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Commit cf8a03e8 authored by peastman's avatar peastman
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Merged changes from main branch

parents f7f70136 31d02cdc
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Showing with 809 additions and 192 deletions
serialization/src/CustomGBForceProxy.cpp
View file @ cf8a03e8
......@@ -87,16 +87,8 @@ void CustomGBForceProxy::serialize(const void* object, SerializationNode& node)
exclusions.createChildNode("Exclusion").setIntProperty("p1", particle1).setIntProperty("p2", particle2);
}
SerializationNode& functions = node.createChildNode("Functions");
for (int i = 0; i < force.getNumFunctions(); i++) {
string name;
vector<double> values;
double min, max;
force.getFunctionParameters(i, name, values, min, max);
SerializationNode& node = functions.createChildNode("Function").setStringProperty("name", name).setDoubleProperty("min", min).setDoubleProperty("max", max);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
}
void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
......@@ -147,11 +139,18 @@ void* CustomGBForceProxy::deserialize(const SerializationNode& node) const {
const SerializationNode& functions = node.getChildNode("Functions");
for (int i = 0; i < (int) functions.getChildren().size(); i++) {
const SerializationNode& function = functions.getChildren()[i];
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
force->addFunction(function.getStringProperty("name"), values, function.getDoubleProperty("min"), function.getDoubleProperty("max"));
if (function.hasProperty("type")) {
force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
}
else {
// This is an old file created before TabulatedFunction existed.
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
}
}
return force;
}
......
serialization/src/CustomHbondForceProxy.cpp
View file @ cf8a03e8
......@@ -92,16 +92,8 @@ void CustomHbondForceProxy::serialize(const void* object, SerializationNode& nod
exclusions.createChildNode("Exclusion").setIntProperty("donor", donor).setIntProperty("acceptor", acceptor);
}
SerializationNode& functions = node.createChildNode("Functions");
for (int i = 0; i < force.getNumFunctions(); i++) {
string name;
vector<double> values;
double min, max;
force.getFunctionParameters(i, name, values, min, max);
SerializationNode& node = functions.createChildNode("Function").setStringProperty("name", name).setDoubleProperty("min", min).setDoubleProperty("max", max);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
}
void* CustomHbondForceProxy::deserialize(const SerializationNode& node) const {
......@@ -159,11 +151,18 @@ void* CustomHbondForceProxy::deserialize(const SerializationNode& node) const {
const SerializationNode& functions = node.getChildNode("Functions");
for (int i = 0; i < (int) functions.getChildren().size(); i++) {
const SerializationNode& function = functions.getChildren()[i];
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
force->addFunction(function.getStringProperty("name"), values, function.getDoubleProperty("min"), function.getDoubleProperty("max"));
if (function.hasProperty("type")) {
force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
}
else {
// This is an old file created before TabulatedFunction existed.
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
}
}
return force;
}
......
serialization/src/CustomNonbondedForceProxy.cpp
View file @ cf8a03e8
......@@ -74,16 +74,8 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
exclusions.createChildNode("Exclusion").setIntProperty("p1", particle1).setIntProperty("p2", particle2);
}
SerializationNode& functions = node.createChildNode("Functions");
for (int i = 0; i < force.getNumFunctions(); i++) {
string name;
vector<double> values;
double min, max;
force.getFunctionParameters(i, name, values, min, max);
SerializationNode& node = functions.createChildNode("Function").setStringProperty("name", name).setDoubleProperty("min", min).setDoubleProperty("max", max);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
}
void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) const {
......@@ -124,11 +116,18 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
const SerializationNode& functions = node.getChildNode("Functions");
for (int i = 0; i < (int) functions.getChildren().size(); i++) {
const SerializationNode& function = functions.getChildren()[i];
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
force->addFunction(function.getStringProperty("name"), values, function.getDoubleProperty("min"), function.getDoubleProperty("max"));
if (function.hasProperty("type")) {
force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
}
else {
// This is an old file created before TabulatedFunction existed.
const SerializationNode& valuesNode = function.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
}
}
return force;
}
......
serialization/src/SerializationProxyRegistration.cpp
View file @ cf8a03e8
......@@ -30,6 +30,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/AndersenThermostat.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/CustomAngleForce.h"
......@@ -38,26 +39,26 @@
#include "openmm/CustomExternalForce.h"
#include "openmm/CustomGBForce.h"
#include "openmm/CustomHbondForce.h"
#include "openmm/CustomIntegrator.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/CustomTorsionForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/MonteCarloBarostat.h"
#include "openmm/NonbondedForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/RBTorsionForce.h"
#include "openmm/System.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/CustomIntegrator.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/TabulatedFunction.h"
#include "openmm/VariableLangevinIntegrator.h"
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/serialization/SerializationProxy.h"
#include "openmm/serialization/BrownianIntegratorProxy.h"
#include "openmm/serialization/AndersenThermostatProxy.h"
#include "openmm/serialization/CMAPTorsionForceProxy.h"
#include "openmm/serialization/CMMotionRemoverProxy.h"
......@@ -67,23 +68,21 @@
#include "openmm/serialization/CustomExternalForceProxy.h"
#include "openmm/serialization/CustomGBForceProxy.h"
#include "openmm/serialization/CustomHbondForceProxy.h"
#include "openmm/serialization/CustomIntegratorProxy.h"
#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"
#include "openmm/serialization/MonteCarloBarostatProxy.h"
#include "openmm/serialization/NonbondedForceProxy.h"
#include "openmm/serialization/PeriodicTorsionForceProxy.h"
#include "openmm/serialization/RBTorsionForceProxy.h"
#include "openmm/serialization/SystemProxy.h"
#include "openmm/serialization/StateProxy.h"
#include "openmm/serialization/BrownianIntegratorProxy.h"
#include "openmm/serialization/CustomIntegratorProxy.h"
#include "openmm/serialization/LangevinIntegratorProxy.h"
#include "openmm/serialization/SystemProxy.h"
#include "openmm/serialization/TabulatedFunctionProxies.h"
#include "openmm/serialization/VariableLangevinIntegratorProxy.h"
#include "openmm/serialization/VariableVerletIntegratorProxy.h"
#include "openmm/serialization/VerletIntegratorProxy.h"
......@@ -104,29 +103,35 @@ using namespace OpenMM;
extern "C" void registerSerializationProxies() {
SerializationProxy::registerProxy(typeid(AndersenThermostat), new AndersenThermostatProxy());
SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy());
SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy());
SerializationProxy::registerProxy(typeid(Continuous1DFunction), new Continuous1DFunctionProxy());
SerializationProxy::registerProxy(typeid(Continuous2DFunction), new Continuous2DFunctionProxy());
SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy());
SerializationProxy::registerProxy(typeid(CustomAngleForce), new CustomAngleForceProxy());
SerializationProxy::registerProxy(typeid(CustomBondForce), new CustomBondForceProxy());
SerializationProxy::registerProxy(typeid(CustomCompoundBondForce), new CustomCompoundBondForceProxy());
SerializationProxy::registerProxy(typeid(CustomExternalForce), new CustomExternalForceProxy());
SerializationProxy::registerProxy(typeid(CustomGBForce), new CustomGBForceProxy());
SerializationProxy::registerProxy(typeid(CustomHbondForce), new CustomHbondForceProxy());
SerializationProxy::registerProxy(typeid(CustomIntegrator), new CustomIntegratorProxy());
SerializationProxy::registerProxy(typeid(CustomNonbondedForce), new CustomNonbondedForceProxy());
SerializationProxy::registerProxy(typeid(CustomTorsionForce), new CustomTorsionForceProxy());
SerializationProxy::registerProxy(typeid(Discrete1DFunction), new Discrete1DFunctionProxy());
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());
SerializationProxy::registerProxy(typeid(MonteCarloBarostat), new MonteCarloBarostatProxy());
SerializationProxy::registerProxy(typeid(NonbondedForce), new NonbondedForceProxy());
SerializationProxy::registerProxy(typeid(PeriodicTorsionForce), new PeriodicTorsionForceProxy());
SerializationProxy::registerProxy(typeid(RBTorsionForce), new RBTorsionForceProxy());
SerializationProxy::registerProxy(typeid(System), new SystemProxy());
SerializationProxy::registerProxy(typeid(State), new StateProxy());
SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
SerializationProxy::registerProxy(typeid(CustomIntegrator), new CustomIntegratorProxy());
SerializationProxy::registerProxy(typeid(LangevinIntegrator), new LangevinIntegratorProxy());
SerializationProxy::registerProxy(typeid(VariableLangevinIntegrator), new VariableLangevinIntegratorProxy());
SerializationProxy::registerProxy(typeid(VariableVerletIntegrator), new VariableVerletIntegratorProxy());
SerializationProxy::registerProxy(typeid(VerletIntegrator), new VerletIntegratorProxy());
......
