mirror of
https://github.com/openmm/openmm
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166 lines
6.1 KiB
C++
166 lines
6.1 KiB
C++
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/* Portions copyright (c) 2006 Stanford University and Simbios.
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* Contributors: Pande Group
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*
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* Permission is hereby granted, free of charge, to any person obtaining
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* a copy of this software and associated documentation files (the
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* "Software"), to deal in the Software without restriction, including
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* without limitation the rights to use, copy, modify, merge, publish,
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* distribute, sublicense, and/or sell copies of the Software, and to
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* permit persons to whom the Software is furnished to do so, subject
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* to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included
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* in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
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* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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#ifndef __ReferenceObc_H__
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#define __ReferenceObc_H__
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#include "ObcParameters.h"
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namespace OpenMM {
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class ReferenceObc {
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private:
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// GBSA/OBC parameters
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ObcParameters* _obcParameters;
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// arrays containing OBC chain derivative
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std::vector<double> _obcChain;
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// flag to signal whether ACE approximation
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// is to be included
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int _includeAceApproximation;
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public:
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/**---------------------------------------------------------------------------------------
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Constructor
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@param implicitSolventParameters ImplicitSolventParameters reference
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@return CpuImplicitSolvent object
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--------------------------------------------------------------------------------------- */
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ReferenceObc(ObcParameters* obcParameters);
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/**---------------------------------------------------------------------------------------
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Destructor
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--------------------------------------------------------------------------------------- */
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~ReferenceObc();
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/**---------------------------------------------------------------------------------------
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Return ObcParameters
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@return ObcParameters
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--------------------------------------------------------------------------------------- */
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ObcParameters* getObcParameters() const;
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/**---------------------------------------------------------------------------------------
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Set ImplicitSolventParameters
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@param ImplicitSolventParameters
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--------------------------------------------------------------------------------------- */
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void setObcParameters(ObcParameters* obcParameters);
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/**---------------------------------------------------------------------------------------
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Return flag signalling whether AceApproximation for nonpolar term is to be included
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@return flag
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--------------------------------------------------------------------------------------- */
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int includeAceApproximation() const;
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/**---------------------------------------------------------------------------------------
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Set flag indicating whether AceApproximation is to be included
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@param includeAceApproximation new includeAceApproximation value
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--------------------------------------------------------------------------------------- */
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void setIncludeAceApproximation(int includeAceApproximation);
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/**---------------------------------------------------------------------------------------
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Return OBC chain derivative: size = _implicitSolventParameters->getNumberOfAtoms()
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@return array
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--------------------------------------------------------------------------------------- */
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std::vector<double>& getObcChain();
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/**---------------------------------------------------------------------------------------
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Get Born radii based on OBC
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@param atomCoordinates atomic coordinates
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@param bornRadii output array of Born radii
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--------------------------------------------------------------------------------------- */
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void computeBornRadii(const std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<double>& bornRadii);
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/**---------------------------------------------------------------------------------------
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Get nonpolar solvation force constribution via ACE approximation
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@param obcParameters parameters
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@param vdwRadii Vdw radii
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@param bornRadii Born radii
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@param energy energy (output): value is incremented from input value
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@param forces forces: values are incremented from input values
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--------------------------------------------------------------------------------------- */
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void computeAceNonPolarForce(const ObcParameters* obcParameters, const std::vector<double>& bornRadii,
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double* energy, std::vector<double>& forces) const;
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/**---------------------------------------------------------------------------------------
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Get Born energy and forces based on OBC
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@param atomCoordinates atomic coordinates
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@param partialCharges partial charges
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@param forces forces
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--------------------------------------------------------------------------------------- */
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double computeBornEnergyForces(const std::vector<OpenMM::Vec3>& atomCoordinates,
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const std::vector<double>& partialCharges, std::vector<OpenMM::Vec3>& forces);
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};
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} // namespace OpenMM
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#endif // __ReferenceObc_H__
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