#ifndef OPENMM_RMSDFORCE_H_ #define OPENMM_RMSDFORCE_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) 2018 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 is a force whose energy equals the root mean squared deviation (RMSD) * between the current coordinates and a reference structure. It is intended for * use with CustomCVForce. You will not normally want a force that exactly equals * the RMSD, but there are many situations where it is useful to have a restraining * or biasing force that depends on the RMSD in some way. * * The force is computed by first aligning the particle positions to the reference * structure, then computing the RMSD between the aligned positions and the reference. * The computation can optionally be done based on only a subset of the particles * in the system. */ class OPENMM_EXPORT RMSDForce : public Force { public: /** * Create an RMSDForce. * * @param referencePositions the reference positions to compute the deviation * from. The length of this vector must equal the * number of particles in the system, even if not * all particles are used in computing the RMSD. * @param particles the indices of the particles to use when computing * the RMSD. If this is empty (the default), all * particles in the system will be used. */ explicit RMSDForce(const std::vector& referencePositions, const std::vector& particles=std::vector()); /** * Get the reference positions to compute the deviation from. */ const std::vector& getReferencePositions() const { return referencePositions; } /** * Set the reference positions to compute the deviation from. */ void setReferencePositions(const std::vector& positions); /** * Get the indices of the particles to use when computing the RMSD. If this * is empty, all particles in the system will be used. */ const std::vector& getParticles() const { return particles; } /** * Set the indices of the particles to use when computing the RMSD. If this * is empty, all particles in the system will be used. */ void setParticles(const std::vector& particles); /** * Update the reference positions and particle indices 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 setReferencePositions() * and setParticles() to modify this object's parameters, then call updateParametersInContext() * to copy them over to the Context. */ void updateParametersInContext(Context& context); /** * Returns whether or not this force makes use of periodic boundary * conditions. * * @returns true if force uses PBC and false otherwise */ bool usesPeriodicBoundaryConditions() const { return false; } protected: ForceImpl* createImpl() const; private: std::vector referencePositions; std::vector particles; }; } // namespace OpenMM #endif /*OPENMM_RMSDFORCE_H_*/