serialization/src/TabulatedFunctionProxies.cpp 0 → 100644
View file @ cf8a03e8
/* -------------------------------------------------------------------------- *
* 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) 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/TabulatedFunctionProxies.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/TabulatedFunction.h"
#include <sstream>
using namespace OpenMM;
using namespace std;
Continuous1DFunctionProxy::Continuous1DFunctionProxy() : SerializationProxy("Continuous1DFunction") {
}
void Continuous1DFunctionProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const Continuous1DFunction& function = *reinterpret_cast<const Continuous1DFunction*>(object);
double min, max;
vector<double> values;
function.getFunctionParameters(values, min, max);
node.setDoubleProperty("min", min);
node.setDoubleProperty("max", max);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
void* Continuous1DFunctionProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
return new Continuous1DFunction(values, node.getDoubleProperty("min"), node.getDoubleProperty("max"));
}
Continuous2DFunctionProxy::Continuous2DFunctionProxy() : SerializationProxy("Continuous2DFunction") {
}
void Continuous2DFunctionProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const Continuous2DFunction& function = *reinterpret_cast<const Continuous2DFunction*>(object);
int xsize, ysize;
double xmin, xmax, ymin, ymax;
vector<double> values;
function.getFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
node.setDoubleProperty("xsize", xsize);
node.setDoubleProperty("ysize", ysize);
node.setDoubleProperty("xmin", xmin);
node.setDoubleProperty("xmax", xmax);
node.setDoubleProperty("ymin", ymin);
node.setDoubleProperty("ymax", ymax);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
void* Continuous2DFunctionProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
return new Continuous2DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), values,
node.getDoubleProperty("xmin"), node.getDoubleProperty("xmax"), node.getDoubleProperty("ymin"), node.getDoubleProperty("ymax"));
}
Continuous3DFunctionProxy::Continuous3DFunctionProxy() : SerializationProxy("Continuous3DFunction") {
}
void Continuous3DFunctionProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const Continuous3DFunction& function = *reinterpret_cast<const Continuous3DFunction*>(object);
int xsize, ysize, zsize;
double xmin, xmax, ymin, ymax, zmin, zmax;
vector<double> values;
function.getFunctionParameters(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
node.setDoubleProperty("xsize", xsize);
node.setDoubleProperty("ysize", ysize);
node.setDoubleProperty("zsize", zsize);
node.setDoubleProperty("xmin", xmin);
node.setDoubleProperty("xmax", xmax);
node.setDoubleProperty("ymin", ymin);
node.setDoubleProperty("ymax", ymax);
node.setDoubleProperty("zmin", zmin);
node.setDoubleProperty("zmax", zmax);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
void* Continuous3DFunctionProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
return new Continuous3DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), node.getIntProperty("zsize"), values,
node.getDoubleProperty("xmin"), node.getDoubleProperty("xmax"), node.getDoubleProperty("ymin"), node.getDoubleProperty("ymax"),
node.getDoubleProperty("zmin"), node.getDoubleProperty("zmax"));
}
Discrete1DFunctionProxy::Discrete1DFunctionProxy() : SerializationProxy("Discrete1DFunction") {
}
void Discrete1DFunctionProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const Discrete1DFunction& function = *reinterpret_cast<const Discrete1DFunction*>(object);
vector<double> values;
function.getFunctionParameters(values);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
void* Discrete1DFunctionProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
return new Discrete1DFunction(values);
}
Discrete2DFunctionProxy::Discrete2DFunctionProxy() : SerializationProxy("Discrete2DFunction") {
}
void Discrete2DFunctionProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const Discrete2DFunction& function = *reinterpret_cast<const Discrete2DFunction*>(object);
int xsize, ysize;
vector<double> values;
function.getFunctionParameters(xsize, ysize, values);
node.setDoubleProperty("xsize", xsize);
node.setDoubleProperty("ysize", ysize);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
void* Discrete2DFunctionProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
return new Discrete2DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), values);
}
Discrete3DFunctionProxy::Discrete3DFunctionProxy() : SerializationProxy("Discrete3DFunction") {
}
void Discrete3DFunctionProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1);
const Discrete3DFunction& function = *reinterpret_cast<const Discrete3DFunction*>(object);
int xsize, ysize, zsize;
vector<double> values;
function.getFunctionParameters(xsize, ysize, zsize, values);
node.setDoubleProperty("xsize", xsize);
node.setDoubleProperty("ysize", ysize);
node.setDoubleProperty("zsize", zsize);
SerializationNode& valuesNode = node.createChildNode("Values");
for (int j = 0; j < (int) values.size(); j++)
valuesNode.createChildNode("Value").setDoubleProperty("v", values[j]);
}
void* Discrete3DFunctionProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
const SerializationNode& valuesNode = node.getChildNode("Values");
vector<double> values;
for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
return new Discrete3DFunction(node.getIntProperty("xsize"), node.getIntProperty("ysize"), node.getIntProperty("zsize"), values);
}
serialization/tests/TestSerializeCustomCompoundBondForce.cpp
View file @ cf8a03e8
......@@ -62,6 +62,10 @@ void testSerialization() {
particles[2] = 1;
params[0] = 2.1;
force.addBond(particles, params);
vector<double> values(10);
for (int i = 0; i < 10; i++)
values[i] = sin((double) i);
force.addTabulatedFunction("f", new Continuous1DFunction(values, 0.5, 1.5));
// Serialize and then deserialize it.
