ReferenceObc.h

/* 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
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 * 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
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 */

#ifndef __ReferenceObc_H__
#define __ReferenceObc_H__

#include "ObcParameters.h"

namespace OpenMM {

class ReferenceObc {

   private:

      // GBSA/OBC parameters

      ObcParameters* _obcParameters;

      // arrays containing OBC chain derivative 

      std::vector<RealOpenMM> _obcChain;

      // flag to signal whether ACE approximation
      // is to be included

      int _includeAceApproximation;


   public:

      /**---------------------------------------------------------------------------------------
      
         Constructor
      
         @param implicitSolventParameters    ImplicitSolventParameters reference
      
         @return CpuImplicitSolvent object
      
         --------------------------------------------------------------------------------------- */

       ReferenceObc(ObcParameters* obcParameters);

      /**---------------------------------------------------------------------------------------
      
         Destructor
      
         --------------------------------------------------------------------------------------- */

       ~ReferenceObc();

      /**---------------------------------------------------------------------------------------
      
         Return ObcParameters
      
         @return ObcParameters
      
         --------------------------------------------------------------------------------------- */

      ObcParameters* getObcParameters() 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() 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
      
         --------------------------------------------------------------------------------------- */
      
      std::vector<RealOpenMM>& getObcChain();
      
      /**---------------------------------------------------------------------------------------
      
         Get Born radii based on OBC 

         @param atomCoordinates   atomic coordinates
         @param bornRadii         output array of Born radii
      
         --------------------------------------------------------------------------------------- */
      
      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& 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 std::vector<RealOpenMM>& bornRadii,
                                   RealOpenMM* energy, std::vector<RealOpenMM>& 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<OpenMM::RealVec>& atomCoordinates,
                                         const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& 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<OpenMM::RealVec>& atomCoordinates,
                  const std::vector<RealOpenMM>& partialCharges,
                  const std::vector<RealOpenMM>& bornRadii,
                  const std::vector<RealOpenMM>& bornForces,
                  const std::vector<OpenMM::RealVec>& forces,
                  const std::string& idString, FILE* log);
    
};

} // namespace OpenMM

#endif // __ReferenceObc_H__