#ifndef OPENMM_AMOEBA_TORSION_TORSION_FORCE_H_ #define OPENMM_AMOEBA_TORSION_TORSION_FORCE_H_ /* -------------------------------------------------------------------------- * * AmoebaOpenMM * * -------------------------------------------------------------------------- * * 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) 2008-2009 Stanford University and the Authors. * * Authors: * * 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/Force.h" #include #include #include "openmm/internal/windowsExport.h" namespace OpenMM { typedef std::vector< std::vector< std::vector > > TorsionTorsionGrid; /** * This class implements the Amoeba torsion-torsion interaction * To use it, create a TorsionTorsionForce object then call addTorsionTorsion() once for each torsionTorsion. After * a torsionTorsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters(). */ class OPENMM_EXPORT AmoebaTorsionTorsionForce : public Force { public: /** * Create a Amoeba TorsionTorsionForce. */ AmoebaTorsionTorsionForce( void ); /** * Get the number of torsionTorsion terms in the potential function */ int getNumTorsionTorsions( void ) const { return torsionTorsions.size(); } /** * Get the number of torsionTorsion grids */ int getNumTorsionTorsionGrids( void ) const { return torsionTorsionGrids.size(); } /** * Add a torsionTorsion term to the force field. * * @param particle1 the index of the first particle connected by the torsionTorsion * @param particle2 the index of the second particle connected by the torsionTorsion * @param particle3 the index of the third particle connected by the torsionTorsion * @param particle4 the index of the fourth particle connected by the torsionTorsion * @param particle5 the index of the fifth particle connected by the torsionTorsion * @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check * @param gridIndex the index to the grid to be used * @return the index of the torsionTorsion that was added */ int addTorsionTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex ); /** * Get the force field parameters for a torsionTorsion term. * * @param index the index of the torsionTorsion for which to get parameters * @param particle1 the index of the first particle connected by the torsionTorsion * @param particle2 the index of the second particle connected by the torsionTorsion * @param particle3 the index of the third particle connected by the torsionTorsion * @param particle4 the index of the fourth particle connected by the torsionTorsion * @param particle5 the index of the fifth particle connected by the torsionTorsion * @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check * @param gridIndex the grid index */ void getTorsionTorsionParameters( int index, int& particle1, int& particle2, int& particle3, int& particle4, int& particle5, int& chiralCheckAtomIndex, int& gridIndex ) const; /** * Set the force field parameters for a torsionTorsion term. * * @param index the index of the torsionTorsion for which to set parameters * @param particle1 the index of the first particle connected by the torsionTorsion * @param particle2 the index of the second particle connected by the torsionTorsion * @param particle3 the index of the third particle connected by the torsionTorsion * @param particle4 the index of the fourth particle connected by the torsionTorsion * @param particle5 the index of the fifth particle connected by the torsionTorsion * @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check * @param gridIndex the grid index */ void setTorsionTorsionParameters( int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex ); /** * Get the torsion-torsion grid at the specified index * * @param gridIndex the grid index * @return grid return grid reference */ const TorsionTorsionGrid& getTorsionTorsionGrid( int index ) const; /** * Set the torsion-torsion grid at the specified index * * @param index the index of the torsionTorsion for which to get parameters * @param grid grid * grid[x][y][0] = x value * grid[x][y][1] = y value * grid[x][y][2] = function value * grid[x][y][3] = dfdx value * grid[x][y][4] = dfdy value * grid[x][y][5] = dfd(xy) value */ void setTorsionTorsionGrid(int index, TorsionTorsionGrid& grid ); protected: ForceImpl* createImpl(); private: class TorsionTorsionInfo; class TorsionTorsionGridInfo; // Retarded visual studio compiler complains about being unable to // export private stl class members. // This stanza explains that it should temporarily shut up. #if defined(_MSC_VER) #pragma warning(push) #pragma warning(disable:4251) #endif std::vector torsionTorsions; std::vector torsionTorsionGrids; #if defined(_MSC_VER) #pragma warning(pop) #endif }; class AmoebaTorsionTorsionForce::TorsionTorsionInfo { public: int particle1, particle2, particle3, particle4, particle5; int chiralCheckAtomIndex; int gridIndex; TorsionTorsionInfo() { particle1 = particle2 = particle3 = particle4 = particle5 = chiralCheckAtomIndex = -1; gridIndex = 0; } TorsionTorsionInfo(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex ) : particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4), particle5(particle5), gridIndex(gridIndex), chiralCheckAtomIndex(chiralCheckAtomIndex) { } }; class AmoebaTorsionTorsionForce::TorsionTorsionGridInfo { public: TorsionTorsionGridInfo( ) { _size[0] = _size[1] = 0; _startValues[0] = _startValues[1] = 0.0; _spacing[0] = _spacing[1] = 1.0; } TorsionTorsionGridInfo( const TorsionTorsionGrid& grid ) { _grid.resize( grid.size() ); for( unsigned int kk = 0; kk < grid.size(); kk++ ){ _grid[kk].resize( grid[kk].size() ); for( unsigned int jj = 0; jj < grid[kk].size(); jj++ ){ _grid[kk][jj].resize( grid[kk][jj].size() ); for( unsigned int ii = 0; ii < grid[kk][jj].size(); ii++ ){ _grid[kk][jj][ii] = grid[kk][jj][ii]; } } } _startValues[0] = _grid[0][0][0]; _startValues[1] = _grid[0][0][1]; //_spacing[0] = fabs( _grid[1][0][0] - _grid[0][0][0] ); //_spacing[1] = fabs( _grid[0][1][1] - _grid[0][0][1] ); _spacing[0] = static_cast(_grid.size()-1)/360.0; _spacing[1] = static_cast(grid.size()-1)/360.0; _size[0] = static_cast(grid.size()); _size[1] = static_cast(grid[0].size()); } const TorsionTorsionGrid& getTorsionTorsionGrid( void ) const { return _grid; } int getDimensionSize( int index ) const { return _size[index]; } double getStartValue( int index ) const { return _startValues[index]; } double getSpacing( int index ) const { return _spacing[index]; } private: TorsionTorsionGrid _grid; int _size[2]; double _startValues[2]; double _spacing[2]; }; } // namespace OpenMM #endif /*OPENMM_AMOEBA_TORSION_TORSION_FORCE_H_*/