......@@ -95,6 +99,19 @@ void testSerialization() {
for (int j = 0; j < (int) particles1.size(); j++)
ASSERT_EQUAL(particles1[j], particles2[j]);
}
ASSERT_EQUAL(force.getNumTabulatedFunctions(), force2.getNumTabulatedFunctions());
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
double min1, min2, max1, max2;
vector<double> val1, val2;
dynamic_cast<Continuous1DFunction&>(force.getTabulatedFunction(i)).getFunctionParameters(val1, min1, max1);
dynamic_cast<Continuous1DFunction&>(force2.getTabulatedFunction(i)).getFunctionParameters(val2, min2, max2);
ASSERT_EQUAL(force.getTabulatedFunctionName(i), force2.getTabulatedFunctionName(i));
ASSERT_EQUAL(min1, min2);
ASSERT_EQUAL(max1, max2);
ASSERT_EQUAL(val1.size(), val2.size());
for (int j = 0; j < (int) val1.size(); j++)
ASSERT_EQUAL(val1[j], val2[j]);
}
}
int main() {
......
serialization/tests/TestSerializeCustomGBForce.cpp
View file @ cf8a03e8
......@@ -63,7 +63,7 @@ void testSerialization() {
vector<double> values(10);
for (int i = 0; i < 10; i++)
values[i] = sin((double) i);
force.addFunction("f", values, 0.5, 1.5);
force.addTabulatedFunction("f", new Discrete1DFunction(values));
// Serialize and then deserialize it.
......@@ -120,16 +120,12 @@ void testSerialization() {
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
}
ASSERT_EQUAL(force.getNumFunctions(), force2.getNumFunctions());
for (int i = 0; i < force.getNumFunctions(); i++) {
string name1, name2;
double min1, min2, max1, max2;
ASSERT_EQUAL(force.getNumTabulatedFunctions(), force2.getNumTabulatedFunctions());
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
vector<double> val1, val2;
force.getFunctionParameters(i, name1, val1, min1, max1);
force2.getFunctionParameters(i, name2, val2, min2, max2);
ASSERT_EQUAL(name1, name2);
ASSERT_EQUAL(min1, min2);
ASSERT_EQUAL(max1, max2);
dynamic_cast<Discrete1DFunction&>(force.getTabulatedFunction(i)).getFunctionParameters(val1);
dynamic_cast<Discrete1DFunction&>(force2.getTabulatedFunction(i)).getFunctionParameters(val2);
ASSERT_EQUAL(force.getTabulatedFunctionName(i), force2.getTabulatedFunctionName(i));
ASSERT_EQUAL(val1.size(), val2.size());
for (int j = 0; j < (int) val1.size(); j++)
ASSERT_EQUAL(val1[j], val2[j]);
......
serialization/tests/TestSerializeCustomHbondForce.cpp
View file @ cf8a03e8
......@@ -66,7 +66,7 @@ void testSerialization() {
vector<double> values(10);
for (int i = 0; i < 10; i++)
values[i] = sin((double) i);
force.addFunction("f", values, 0.5, 1.5);
force.addTabulatedFunction("f", new Discrete1DFunction(values));
// Serialize and then deserialize it.
......@@ -125,16 +125,12 @@ void testSerialization() {
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
}
ASSERT_EQUAL(force.getNumFunctions(), force2.getNumFunctions());
for (int i = 0; i < force.getNumFunctions(); i++) {
string name1, name2;
double min1, min2, max1, max2;
ASSERT_EQUAL(force.getNumTabulatedFunctions(), force2.getNumTabulatedFunctions());
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
vector<double> val1, val2;
force.getFunctionParameters(i, name1, val1, min1, max1);
force2.getFunctionParameters(i, name2, val2, min2, max2);
ASSERT_EQUAL(name1, name2);
ASSERT_EQUAL(min1, min2);
ASSERT_EQUAL(max1, max2);
dynamic_cast<Discrete1DFunction&>(force.getTabulatedFunction(i)).getFunctionParameters(val1);
dynamic_cast<Discrete1DFunction&>(force2.getTabulatedFunction(i)).getFunctionParameters(val2);
ASSERT_EQUAL(force.getTabulatedFunctionName(i), force2.getTabulatedFunctionName(i));
ASSERT_EQUAL(val1.size(), val2.size());
for (int j = 0; j < (int) val1.size(); j++)
ASSERT_EQUAL(val1[j], val2[j]);
......
serialization/tests/TestSerializeCustomNonbondedForce.cpp
View file @ cf8a03e8
......@@ -98,14 +98,13 @@ void testSerialization() {
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
}
ASSERT_EQUAL(force.getNumFunctions(), force2.getNumFunctions());
for (int i = 0; i < force.getNumFunctions(); i++) {
string name1, name2;
ASSERT_EQUAL(force.getNumTabulatedFunctions(), force2.getNumTabulatedFunctions());
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
double min1, min2, max1, max2;
vector<double> val1, val2;
force.getFunctionParameters(i, name1, val1, min1, max1);
force2.getFunctionParameters(i, name2, val2, min2, max2);
ASSERT_EQUAL(name1, name2);
dynamic_cast<Continuous1DFunction&>(force.getTabulatedFunction(i)).getFunctionParameters(val1, min1, max1);
dynamic_cast<Continuous1DFunction&>(force2.getTabulatedFunction(i)).getFunctionParameters(val2, min2, max2);
ASSERT_EQUAL(force.getTabulatedFunctionName(i), force2.getTabulatedFunctionName(i));
ASSERT_EQUAL(min1, min2);
ASSERT_EQUAL(max1, max2);
ASSERT_EQUAL(val1.size(), val2.size());
......
serialization/tests/TestSerializeTabulatedFunctions.cpp 0 → 100644
View file @ cf8a03e8
/* -------------------------------------------------------------------------- *
* 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/TabulatedFunction.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
void testContinuous1DFunction() {
// Create a function.
double min = 0.5, max = 1.5;
vector<double> values(60);
for (int i = 0; i < (int) values.size(); i++)
values[i] = sin((double) i);
Continuous1DFunction function(values, min, max);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<Continuous1DFunction>(&function, "Function", buffer);
Continuous1DFunction* copy = XmlSerializer::deserialize<Continuous1DFunction>(buffer);
// Compare the two forces to see if they are identical.
double min2, max2;
vector<double> values2;
copy->getFunctionParameters(values2, min2, max2);
ASSERT_EQUAL(min, min2);
ASSERT_EQUAL(max, max2);
ASSERT_EQUAL(values.size(), values2.size());
for (int j = 0; j < (int) values.size(); j++)
ASSERT_EQUAL(values[j], values2[j]);
}
void testContinuous2DFunction() {
// Create a function.
int xsize = 5, ysize = 12;
double xmin = 0.5, xmax = 1.5, ymin = 0.1, ymax = 5.0;
vector<double> values(xsize*ysize);
for (int i = 0; i < (int) values.size(); i++)
values[i] = sin((double) i);
Continuous2DFunction function(xsize, ysize, values, xmin, xmax, ymin, ymax);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<Continuous2DFunction>(&function, "Function", buffer);
Continuous2DFunction* copy = XmlSerializer::deserialize<Continuous2DFunction>(buffer);
// Compare the two forces to see if they are identical.
