CustomBondForce.h

#ifndef OPENMM_CUSTOMBONDEDFORCE_H_
#define OPENMM_CUSTOMBONDEDFORCE_H_

/* -------------------------------------------------------------------------- *
 *                                   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) 2008-2012 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 "Force.h"
#include "Vec3.h"
#include <vector>
#include "internal/windowsExport.h"

namespace OpenMM {

class OPENMM_EXPORT CustomBondForce : public Force {
public:
    explicit CustomBondForce(const std::string& energy);
    int getNumBonds() const {
        return bonds.size();
    }
    int getNumPerBondParameters() const {
        return parameters.size();
    }
    int getNumGlobalParameters() const {
        return globalParameters.size();
    }
    const std::string& getEnergyFunction() const;
    void setEnergyFunction(const std::string& energy);
    int addPerBondParameter(const std::string& name);
    const std::string& getPerBondParameterName(int index) const;
    void setPerBondParameterName(int index, const std::string& name);
    int addGlobalParameter(const std::string& name, double defaultValue);
    const std::string& getGlobalParameterName(int index) const;
    void setGlobalParameterName(int index, const std::string& name);
    double getGlobalParameterDefaultValue(int index) const;
    void setGlobalParameterDefaultValue(int index, double defaultValue);
    int addBond(int particle1, int particle2, const std::vector<double>& parameters);
    void getBondParameters(int index, int& particle1, int& particle2, std::vector<double>& parameters) const;
    void setBondParameters(int index, int particle1, int particle2, const std::vector<double>& parameters);
    void updateParametersInContext(Context& context);
protected:
    ForceImpl* createImpl();
private:
    class BondInfo;
    class BondParameterInfo;
    class GlobalParameterInfo;
    std::string energyExpression;
    std::vector<BondParameterInfo> parameters;
    std::vector<GlobalParameterInfo> globalParameters;
    std::vector<BondInfo> bonds;
};

class CustomBondForce::BondInfo {
public:
    int particle1, particle2;
    std::vector<double> parameters;
    BondInfo() : particle1(-1), particle2(-1) {
    }
    BondInfo(int particle1, int particle2, const std::vector<double>& parameters) :
            particle1(particle1), particle2(particle2), parameters(parameters) {
    }
};

class CustomBondForce::BondParameterInfo {
public:
    std::string name;
    BondParameterInfo() {
    }
    BondParameterInfo(const std::string& name) : name(name) {
    }
};

class CustomBondForce::GlobalParameterInfo {
public:
    std::string name;
    double defaultValue;
    GlobalParameterInfo() {
    }
    GlobalParameterInfo(const std::string& name, double defaultValue) : name(name), defaultValue(defaultValue) {
    }
};

} // namespace OpenMM

#endif /*OPENMM_CUSTOMBONDEDFORCE_H_*/