optunit(thing, unit):
+    """
+    Strips optional units, converting to specified unit type. If no unit
+    present, it just returns the number
+    """
+    if u.is_quantity(thing):
+        return thing.value_in_unit(unit)
+    return thing
+
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
 _resre = re.compile(r'(\d+)([a-zA-Z]*)')
 
 class CharmmPsfFile(object):
-    """
-    A chemical structure instantiated from CHARMM files.
+    """A chemical structure instantiated from CHARMM files.
 
-    Example:
-    >>> cs = CharmmPsfFile("testfiles/test.psf")
-    
     This structure has numerous attributes that are lists of the elements of
     this structure, including atoms, bonds, torsions, etc. The attributes are
         - residue_list
@@ -129,13 +134,14 @@ class CharmmPsfFile(object):
 
     Additional attribute is available if a CharmmParameterSet is loaded into
     this structure.
-        
+
         - urey_bradley_list
 
     The lengths of each of these lists gives the pointers (e.g., natom, nres,
     etc.)
 
-    Example:
+    Examples
+    --------
     >>> cs = CharmmPsfFile("testfiles/test.psf")
     >>> len(cs.atom_list)
     33
@@ -154,19 +160,21 @@ class CharmmPsfFile(object):
     CMAP_FORCE_GROUP = 5
     NONBONDED_FORCE_GROUP = 6
     GB_FORCE_GROUP = 6
-    
+
     @_catchindexerror
     def __init__(self, psf_name):
-        """
-        Opens and parses a PSF file, then instantiates a CharmmPsfFile
+        """Opens and parses a PSF file, then instantiates a CharmmPsfFile
         instance from the data.
-            
-        Parameters:
-            psf_name (str) : Name of the PSF file (it must exist)
-        
-        Exceptions Raised:
-            IOError : If file "psf_name" does not exist
-            CharmmPSFError: If any parsing errors are encountered
+
+        Parameters
+        ----------
+        psf_name : str
+            Name of the PSF file (it must exist)
+
+        Raises
+        ------
+        IOError : If file "psf_name" does not exist
+        CharmmPSFError: If any parsing errors are encountered
         """
         conv = CharmmPsfFile._convert
         # Make sure the file exists
@@ -379,14 +387,17 @@ class CharmmPsfFile(object):
 
     @staticmethod
     def _convert(string, type, message):
-        """
-        Converts a string to a specific type, making sure to raise
+        """Converts a string to a specific type, making sure to raise
         CharmmPSFError with the given message in the event of a failure.
 
-        Parameters:
-            - string (str) : Input string to process
-            - type (type) : Type of data to convert to
-            - message (str) : Error message to put in exception if failed
+        Parameters
+        ----------
+        string : str
+            Input string to process
+        type : type
+            Type of data to convert to
+        message : str
+            Error message to put in exception if failed
         """
         try:
             return type(string)
@@ -396,23 +407,24 @@ class CharmmPsfFile(object):
 
     @staticmethod
     def _parse_psf_section(psf):
-        """
-        This method parses a section of the PSF file
-
-        Parameters:
-            - psf (CharmmFile) : Open file that is pointing to the first line
-                                 of the section that is to be parsed
-        
-        Returns:
-            (title, pointers, data)
-
-            - title (str) : The label of the PSF section we are parsing
-            - pointers (int/tuple of ints) : If one pointer is set, pointers is
-                    simply the integer that is value of that pointer. Otherwise
-                    it is a tuple with every pointer value defined in the first
-                    line
-            - data (list) : A list of all data in the parsed section converted
-                    to `dtype'
+        """This method parses a section of the PSF file
+
+        Parameters
+        ----------
+         psf : CharmmFile
+             Open file that is pointing to the first line of the section
+             that is to be parsed
+
+        Returns
+        --------
+        str
+            The label of the PSF section we are parsing
+        int/tuple of ints
+            If one pointer is set, pointers is simply the integer that is
+            value of that pointer. Otherwise it is a tuple with every pointer
+            value defined in the first line
+        list
+            A list of all data in the parsed section converted to `dtype'
         """
         conv = CharmmPsfFile._convert
         line = psf.readline()
@@ -453,25 +465,25 @@ class CharmmPsfFile(object):
         return title, pointers, data
 
     def loadParameters(self, parmset):
-        """
-        Loads parameters from a parameter set that was loaded via CHARMM RTF,
+        """Loads parameters from a parameter set that was loaded via CHARMM RTF,
         PAR, and STR files.
 