int xsize2, ysize2;
double xmin2, xmax2, ymin2, ymax2;
vector<double> values2;
copy->getFunctionParameters(xsize2, ysize2, values2, xmin2, xmax2, ymin2, ymax2);
ASSERT_EQUAL(xsize, xsize2);
ASSERT_EQUAL(ysize, ysize2);
ASSERT_EQUAL(xmin, xmin2);
ASSERT_EQUAL(xmax, xmax2);
ASSERT_EQUAL(ymin, ymin2);
ASSERT_EQUAL(ymax, ymax2);
ASSERT_EQUAL(values.size(), values2.size());
for (int j = 0; j < (int) values.size(); j++)
ASSERT_EQUAL(values[j], values2[j]);
}
void testContinuous3DFunction() {
// Create a function.
int xsize = 5, ysize = 4, zsize = 3;
double xmin = 0.5, xmax = 1.5, ymin = 0.1, ymax = 5.0, zmin = 0.3, zmax = 0.9;
vector<double> values(xsize*ysize*zsize);
for (int i = 0; i < (int) values.size(); i++)
values[i] = sin((double) i);
Continuous3DFunction function(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<Continuous3DFunction>(&function, "Function", buffer);
Continuous3DFunction* copy = XmlSerializer::deserialize<Continuous3DFunction>(buffer);
// Compare the two forces to see if they are identical.
int xsize2, ysize2, zsize2;
double xmin2, xmax2, ymin2, ymax2, zmin2, zmax2;
vector<double> values2;
copy->getFunctionParameters(xsize2, ysize2, zsize2, values2, xmin2, xmax2, ymin2, ymax2, zmin2, zmax2);
ASSERT_EQUAL(xsize, xsize2);
ASSERT_EQUAL(ysize, ysize2);
ASSERT_EQUAL(zsize, zsize2);
ASSERT_EQUAL(xmin, xmin2);
ASSERT_EQUAL(xmax, xmax2);
ASSERT_EQUAL(ymin, ymin2);
ASSERT_EQUAL(ymax, ymax2);
ASSERT_EQUAL(zmin, zmin2);
ASSERT_EQUAL(zmax, zmax2);
ASSERT_EQUAL(values.size(), values2.size());
for (int j = 0; j < (int) values.size(); j++)
ASSERT_EQUAL(values[j], values2[j]);
}
void testDiscrete1DFunction() {
// Create a function.
vector<double> values(60);
for (int i = 0; i < (int) values.size(); i++)
values[i] = sin((double) i);
Discrete1DFunction function(values);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<Discrete1DFunction>(&function, "Function", buffer);
Discrete1DFunction* copy = XmlSerializer::deserialize<Discrete1DFunction>(buffer);
// Compare the two forces to see if they are identical.
vector<double> values2;
copy->getFunctionParameters(values2);
ASSERT_EQUAL(values.size(), values2.size());
for (int j = 0; j < (int) values.size(); j++)
ASSERT_EQUAL(values[j], values2[j]);
}
void testDiscrete2DFunction() {
// Create a function.
int xsize = 5, ysize = 12;
vector<double> values(xsize*ysize);
for (int i = 0; i < (int) values.size(); i++)
values[i] = sin((double) i);
Discrete2DFunction function(xsize, ysize, values);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<Discrete2DFunction>(&function, "Function", buffer);
Discrete2DFunction* copy = XmlSerializer::deserialize<Discrete2DFunction>(buffer);
// Compare the two forces to see if they are identical.
int xsize2, ysize2;
vector<double> values2;
copy->getFunctionParameters(xsize2, ysize2, values2);
ASSERT_EQUAL(xsize, xsize2);
ASSERT_EQUAL(ysize, ysize2);
ASSERT_EQUAL(values.size(), values2.size());
for (int j = 0; j < (int) values.size(); j++)
ASSERT_EQUAL(values[j], values2[j]);
}
void testDiscrete3DFunction() {
// Create a function.
int xsize = 5, ysize = 4, zsize = 3;
vector<double> values(xsize*ysize*zsize);
for (int i = 0; i < (int) values.size(); i++)
values[i] = sin((double) i);
Discrete3DFunction function(xsize, ysize, zsize, values);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<Discrete3DFunction>(&function, "Function", buffer);
Discrete3DFunction* copy = XmlSerializer::deserialize<Discrete3DFunction>(buffer);
// Compare the two forces to see if they are identical.
int xsize2, ysize2, zsize2;
vector<double> values2;
copy->getFunctionParameters(xsize2, ysize2, zsize2, values2);
ASSERT_EQUAL(xsize, xsize2);
ASSERT_EQUAL(ysize, ysize2);
ASSERT_EQUAL(zsize, zsize2);
ASSERT_EQUAL(values.size(), values2.size());
for (int j = 0; j < (int) values.size(); j++)
ASSERT_EQUAL(values[j], values2[j]);
}
int main() {
try {
testContinuous1DFunction();
testContinuous2DFunction();
testContinuous3DFunction();
testDiscrete1DFunction();
testDiscrete2DFunction();
testDiscrete3DFunction();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
tests/TestSplineFitter.cpp
View file @ cf8a03e8
......@@ -84,10 +84,91 @@ void testPeriodicSpline() {
}
}
void test2DSpline() {
const int xsize = 15;
const int ysize = 17;
vector<double> x(xsize);
vector<double> y(ysize);
vector<double> f(xsize*ysize);
for (int i = 0; i < xsize; i++)
x[i] = 0.5*i+0.1*sin(double(i));
for (int i = 0; i < ysize; i++)
y[i] = 0.6*i+0.1*sin(double(i));
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++)
f[i+j*xsize] = sin(x[i])*cos(0.4*y[j]);
vector<vector<double> > c;
SplineFitter::create2DNaturalSpline(x, y, f, c);
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++) {
double value = SplineFitter::evaluate2DSpline(x, y, f, c, x[i], y[j]);
ASSERT_EQUAL_TOL(f[i+j*xsize], value, 1e-6);
}
for (int i = 0; i < 10; i++) {
for (int j = 0; j < 10; j++) {
double s = x[0]+(i+1)*(x[xsize-1]-x[0])/12.0;
double t = y[0]+(j+1)*(y[ysize-1]-y[0])/12.0;
double value = SplineFitter::evaluate2DSpline(x, y, f, c, s, t);
ASSERT_EQUAL_TOL(sin(s)*cos(0.4*t), value, 0.02);
double dx, dy;
SplineFitter::evaluate2DSplineDerivatives(x, y, f, c, s, t, dx, dy);
ASSERT_EQUAL_TOL(cos(s)*cos(0.4*t), dx, 0.05);
ASSERT_EQUAL_TOL(-0.4*sin(s)*sin(0.4*t), dy, 0.05);
}
}
}
void test3DSpline() {
const int xsize = 8;
const int ysize = 9;
const int zsize = 10;
vector<double> x(xsize);
vector<double> y(ysize);
vector<double> z(zsize);
vector<double> f(xsize*ysize*zsize);
for (int i = 0; i < xsize; i++)
x[i] = 0.2*i+0.02*sin(0.4*double(i));
for (int i = 0; i < ysize; i++)
y[i] = 0.2*i+0.02*sin(0.45*double(i));
for (int i = 0; i < zsize; i++)
z[i] = 0.2*i+0.02*sin(0.5*double(i));
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++)
for (int k = 0; k < zsize; k++)
f[i+j*xsize+k*xsize*ysize] = sin(x[i])*cos(0.4*y[j])*(1+z[k]);
vector<vector<double> > c;
SplineFitter::create3DNaturalSpline(x, y, z, f, c);
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++) {
for (int k = 0; k < zsize; k++) {
double value = SplineFitter::evaluate3DSpline(x, y, z, f, c, x[i], y[j], z[k]);
