#ifndef OPENMM_CMAPTORSIONFORCE_H_ #define OPENMM_CMAPTORSIONFORCE_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) 2010-2016 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 #include "internal/windowsExport.h" namespace OpenMM { /** * This class implements an interaction between pairs of dihedral angles. The interaction energy is * defined by an "energy correction map" (CMAP), which is simply a set of tabulated energy values * on a regular grid of (phi, psi) angles. Natural cubic spline interpolation is used to compute * forces and energies at arbitrary values of the two angles. * * To use this class, first create one or more energy correction maps by calling addMap(). For each * one, you provide an array of energies at uniformly spaced values of the two angles. Next, * add interactions by calling addTorsion(). For each one, you specify the sequence of particles used * to calculate each of the two dihedral angles, and the index of the map used to calculate their * interaction energy. */ class OPENMM_EXPORT CMAPTorsionForce : public Force { public: /** * Create a CMAPTorsionForce. */ CMAPTorsionForce(); /** * Get the number of maps that have been defined. */ int getNumMaps() const { return maps.size(); } /** * Get the number of CMAP torsion terms in the potential function */ int getNumTorsions() const { return torsions.size(); } /** * Create a new map that can be used for torsion pairs. * * @param size the size of the map along each dimension * @param energy the energy values for the map. This must be of length size*size. * The element energy[i+size*j] contains the energy when the first * torsion angle equals i*2*PI/size and the second torsion angle * equals j*2*PI/size. * @return the index of the map that was added */ int addMap(int size, const std::vector& energy); /** * Get the energy values of a map. * * @param index the index of the map for which to get energy values * @param[out] size the size of the map along each dimension * @param[out] energy the energy values for the map. This must be of length size*size. * The element energy[i+size*j] contains the energy when the first * torsion angle equals i*2*PI/size and the second torsion angle * equals j*2*PI/size. */ void getMapParameters(int index, int& size, std::vector& energy) const; /** * Set the energy values of a map. * * @param index the index of the map for which to set energy values * @param size the size of the map along each dimension * @param energy the energy values for the map. This must be of length size*size. * The element energy[i+size*j] contains the energy when the first * torsion angle equals i*2*PI/size and the second torsion angle * equals j*2*PI/size. */ void setMapParameters(int index, int size, const std::vector& energy); /** * Add a CMAP torsion term to the force field. * * @param map the index of the map to use for this term * @param a1 the index of the first particle forming the first torsion * @param a2 the index of the second particle forming the first torsion * @param a3 the index of the third particle forming the first torsion * @param a4 the index of the fourth particle forming the first torsion * @param b1 the index of the first particle forming the second torsion * @param b2 the index of the second particle forming the second torsion * @param b3 the index of the third particle forming the second torsion * @param b4 the index of the fourth particle forming the second torsion * @return the index of the torsion that was added */ int addTorsion(int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4); /** * Get the force field parameters for a CMAP torsion term. * * @param index the index of the torsion for which to get parameters * @param[out] map the index of the map to use for this term * @param[out] a1 the index of the first particle forming the first torsion * @param[out] a2 the index of the second particle forming the first torsion * @param[out] a3 the index of the third particle forming the first torsion * @param[out] a4 the index of the fourth particle forming the first torsion * @param[out] b1 the index of the first particle forming the second torsion * @param[out] b2 the index of the second particle forming the second torsion * @param[out] b3 the index of the third particle forming the second torsion * @param[out] b4 the index of the fourth particle forming the second torsion */ void getTorsionParameters(int index, int& map, int& a1, int& a2, int& a3, int& a4, int& b1, int& b2, int& b3, int& b4) const; /** * Set the force field parameters for a CMAP torsion term. * * @param index the index of the torsion for which to set parameters * @param map the index of the map to use for this term * @param a1 the index of the first particle forming the first torsion * @param a2 the index of the second particle forming the first torsion * @param a3 the index of the third particle forming the first torsion * @param a4 the index of the fourth particle forming the first torsion * @param b1 the index of the first particle forming the second torsion * @param b2 the index of the second particle forming the second torsion * @param b3 the index of the third particle forming the second torsion * @param b4 the index of the fourth particle forming the second torsion */ void setTorsionParameters(int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4); /** * Update the map and torsion parameters in a Context to match those stored in this Force object. This method provides * an efficient method to update certain parameters in an existing Context without needing to reinitialize it. * Simply call setMapParameters() and setTorsionParameters() to modify this object's parameters, then call updateParametersInContext() * to copy them over to the Context. * * The only information that can be updated with this method is the energy values for a map, and the map index * for a torsion. The size of a map and the set of particles involved in a torsion cannot be changed. Also, * new bonds and torsions cannot be added. */ void updateParametersInContext(Context& context); /** * Set whether this force should apply periodic boundary conditions when calculating displacements. * Usually this is not appropriate for bonded forces, but there are situations when it can be useful. */ void setUsesPeriodicBoundaryConditions(bool periodic); /** * Returns whether or not this force makes use of periodic boundary * conditions. * * @returns true if force uses PBC and false otherwise */ bool usesPeriodicBoundaryConditions() const; protected: ForceImpl* createImpl() const; private: class MapInfo; class CMAPTorsionInfo; std::vector maps; std::vector torsions; bool usePeriodic; }; /** * This is an internal class used to record information about a map. * @private */ class CMAPTorsionForce::MapInfo { public: int size; std::vector energy; MapInfo() { size = -1; } MapInfo(int size, const std::vector& energy) : size(size), energy(energy) { } }; /** * This is an internal class used to record information about a torsion. * @private */ class CMAPTorsionForce::CMAPTorsionInfo { public: int map, a1, a2, a3, a4, b1, b2, b3, b4; CMAPTorsionInfo() { map = a1 = a2 = a3 = a4 = b1 = b2 = b3 = b4 = -1; } CMAPTorsionInfo(int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) : map(map), a1(a1), a2(a2), a3(a3), a4(a4), b1(b1), b2(b2), b3(b3), b4(b4) { } }; } // namespace OpenMM #endif /*OPENMM_CMAPTORSIONFORCE_H_*/