/* 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 __CpuObcInterface_H__ #define __CpuObcInterface_H__ #ifdef __cplusplus #define externC extern "C" #else #define externC extern #endif #include "../SimTKUtilities/RealVec.h" #include #include /**--------------------------------------------------------------------------------------- Retrieve the calculated implicit solvation energy from the static class member @return the calculated energy from the static class member --------------------------------------------------------------------------------------- */ externC RealOpenMM cpuGetImplicitSolventEnergy( void ); /**--------------------------------------------------------------------------------------- Delete the Obc associated object(s) @return 0 if static CpuObc object was set; else return -1 --------------------------------------------------------------------------------------- */ externC int cpuDeleteObcParameters( void ); /**--------------------------------------------------------------------------------------- Setup for Obc calculations from Gromacs @param numberOfAtoms number of atoms @param obcScaleFactors array of OBC scale factors (one entry each atom) @param atomicRadii atomic radii in Angstrom (one entry each atom) @param includeAceApproximation if true, then include nonpolar ACE term in calculations @param soluteDielectric solute dielectric @param solventDielectric solvent dielectric @param log log reference -- if NULL, then errors/warnings output to stderr The method creates a CpuObc instance -- currently the OBC type II model is the default (see paper). If the OBC type I model is desired change ObcParameters* obcParameters = new ObcParameters( numberOfAtoms, ObcParameters::ObcTypeII ); to ObcParameters* obcParameters = new ObcParameters( numberOfAtoms, ObcParameters::ObcTypeI ); The created object is a static member of the class CpuObc; when the force routine, cpuCalculateObcForces(), is called, the static object is used to compute the forces and energy @return 0 --------------------------------------------------------------------------------------- */ externC int cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obcScaleFactors, int includeAceApproximation, RealOpenMM soluteDielectric, RealOpenMM solventDielectric, FILE* log ); /**--------------------------------------------------------------------------------------- Calculate implicit solvent forces and energy @param atomCoordinates atom coordinates in Angstrom; format of array is atomCoordinates[atom][3] @param partialCharges partial atom charges @param forces output forces in kcal/mol.A; format of array is forces[atom][3] @param energy energy @param updateBornRadii if set, then Born radii are updated for current configuration; otherwise radii correspond to configuration from previous iteration Function calls a static method in CpuImplicitSolvent class to calculate forces/energy @return result from CpuImplicitSolvent::computeImplicitSolventForces --------------------------------------------------------------------------------------- */ externC int cpuCalculateImplicitSolventForces( std::vector& atomCoordinates, const RealOpenMM* partialChargesIn, std::vector& forces, RealOpenMM* energy, int updateBornRadii ); /**--------------------------------------------------------------------------------------- Get OBC scale factors given masses @param numberOfAtoms number of atoms @param masses input masses @param scaleFactors output atomic numbers @return SimTKOpenMMCommon::DefaultReturn --------------------------------------------------------------------------------------- */ externC int getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealOpenMM* masses, RealOpenMM* scaleFactors ); /**--------------------------------------------------------------------------------------- Get OBC scale factors given atomic numbers @param numberOfAtoms number of atoms @param atomicNumber input atomic number for each atom @param scaleFactors output atomic numbers @return SimTKOpenMMCommon::DefaultReturn --------------------------------------------------------------------------------------- */ externC int getObcScaleFactors( int numberOfAtoms, const int* atomicNumber, RealOpenMM* scaleFactors ); /**--------------------------------------------------------------------------------------- Get GBSA radii @param numberOfAtoms number of atoms @param atomicNumber input atomic number for each atom @param numberOfCovalentPartners input number of covalent partners for each atom 1 for H, ...; only used for C, N & O @param indexOfCovalentPartner index of covalent partner -- only used for H e.g. if atom 22 is a H and it is bonded to atom 24 then indexOfCovalentPartner[22] = 24 @param gbsaRadii output GBSA radii @return SimTKOpenMMCommon::DefaultReturn --------------------------------------------------------------------------------------- */ externC int getGbsaRadii( int numberOfAtoms, const int* atomicNumber, const int* numberOfCovalentPartners, const int* indexOfCovalentPartner, RealOpenMM* gbsaRadii ); #undef externC #endif