ASSERT_EQUAL_TOL(f[i+j*xsize+k*xsize*ysize], value, 1e-6);
}
}
for (int i = 0; i < 10; i++) {
for (int j = 0; j < 10; j++) {
for (int k = 0; k < 10; k++) {
double s = x[0]+(i+1)*(x[xsize-1]-x[0])/12.0;
double t = y[0]+(j+1)*(y[ysize-1]-y[0])/12.0;
double u = z[0]+(k+1)*(z[zsize-1]-z[0])/12.0;
double value = SplineFitter::evaluate3DSpline(x, y, z, f, c, s, t, u);
ASSERT_EQUAL_TOL(sin(s)*cos(0.4*t)*(1+u), value, 0.02);
double dx, dy, dz;
SplineFitter::evaluate3DSplineDerivatives(x, y, z, f, c, s, t, u, dx, dy, dz);
ASSERT_EQUAL_TOL(cos(s)*cos(0.4*t)*(1+u), dx, 0.1);
ASSERT_EQUAL_TOL(-0.4*sin(s)*sin(0.4*t)*(1+u), dy, 0.1);
ASSERT_EQUAL_TOL(sin(s)*cos(0.4*t), dz, 0.1);
}
}
}
}
int main() {
try {
testNaturalSpline();
testPeriodicSpline();
test2DSpline();
test3DSpline();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
wrappers/generateWrappers.py
View file @ cf8a03e8
......@@ -42,7 +42,7 @@ def getText(subNodePath, node):
def convertOpenMMPrefix(name):
return name.replace('OpenMM::', 'OpenMM_')
OPENMM_RE_PATTERN=re.compile("(.*)OpenMM:[a-zA-Z:]*:(.*)")
OPENMM_RE_PATTERN=re.compile("(.*)OpenMM:[a-zA-Z0-9_:]*:(.*)")
def stripOpenMMPrefix(name, rePattern=OPENMM_RE_PATTERN):
try:
m=rePattern.search(name)
......@@ -75,9 +75,10 @@ class WrapperGenerator:
# Read all the XML files and merge them into a single document.
self.doc = etree.ElementTree(etree.Element('root'))
for file in os.listdir(inputDirname):
root = etree.parse(os.path.join(inputDirname, file)).getroot()
for node in root:
self.doc.getroot().append(node)
if file.lower().endswith('xml'):
root = etree.parse(os.path.join(inputDirname, file)).getroot()
for node in root:
self.doc.getroot().append(node)
self.out = output
......@@ -623,6 +624,8 @@ class CSourceGenerator(WrapperGenerator):
unwrappedType = type[:-1].strip()
if unwrappedType in self.classesByShortName:
unwrappedType = self.classesByShortName[unwrappedType]
if unwrappedType == 'const std::string':
return 'std::string(%s)' % value
return '*'+self.unwrapValue(unwrappedType+'*', value)
if type in self.classesByShortName:
return 'static_cast<%s>(%s)' % (self.classesByShortName[type], value)
......@@ -1664,14 +1667,14 @@ class FortranSourceGenerator(WrapperGenerator):
return type
def isHandleType(self, type):
if type.startswith('OpenMM_'):
return True;
if type == 'Vec3':
return True
if type == 'OpenMM_Vec3':
return False
if type.endswith('*') or type.endswith('&'):
return self.isHandleType(type[:-1].strip())
if type.startswith('const '):
return self.isHandleType(type[6:].strip())
if type.startswith('OpenMM_'):
return True;
return False
def writeOutput(self):
......
wrappers/python/CMakeLists.txt
View file @ cf8a03e8
find_program(PYTHON_EXECUTABLE NAMES python)
#############################################
### Copy all source files to staging area ###
#############################################
......@@ -57,6 +55,7 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
)
foreach(file ${STAGING_INPUT_FILES1})
......
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @ cf8a03e8
......@@ -31,6 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
__author__ = "Peter Eastman"
__version__ = "1.0"
from math import sqrt
from simtk.openmm.app import Topology
from simtk.openmm.app import PDBFile
from simtk.openmm.app.internal import amber_file_parser
......@@ -118,6 +119,8 @@ class AmberPrmtopFile(object):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('ZN'):
element = elem.zinc
else:
try:
element = elem.get_by_symbol(atomName[0])
......@@ -142,7 +145,8 @@ class AmberPrmtopFile(object):
def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
constraints=None, rigidWater=True, implicitSolvent=None,
implicitSolventKappa=0.0*(1/unit.nanometer),
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):
"""Construct an OpenMM System representing the topology described by this prmtop file.
......@@ -155,7 +159,12 @@ class AmberPrmtopFile(object):
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.
- implicitSolventKappa (float=0.0*1/unit.nanometer) The Debye-screening parameter corresponding to ionic strength used for implicit solvent
- 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
......@@ -197,10 +206,29 @@ class AmberPrmtopFile(object):
implicitString = 'GBn2'
else:
raise ValueError('Illegal value for implicit solvent model')
sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString, nonbondedCutoff=nonbondedCutoff,
nonbondedMethod=methodMap[nonbondedMethod], flexibleConstraints=False, gbmodel=implicitString,
soluteDielectric=soluteDielectric, solventDielectric=solventDielectric, implicitSolventKappa=implicitSolventKappa,
rigidWater=rigidWater, elements=self.elements)
# If implicitSolventKappa is None, compute it from the salt concentration
if implicitSolvent is not None and implicitSolventKappa is None:
if unit.is_quantity(implicitSolventSaltConc):
implicitSolventSaltConc = implicitSolventSaltConc.value_in_unit(unit.moles/unit.liter)
if unit.is_quantity(temperature):
temperature = temperature.value_in_unit(unit.kelvin)
# The constant is 1 / sqrt( epsilon_0 * kB / (2 * NA * q^2 * 1000) )
# where NA is avogadro's number, epsilon_0 is the permittivity of
# free space, q is the elementary charge (this number matches
# Amber's kappa conversion factor)
implicitSolventKappa = 50.33355 * sqrt(implicitSolventSaltConc / solventDielectric / temperature)
# Multiply by 0.73 to account for ion exclusions, and multiply by 10
# to convert to 1/nm from 1/angstroms
implicitSolventKappa *= 7.3
elif implicitSolvent is None:
implicitSolventKappa = 0.0
sys = amber_file_parser.readAmberSystem(prmtop_loader=self._prmtop, shake=constraintString,
nonbondedCutoff=nonbondedCutoff, nonbondedMethod=methodMap[nonbondedMethod],
flexibleConstraints=False, gbmodel=implicitString, soluteDielectric=soluteDielectric,
solventDielectric=solventDielectric, implicitSolventKappa=implicitSolventKappa,
rigidWater=rigidWater, elements=self.elements)
if hydrogenMass is not None:
for atom1, atom2 in self.topology.bonds():
if atom1.element == elem.hydrogen:
......