-        Parameters:
-            - parmset (CharmmParameterSet) : List of all parameters
-
-        Notes:
-            - If any parameters that are necessary cannot be found, a
-              MissingParameter exception is raised.
-
-            - If any dihedral or improper parameters cannot be found, I will try
-              inserting wildcards (at either end for dihedrals and as the two
-              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_parameter_list attribute by
-              adding a separate Dihedral object for each term for types that
-              have a multi-term expansion
+        Parameters
+        ----------
+        parmset : CharmmParameterSet
+            List of all parameters
+
+        Notes
+        -----
+        - If any parameters that are necessary cannot be found, a
+          MissingParameter exception is raised.
+        - If any dihedral or improper parameters cannot be found, I will try
+          inserting wildcards (at either end for dihedrals and as the two
+          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_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
@@ -579,13 +591,22 @@ class CharmmPsfFile(object):
 
     def setBox(self, a, b, c, alpha=90.0*u.degrees, beta=90.0*u.degrees,
                gamma=90.0*u.degrees):
-        """
-        Sets the periodic box boundary conditions.
-
-        Parameters:
-            - a, b, c (floats) : Lengths of the periodic cell
-            - alpha, beta, gamma (floats, optional) : Angles between the
-                periodic cell vectors.
+        """Sets the periodic box boundary conditions.
+
+        Parameters
+        ----------
+        a : length
+            Lengths of the periodic cell
+        b : length
+            Lengths of the periodic cell
+        c : length
+            Lengths of the periodic cell
+        alpha : floats, optional
+            Angles between the periodic cell vectors.
+        beta : floats, optional
+            Angles between the periodic cell vectors.
+        gamma : floats, optional
+            Angles between the periodic cell vectors.
         """
         try:
             # Since we are setting the box, delete the cached box lengths if we
@@ -611,7 +632,7 @@ class CharmmPsfFile(object):
             pass
         # Cache the topology for easy returning later
         self._topology = topology = Topology()
-        
+
         last_chain = None
         last_residue = None
         # Add each chain (separate 'system's) and residue
@@ -743,52 +764,60 @@ class CharmmPsfFile(object):
                      ewaldErrorTolerance=0.0005,
                      flexibleConstraints=True,
                      verbose=False):
-        """
-        Construct an OpenMM System representing the topology described by the
+        """Construct an OpenMM System representing the topology described by the
         prmtop file. You MUST have loaded a parameter set into this PSF before
         calling createSystem. If not, AttributeError will be raised. ValueError
         is raised for illegal input.
 
