/* Portions copyright (c) 2006 Stanford University and Simbios. * Contributors: Pande Group * * 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. */ #ifndef __CpuObc_H__ #define __CpuObc_H__ #include "ObcParameters.h" // --------------------------------------------------------------------------------------- class CpuObc { private: // GBSA/OBC parameters ObcParameters* _obcParameters; // arrays containing OBC chain derivative RealOpenMMVector _obcChain; // flag to signal whether ACE approximation // is to be included int _includeAceApproximation; public: /**--------------------------------------------------------------------------------------- Constructor @param implicitSolventParameters ImplicitSolventParameters reference @return CpuImplicitSolvent object --------------------------------------------------------------------------------------- */ CpuObc( ObcParameters* obcParameters ); /**--------------------------------------------------------------------------------------- Destructor --------------------------------------------------------------------------------------- */ ~CpuObc( ); /**--------------------------------------------------------------------------------------- Return ObcParameters @return ObcParameters --------------------------------------------------------------------------------------- */ ObcParameters* getObcParameters( void ) const; /**--------------------------------------------------------------------------------------- Set ImplicitSolventParameters @param ImplicitSolventParameters --------------------------------------------------------------------------------------- */ void setObcParameters( ObcParameters* obcParameters ); /**--------------------------------------------------------------------------------------- Return flag signalling whether AceApproximation for nonpolar term is to be included @return flag --------------------------------------------------------------------------------------- */ int includeAceApproximation( void ) const; /**--------------------------------------------------------------------------------------- Set flag indicating whether AceApproximation is to be included @param includeAceApproximation new includeAceApproximation value --------------------------------------------------------------------------------------- */ void setIncludeAceApproximation( int includeAceApproximation ); /**--------------------------------------------------------------------------------------- Return OBC chain derivative: size = _implicitSolventParameters->getNumberOfAtoms() @return array --------------------------------------------------------------------------------------- */ RealOpenMMVector& getObcChain( void ); /**--------------------------------------------------------------------------------------- Get Born radii based on OBC @param atomCoordinates atomic coordinates @param bornRadii output array of Born radii --------------------------------------------------------------------------------------- */ void computeBornRadii( const std::vector& atomCoordinates, RealOpenMMVector& bornRadii ); /**--------------------------------------------------------------------------------------- Get nonpolar solvation force constribution via ACE approximation @param obcParameters parameters @param vdwRadii Vdw radii @param bornRadii Born radii @param energy energy (output): value is incremented from input value @param forces forces: values are incremented from input values --------------------------------------------------------------------------------------- */ void computeAceNonPolarForce( const ObcParameters* obcParameters, const RealOpenMMVector& bornRadii, RealOpenMM* energy, RealOpenMMVector& forces ) const; /**--------------------------------------------------------------------------------------- Get Born energy and forces based on OBC @param atomCoordinates atomic coordinates @param partialCharges partial charges @param forces forces --------------------------------------------------------------------------------------- */ RealOpenMM computeBornEnergyForces( const std::vector& atomCoordinates, const RealOpenMMVector& partialCharges, std::vector& forces ); /**--------------------------------------------------------------------------------------- Print Obc parameters, radii, forces, ... @param atomCoordinates atomic coordinates @param partialCharges partial charges @param bornRadii Born radii (may be empty) @param bornForces Born forces (may be empty) @param forces forces (may be empty) @param idString id string (who is calling) @param log log file --------------------------------------------------------------------------------------- */ void printObc( const std::vector& atomCoordinates, const RealOpenMMVector& partialCharges, const RealOpenMMVector& bornRadii, const RealOpenMMVector& bornForces, const std::vector& forces, const std::string& idString, FILE* log ); }; // --------------------------------------------------------------------------------------- #endif // __CpuObc_H__