wrappers/python/simtk/openmm/app/data/absinth.xml
View file @ cf8a03e8
......@@ -4151,7 +4151,7 @@
<EnergyTerm type="ParticlePairNoExclusions">
include(chargeGroup1*numChargeGroups+chargeGroup2)*screening1*screening2*138.935456*charge1*charge2/r
</EnergyTerm>
<Function name="sigma" min="0" max="675">
<Function name="sigma" type="Discrete1D">
0.27 0.3 0.285 0.185 0.27 0.285 0.315 0.27 0.235 0.295 0.27 0.30152225 0.355862 0.2932777648 0.235 0.29253280555 0.235 0.29267889715 0.235 0.3817314 0.366188 0.47079995 0.405 0.315 0.3099 0.241
0.3 0.33 0.315 0.265 0.3 0.315 0.345 0.3 0.265 0.325 0.3 0.33152225 0.385862 0.3232777648 0.265 0.32253280555 0.265 0.32267889715 0.265 0.4117314 0.396188 0.50079995 0.435 0.345 0.3399 0.271
0.285 0.315 0.3 0.25 0.285 0.3 0.33 0.285 0.25 0.31 0.285 0.31652225 0.370862 0.3082777648 0.25 0.30753280555 0.25 0.30767889715 0.25 0.3967314 0.381188 0.48579995 0.42 0.33 0.3249 0.256
......
wrappers/python/simtk/openmm/app/data/iamoeba.xml 0 → 100644
View file @ cf8a03e8
<ForceField>
<AtomTypes>
<Type name="380" class="73" element="O" mass="15.999"/>
<Type name="381" class="74" element="H" mass="1.008"/>
</AtomTypes>
<Residues>
<Residue name="HOH">
<Atom name="H1" type="381"/>
<Atom name="H2" type="381"/>
<Atom name="O" type="380"/>
<Bond from="0" to="2"/>
<Bond from="1" to="2"/>
</Residue>
</Residues>
<AmoebaBondForce bond-cubic="-25.5" bond-quartic="379.3125">
<Bond class1="73" class2="74" length="9.584047e-02" k="2.3331232e+05"/>
</AmoebaBondForce>
<AmoebaAngleForce angle-cubic="-0.014" angle-quartic="5.6e-05" angle-pentic="-7e-07" angle-sextic="2.2e-08">
<Angle class1="74" class2="73" class3="74" k="6.359379296918e-02" angle1="1.064826e+02"/>
</AmoebaAngleForce>
<AmoebaOutOfPlaneBendForce type="ALLINGER" opbend-cubic="-0.014" opbend-quartic="5.6e-05" opbend-pentic="-7e-07" opbend-sextic="2.2e-08">
<!-- LPW: Mark's force field parsing code requires AmoebaOutOfPlaneBendForce in order to read AmoebaAngleForce, even if the clause is empty -->
</AmoebaOutOfPlaneBendForce>
<AmoebaVdwForce type="BUFFERED-14-7" radiusrule="CUBIC-MEAN" radiustype="R-MIN" radiussize="DIAMETER" epsilonrule="HHG" vdw-13-scale="0.0" vdw-14-scale="1.0" vdw-15-scale="1.0">
<Vdw class="73" sigma="3.645297e-01" epsilon="8.2348e-01" reduction="1.0"/>
<Vdw class="74" sigma="0.0" epsilon="0.0" reduction="1.0"/>
</AmoebaVdwForce>
<AmoebaMultipoleForce direct11Scale="0.0" direct12Scale="1.0" direct13Scale="1.0" direct14Scale="1.0" mpole12Scale="0.0" mpole13Scale="0.0" mpole14Scale="0.4" mpole15Scale="0.8" mutual11Scale="1.0" mutual12Scale="1.0" mutual13Scale="1.0" mutual14Scale="1.0" polar12Scale="0.0" polar13Scale="0.0" polar14Intra="0.5" polar14Scale="1.0" polar15Scale="1.0">
<Multipole type="380" kz="-381" kx="-381" c0="-5.94024e-01" d1="0.0" d2="0.0" d3="4.682021361460e-03" q11="2.111247211390e-04" q21="0.0" q22="-3.009710770960e-04" q31="0.0" q32="0.0" q33="8.984635595700e-05"/>
<Multipole type="381" kz="380" kx="381" c0="2.97012e-01" d1="-4.969244847950e-03" d2="0.0" d3="-6.646702999580e-03" q11="1.750551751017e-04" q21="0.0" q22="2.029112480700e-05" q31="-3.392685963908e-05" q32="0.0" q33="-1.953462999087e-04"/>
<Polarize type="380" polarizability="8.063631227791e-04" thole="2.36164e-01" pgrp1="381"/>
<Polarize type="381" polarizability="5.048434386104e-04" thole="2.36164e-01" pgrp1="380"/>
</AmoebaMultipoleForce>
<AmoebaUreyBradleyForce cubic="0.0" quartic="0.0">
<UreyBradley class1="74" class2="73" class3="74" k="-4.31294e+03" d="1.535676676685e-01"/>
</AmoebaUreyBradleyForce>
</ForceField>
wrappers/python/simtk/openmm/app/desmonddmsfile.py
View file @ cf8a03e8
'''
"""
desmonddmsfile.py: Load Desmond dms files
Portions copyright (c) 2013 Stanford University and the Authors
......@@ -23,7 +23,7 @@ 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.
'''
"""
import os
import math
......@@ -38,16 +38,16 @@ from simtk.unit import (nanometer, angstrom, dalton, radian,
class DesmondDMSFile(object):
'''DesmondDMSFile parses a Desmond DMS (desmond molecular system) and
"""DesmondDMSFile parses a Desmond DMS (desmond molecular system) and
constructs a topology and (optionally) an OpenMM System from it
'''
"""
def __init__(self, file):
'''Load a DMS file
"""Load a DMS file
Parameters:
- file (string) the name of the file to load
'''
- file (string) the name of the file to load
"""
# sqlite3 is included in the standard lib, but at python
# compile time, you can disable support (I think), so it's
......@@ -73,8 +73,8 @@ class DesmondDMSFile(object):
# build the provenance string
provenance = []
q = '''SELECT id, user, timestamp, version, workdir, cmdline, executable
FROM provenance'''
q = """SELECT id, user, timestamp, version, workdir, cmdline, executable
FROM provenance"""
#for id, user, timestamp, version, workdir, cmdline, executable in self._conn.execute(q):
for row in self._conn.execute('SELECT * FROM provenance'):
rowdict = dict(zip(self._tables['provenance'], row))
......@@ -89,23 +89,23 @@ class DesmondDMSFile(object):
self._angleConstraints = [{} for x in range(len(self._topologyAtoms))]
def getPositions(self):
'''Get the positions of each atom in the system
'''
"""Get the positions of each atom in the system
"""
return self.positions
def getTopology(self):
'''Get the topology of the system
'''
"""Get the topology of the system
"""
return self.topology
def getProvenance(self):
'''Get the provenance string of this system
'''
"""Get the provenance string of this system
"""
return self.provenance
def _createTopology(self):
'''Build the topology of the system
'''
"""Build the topology of the system
"""
top = Topology()
positions = []
......@@ -119,8 +119,8 @@ class DesmondDMSFile(object):
lastChain = None
lastResId = None
c = top.addChain()
q = '''SELECT id, name, anum, resname, resid, chain, x, y, z
FROM particle'''
q = """SELECT id, name, anum, resname, resid, chain, x, y, z
FROM particle"""
for (atomId, atomName, atomNumber, resName, resId, chain, x, y, z) in self._conn.execute(q):
newChain = False
if chain != lastChain:
......@@ -156,17 +156,17 @@ class DesmondDMSFile(object):
def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*nanometer,
ewaldErrorTolerance=0.0005, removeCMMotion=True, hydrogenMass=None):
'''Construct an OpenMM System representing the topology described by this dms file
"""Construct an OpenMM System representing the topology described by this dms 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
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
- 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.