-        Parameters:
-         -  params (CharmmParameterSet) The parameter set to use to parametrize
-               this molecule
-         -  nonbondedMethod (object=NoCutoff) The method to use for nonbonded
-               interactions. Allowed values are NoCutoff, CutoffNonPeriodic,
-               CutoffPeriodic, Ewald, or PME.
-         -  nonbondedCutoff (distance=1*nanometer) The cutoff distance to use
-               for nonbonded interactions.
-         -  switchDistance (distance=0*nanometer) The distance at which the
-               switching function is active for nonbonded interactions. If the
-               switchDistance evaluates to boolean False (if it is 0), no
-               switching function will be used. Illegal values will raise a
-               ValueError
-         -  constraints (object=None) Specifies which bonds or angles should be
-               implemented with constraints. Allowed values are None, HBonds,
-               AllBonds, or HAngles.
-         -  rigidWater (boolean=True) If true, water molecules will be fully
-               rigid regardless of the value passed for the constraints argument
-         -  implicitSolvent (object=None) If not None, the implicit solvent
-               model to use. Allowed values are HCT, OBC1, OBC2, or GBn
-         -  implicitSolventKappa (float=None): Debye screening parameter to
-               model salt concentrations in GB solvent.
-         -  implicitSolventSaltConc (float=0.0*u.moles/u.liter): Salt
-               concentration for GB simulations. Converted to Debye length
-               `kappa'
-         -  temperature (float=298.15*u.kelvin): Temperature used in the salt
-               concentration-to-kappa conversion for GB salt concentration term
-         -  soluteDielectric (float=1.0) The solute dielectric constant to use
-               in the implicit solvent model.
-         -  solventDielectric (float=78.5) The solvent dielectric constant to
-               use in the implicit solvent model.
-         -  removeCMMotion (boolean=True) If true, a CMMotionRemover will be
-               added to the System.
-         -  hydrogenMass (mass=None) The mass to use for hydrogen atoms bound to
-               heavy atoms. Any mass added to a hydrogen is subtracted from the
-               heavy atom to keep their total mass the same.
-         -  ewaldErrorTolerance (float=0.0005) The error tolerance to use if the
-               nonbonded method is Ewald or PME.
-         -  flexibleConstraints (bool=True) Are our constraints flexible or not?
-         -  verbose (bool=False) Optionally prints out a running progress report
+        Parameters
+        ----------
+        params : CharmmParameterSet
+            The parameter set to use to parametrize this molecule
+        nonbondedMethod : object=NoCutoff
+            The method to use for nonbonded interactions. Allowed values are
+            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
+        nonbondedCutoff : distance=1*nanometer
+            The cutoff distance to use for nonbonded interactions.
+        switchDistance : distance=0*nanometer
+            The distance at which the switching function is active for nonbonded
+            interactions. If the switchDistance evaluates to boolean False (if
+            it is 0), no switching function will be used. Illegal values will
+            raise a ValueError
+        constraints : object=None
+            Specifies which bonds or angles should be implemented with
+            constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
+        rigidWater : boolean=True
+            If true, water molecules will be fully rigid regardless of the value
+            passed for the constraints argument
+        implicitSolvent : object=None
+            If not None, the implicit solvent model to use. Allowed values are
+            HCT, OBC1, OBC2, or GBn
+        implicitSolventKappa : float=None
+            Debye screening parameter to model salt concentrations in GB
+            solvent.
+        implicitSolventSaltConc : float=0.0*u.moles/u.liter
+            Salt concentration for GB simulations. Converted to Debye length
+            `kappa'
+        temperature : float=298.15*u.kelvin
+            Temperature used in the salt concentration-to-kappa conversion for
+            GB salt concentration term
+        soluteDielectric : float=1.0
+            The solute dielectric constant to use in the implicit solvent model.
+        solventDielectric : float=78.5
+            The solvent dielectric constant to use in the implicit solvent
+            model.
+        removeCMMotion : boolean=True
+            If true, a CMMotionRemover will be added to the System.
+        hydrogenMass : mass=None
+            The mass to use for hydrogen atoms bound to heavy atoms. Any mass
+            added to a hydrogen is subtracted from the heavy atom to keep their
+            total mass the same.
+        ewaldErrorTolerance : float=0.0005
+            The error tolerance to use if the nonbonded method is Ewald or PME.
+        flexibleConstraints : bool=True
+            Are our constraints flexible or not?
+        verbose : bool=False
+            Optionally prints out a running progress report
         """
         # Load the parameter set
         self.loadParameters(params.condense())
@@ -812,7 +841,7 @@ class CharmmPsfFile(object):
             raise ValueError('Illegal implicit solvent model choice.')
         if not constraints in (None, ff.HAngles, ff.HBonds, ff.AllBonds):
             raise ValueError('Illegal constraints choice')
-      
+
         # Define conversion factors
         length_conv = u.angstrom.conversion_factor_to(u.nanometer)
         _chmfrc = u.kilocalorie_per_mole/(u.angstrom*u.angstrom)
@@ -824,7 +853,7 @@ class CharmmPsfFile(object):
         dihe_frc_conv = u.kilocalorie_per_mole.conversion_factor_to(
                             u.kilojoule_per_mole)
         ene_conv = dihe_frc_conv
-      
+
         # Create the system and determine if any of our atoms have NBFIX (and
         # therefore requires a CustomNonbondedForce instead)
         typenames = set()
@@ -1026,10 +1055,11 @@ class CharmmPsfFile(object):
             # See if we need to use a switching function
             if switchDistance and nonbondedMethod is not ff.NoCutoff:
                 # make sure it's legal
-                if switchDistance >= nonbondedCutoff:
+                if (_strip_optunit(switchDistance, u.nanometer) >=
+                        _strip_optunit(nonbondedCutoff, u.nanometer)):
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                if abs(switchDistance) != switchDistance:
+                if _strip_optunit(switchDistance, u.nanometer) < 0:
                     # Detects negatives for both Quantity and float
                     raise ValueError('switchDistance must be non-negative!')
                 force.setUseSwitchingFunction(True)
@@ -1070,10 +1100,11 @@ class CharmmPsfFile(object):
             # See if we need to use a switching function
             if switchDistance and nonbondedMethod is not ff.NoCutoff:
                 # make sure it's legal
-                if switchDistance >= nonbondedCutoff:
+                if (_strip_optunit(switchDistance, u.nanometer) >=
+                        _strip_optunit(nonbondedCutoff, u.nanometer)):
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                if abs(switchDistance) != switchDistance:
+                if _strip_optunit(switchDistance, u.nanometer) < 0:
                     # Detects negatives for both Quantity and float
                     raise ValueError('switchDistance must be non-negative!')
                 force.setUseSwitchingFunction(True)
@@ -1156,11 +1187,15 @@ class CharmmPsfFile(object):
                 raise ValueError('Unrecognized nonbonded method')
             if switchDistance and nonbondedMethod is not ff.NoCutoff:
                 # make sure it's legal
-                if switchDistance >= nonbondedCutoff:
+                if (_strip_optunit(switchDistance, u.nanometer) >=
+                        _strip_optunit(nonbondedCutoff, u.nanometer)):
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                    cforce.setUseSwitchingFunction(True)
-                    cforce.setSwitchingDistance(switchDistance)
+                if _strip_optunit(switchDistance, u.nanometer) < 0:
+                    # Detects negatives for both Quantity and float
+                    raise ValueError('switchDistance must be non-negative!')
+                cforce.setUseSwitchingFunction(True)
+                cforce.setSwitchingDistance(switchDistance)
             for i in lj_idx_list:
                 cforce.addParticle((i - 1,)) # adjust for indexing from 0
 
@@ -1343,7 +1378,7 @@ class CharmmPsfFile(object):
     def boxLengths(self, stuff):
         raise RuntimeError('Use setBox to set a box with lengths and angles '
                            'or set the boxVectors attribute with box vectors')
-    
+
     @property
     def boxVectors(self):
         """ Return the box vectors """
@@ -1388,12 +1423,12 @@ def set_molecules(atom_list):
     owner = []
     # The way I do this is via a recursive algorithm, in which
     # the "set_owner" method is called for each bonded partner an atom
-    # has, which in turn calls set_owner for each of its partners and 
+    # has, which in turn calls set_owner for each of its partners and
     # so on until everything has been assigned.
     molecule_number = 1 # which molecule number we are on
     for i in range(len(atom_list)):
         # If this atom has not yet been "owned", make it the next molecule
-        # However, we only increment which molecule number we're on if 
+        # However, we only increment which molecule number we're on if
         # we actually assigned a new molecule (obviously)
         if not atom_list[i].marked:
             tmp = [i]
@@ -1414,7 +1449,7 @@ def _set_owner(atom_list, owner_array, atm, mol_id):
             owner_array.append(partner.idx)
             _set_owner(atom_list, owner_array, partner.idx, mol_id)
         elif partner.marked != mol_id:
-            raise MoleculeError('Atom %d in multiple molecules' % 
+            raise MoleculeError('Atom %d in multiple molecules' %
                                 partner.idx)
 
 # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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

@@ -8,7 +8,7 @@ Medical Research, grant U54 GM072970. See https://simtk.org.
 
 Portions copyright (c) 2014 Stanford University and the Authors.
 Authors: Robert McGibbon
-Contributors: 
+Contributors:
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -71,10 +71,12 @@ class CheckpointReporter(object):
     def __init__(self, file, reportInterval):
         """Create a CheckpointReporter.
 
-        Parameters:
-         - file (string or open file object) The file to write to. Any current
-           contents will be overwritten.
-         - reportInterval (int) The interval (in time steps) at which to write checkpoints
+        Parameters
+        ----------
+        file : string or open file object
+            The file to write to. Any current contents will be overwritten.
+        reportInterval : int
+            The interval (in time steps) at which to write checkpoints.
         """
 
         self._reportInterval = reportInterval
@@ -88,12 +90,18 @@ class CheckpointReporter(object):
     def describeNextReport(self, simulation):
         """Get information about the next report this object will generate.
 
-        Parameters:
-         - simulation (Simulation) The Simulation to generate a report for
-
-        Returns: A five element tuple.  The first element is the number of steps until the
-        next report.  The remaining elements specify whether that report will require
-        positions, velocities, forces, and energies respectively.
+        Parameters
+        ----------
+        simulation : Simulation
+            The Simulation to generate a report for
+
+        Returns
+        -------
+        tuple
+            A five element tuple. The first element is the number of steps
+            until the next report. The remaining elements specify whether
+            that report will require positions, velocities, forces, and
+            energies respectively.
         """
         steps = self._reportInterval - simulation.currentStep%self._reportInterval
         return (steps, False, False, False, False)
@@ -101,9 +109,12 @@ class CheckpointReporter(object):
     def report(self, simulation, state):
         """Generate a report.
 
-        Parameters:
-         - simulation (Simulation) The Simulation to generate a report for
-         - state (State) The current state of the simulation
+        Parameters
+        ----------
+        simulation : Simulation
+            The Simulation to generate a report for
+        state : State
+            The current state of the simulation
         """
         self._out.seek(0)
         chk = simulation.context.createCheckpoint()