'''
- 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
- ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
- 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.
"""
self._checkForUnsupportedTerms()
sys = mm.System()
......@@ -219,14 +219,14 @@ class DesmondDMSFile(object):
return sys
def _addBondsToSystem(self, sys):
'''Create the harmonic bonds
'''
"""Create the harmonic bonds
"""
bonds = mm.HarmonicBondForce()
sys.addForce(bonds)
q = '''SELECT p0, p1, r0, fc, constrained
q = """SELECT p0, p1, r0, fc, constrained
FROM stretch_harm_term INNER JOIN stretch_harm_param
ON stretch_harm_term.param=stretch_harm_param.id'''
ON stretch_harm_term.param=stretch_harm_param.id"""
for p0, p1, r0, fc, constrained in self._conn.execute(q):
if constrained:
sys.addConstraint(p0, p1, r0*angstrom)
......@@ -242,15 +242,15 @@ class DesmondDMSFile(object):
return bonds
def _addAnglesToSystem(self, sys):
'''Create the harmonic angles
'''
"""Create the harmonic angles
"""
angles = mm.HarmonicAngleForce()
sys.addForce(angles)
degToRad = math.pi/180
q = '''SELECT p0, p1, p2, theta0, fc, constrained
q = """SELECT p0, p1, p2, theta0, fc, constrained
FROM angle_harm_term INNER JOIN angle_harm_param
ON angle_harm_term.param=angle_harm_param.id'''
ON angle_harm_term.param=angle_harm_param.id"""
for p0, p1, p2, theta0, fc, constrained in self._conn.execute(q):
if constrained:
l1 = self._atomBonds[p1][p0]
......@@ -267,15 +267,15 @@ class DesmondDMSFile(object):
return angles
def _addConstraintsToSystem(self, sys):
'''Add constraints to system. Normally these should already be
"""Add constraints to system. Normally these should already be
added by the bonds table, but we want to make sure that there's
no extra information in the constraints table that we're not
including in the system'''
including in the system"""
for term_table in [n for n in self._tables.keys() if n.startswith('constraint_a') and n.endswith('term')]:
param_table = term_table.replace('term', 'param')
q = '''SELECT p0, p1, r1
q = """SELECT p0, p1, r1
FROM %(term)s INNER JOIN %(param)s
ON %(term)s.param=%(param)s.id''' % \
ON %(term)s.param=%(param)s.id""" % \
{'term': term_table, 'param': param_table}
for p0, p1, r1 in self._conn.execute(q):
if not p1 in self._atomBonds[p0]:
......@@ -285,9 +285,9 @@ class DesmondDMSFile(object):
if 'constraint_hoh_term' in self._tables:
degToRad = math.pi/180
q = '''SELECT p0, p1, p2, r1, r2, theta
q = """SELECT p0, p1, p2, r1, r2, theta
FROM constraint_hoh_term INNER JOIN constraint_hoh_param
ON constraint_hoh_term.param=constraint_hoh_param.id'''
ON constraint_hoh_term.param=constraint_hoh_param.id"""
for p0, p1, p2, r1, r2, theta in self._conn.execute(q):
# Here, p0 is the heavy atom and p1 and p2 are the H1 and H2
# wihth O-H1 and O-H2 distances r1 and r2
......@@ -296,14 +296,14 @@ class DesmondDMSFile(object):
sys.addConstraint(p1, p2, length)
def _addPeriodicTorsionsToSystem(self, sys):
'''Create the torsion terms
'''
"""Create the torsion terms
"""
periodic = mm.PeriodicTorsionForce()
sys.addForce(periodic)
q = '''SELECT p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6
q = """SELECT p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6
FROM dihedral_trig_term INNER JOIN dihedral_trig_param
ON dihedral_trig_term.param=dihedral_trig_param.id'''
ON dihedral_trig_term.param=dihedral_trig_param.id"""
for p0, p1, p2, p3, phi0, fc0, fc1, fc2, fc3, fc4, fc5, fc6 in self._conn.execute(q):
for order, fc in enumerate([fc0, fc1, fc2, fc3, fc4, fc5, fc6]):
if fc == 0:
......@@ -312,8 +312,8 @@ class DesmondDMSFile(object):
def _addImproperHarmonicTorsionsToSystem(self, sys):
'''Create the improper harmonic torsion terms
'''
"""Create the improper harmonic torsion terms
"""
if not self._hasTable('improper_harm_term'):
return
......@@ -322,15 +322,15 @@ class DesmondDMSFile(object):
harmonicTorsion.addPerTorsionParameter('k')
sys.addForce(harmonicTorsion)
q = '''SELECT p0, p1, p2, p3, phi0, fc
q = """SELECT p0, p1, p2, p3, phi0, fc
FROM improper_harm_term INNER JOIN improper_harm_param
ON improper_harm_term.param=improper_harm_param.id'''
ON improper_harm_term.param=improper_harm_param.id"""
for p0, p1, p2, p3, phi0, fc in self._conn.execute(q):
harmonicTorsion.addTorsion(p0, p1, p2, p3, [phi0*degree, fc*kilocalorie_per_mole])
def _addCMAPToSystem(self, sys):
'''Create the CMAP terms
'''
"""Create the CMAP terms
"""
if not self._hasTable('torsiontorsion_cmap_term'):
return
......@@ -354,30 +354,30 @@ class DesmondDMSFile(object):
index = cmap.addMap(size, map*kilocalorie_per_mole)
cmap_indices[name] = index
q = '''SELECT p0, p1, p2, p3, p4, p5, p6, p7, cmapid
q = """SELECT p0, p1, p2, p3, p4, p5, p6, p7, cmapid
FROM torsiontorsion_cmap_term INNER JOIN torsiontorsion_cmap_param
ON torsiontorsion_cmap_term.param=torsiontorsion_cmap_param.id'''
ON torsiontorsion_cmap_term.param=torsiontorsion_cmap_param.id"""
for p0, p1, p2, p3, p4, p5, p6, p7, cmapid in self._conn.execute(q):
cmap.addTorsion(cmap_indices[cmapid], p0, p1, p2, p3, p4, p5, p6, p7)
def _addNonbondedForceToSystem(self, sys):
'''Create the nonbonded force
'''
"""Create the nonbonded force
"""
nb = mm.NonbondedForce()
sys.addForce(nb)
q = '''SELECT charge, sigma, epsilon
q = """SELECT charge, sigma, epsilon
FROM particle INNER JOIN nonbonded_param
ON particle.nbtype=nonbonded_param.id'''
ON particle.nbtype=nonbonded_param.id"""
for charge, sigma, epsilon in self._conn.execute(q):
nb.addParticle(charge, sigma*angstrom, epsilon*kilocalorie_per_mole)
for p0, p1 in self._conn.execute('SELECT p0, p1 FROM exclusion'):
nb.addException(p0, p1, 0.0, 1.0, 0.0)
q = '''SELECT p0, p1, aij, bij, qij
q = """SELECT p0, p1, aij, bij, qij
FROM pair_12_6_es_term INNER JOIN pair_12_6_es_param
ON pair_12_6_es_term.param=pair_12_6_es_param.id;'''
ON pair_12_6_es_term.param=pair_12_6_es_param.id;"""
for p0, p1, a_ij, b_ij, q_ij in self._conn.execute(q):
a_ij = (a_ij*kilocalorie_per_mole*(angstrom**12)).in_units_of(kilojoule_per_mole*(nanometer**12))
b_ij = (b_ij*kilocalorie_per_mole*(angstrom**6)).in_units_of(kilojoule_per_mole*(nanometer**6))
......@@ -391,41 +391,41 @@ class DesmondDMSFile(object):
new_sigma = (a_ij / b_ij)**(1.0/6.0)
nb.addException(p0, p1, q_ij, new_sigma, new_epsilon, True)
n_total = self._conn.execute('''SELECT COUNT(*) FROM pair_12_6_es_term''').fetchone()
n_in_exclusions = self._conn.execute('''SELECT COUNT(*)
n_total = self._conn.execute("""SELECT COUNT(*) FROM pair_12_6_es_term""").fetchone()
n_in_exclusions = self._conn.execute("""SELECT COUNT(*)
FROM exclusion INNER JOIN pair_12_6_es_term
ON exclusion.p0==pair_12_6_es_term.p0 AND exclusion.p1==pair_12_6_es_term.p1''').fetchone()
ON exclusion.p0==pair_12_6_es_term.p0 AND exclusion.p1==pair_12_6_es_term.p1""").fetchone()
if not n_total == n_in_exclusions:
raise NotImplementedError('All pair_12_6_es_terms must have a corresponding exclusion')
return nb
def _addVirtualSitesToSystem(self, sys):
'''Create any virtual sites in the systempy
'''
"""Create any virtual sites in the systempy
"""
if not any(t.startswith('virtual_') for t in self._tables.keys()):
return
if 'virtual_lc2_term' in self._tables:
q = '''SELECT p0, p1, p2, c1
q = """SELECT p0, p1, p2, c1
FROM virtual_lc2_term INNER JOIN virtual_lc2_param
ON virtual_lc2_term.param=virtual_lc2_param.id'''
ON virtual_lc2_term.param=virtual_lc2_param.id"""
for p0, p1, p2, c1 in self._conn.execute(q):
vsite = mm.TwoParticleAverageSite(p1, p2, (1-c1), c1)
sys.setVirtualSite(p0, vsite)
if 'virtual_lc3_term' in self._tables:
q = '''SELECT p0, p1, p2, p3, c1, c2
q = """SELECT p0, p1, p2, p3, c1, c2
FROM virtual_lc3_term INNER JOIN virtual_lc3_param
ON virtual_lc3_term.param=virtual_lc3_param.id'''
ON virtual_lc3_term.param=virtual_lc3_param.id"""
for p0, p1, p2, p3, c1, c2 in self._conn.execute(q):
vsite = mm.ThreeParticleAverageSite(p1, p2, p3, (1-c1-c2), c1, c2)
sys.setVirtualSite(p0, vsite)
if 'virtual_out3_term' in self._tables:
q = '''SELECT p0, p1, p2, p3, c1, c2, c3
q = """SELECT p0, p1, p2, p3, c1, c2, c3
FROM virtual_out3_term INNER JOIN virtual_out3_param
ON virtual_out3_term.param=virtual_out3_param.id'''
ON virtual_out3_term.param=virtual_out3_param.id"""
for p0, p1, p2, p3, c1, c2, c3 in self._conn.execute(q):
vsite = mm.OutOfPlaneSite(p1, p2, p3, c1, c2, c3)
sys.setVirtualSite(p0, vsite)
......@@ -436,14 +436,14 @@ class DesmondDMSFile(object):
def _hasTable(self, table_name):
'''Does our DMS file contain this table?
'''
"""Does our DMS file contain this table?
"""
return table_name in self._tables
def _readSchemas(self):
'''Read the schemas of each of the tables in the dms file, populating
"""Read the schemas of each of the tables in the dms file, populating
the `_tables` instance attribute
'''
"""
tables = {}
for table in self._conn.execute("SELECT name FROM sqlite_master WHERE type='table'"):
names = []
......@@ -453,9 +453,9 @@ class DesmondDMSFile(object):
self._tables = tables
def _checkForUnsupportedTerms(self):
'''Check the file for forcefield terms that are not currenty supported,
"""Check the file for forcefield terms that are not currenty supported,
raising a NotImplementedError
'''
"""
if 'posre_harm_term' in self._tables:
raise NotImplementedError('Position restraints are not implemented.')
flat_bottom_potential_terms = ['stretch_fbhw_term', 'angle_fbhw_term',
......@@ -488,8 +488,8 @@ class DesmondDMSFile(object):
raise NotImplementedError('Drude particles are not currently supported')
def close(self):
'''Close the SQL connection
'''
"""Close the SQL connection
"""
if self._open:
self._conn.close()
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ cf8a03e8
......@@ -1509,7 +1509,17 @@ class CustomGBGenerator:
generator.energyTerms.append((term.text, computationMap[term.attrib['type']]))
for function in element.findall("Function"):
values = [float(x) for x in function.text.split()]
generator.functions.append((function.attrib['name'], values, float(function.attrib['min']), float(function.attrib['max'])))
if 'type' in function.attrib:
type = function.attrib['type']
else:
type = 'Continuous1D'
params = {}
for key in function.attrib:
if key.endswith('size'):
params[key] = int(function.attrib[key])
elif key.endswith('min') or key.endswith('max'):
params[key] = float(function.attrib[key])
generator.functions.append((function.attrib['name'], type, values, params))
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.CustomGBForce.NoCutoff,
......@@ -1526,8 +1536,19 @@ class CustomGBGenerator:
force.addComputedValue(value[0], value[1], value[2])
for term in self.energyTerms:
force.addEnergyTerm(term[0], term[1])
for function in self.functions:
force.addFunction(function[0], function[1], function[2], function[3])
for (name, type, values, params) in self.functions:
if type == 'Continuous1D':
force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
elif type == 'Continuous2D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
elif type == 'Continuous3D':
force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
elif type == 'Discrete1D':
force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
elif type == 'Discrete2D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
elif type == 'Discrete3D':
force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
for atom in data.atoms:
t = data.atomType[atom]
if t in self.typeMap:
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ cf8a03e8
......@@ -890,7 +890,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
else:
raise Exception("Illegal value specified for implicit solvent model")
for iAtom in range(prmtop.getNumAtoms()):
if gbmodel == 'OBC2':
if gbmodel == 'OBC2' and implicitSolventKappa == 0:
gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
elif gbmodel == 'GBn2':
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ cf8a03e8
......@@ -6,9 +6,9 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012 University of Virginia and the Authors.
Portions copyright (c) 2012-2014 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts
Contributors: Jason M. Swails
Contributors: Jason M. Swails, Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -31,7 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
from __future__ import division
from simtk.openmm import CustomGBForce
from simtk.openmm import CustomGBForce, Discrete1DFunction
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
......@@ -331,8 +331,8 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
......@@ -380,8 +380,8 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom.addGlobalParameter("neckScale", 0.826836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
......
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