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105 lines
3.9 KiB
C++
105 lines
3.9 KiB
C++
//
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// Copyright (C) 2013 Paolo Tosco
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//
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// Copyright (C) 2004-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef __RD_MMFFNONBONDED_H__
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#define __RD_MMFFNONBONDED_H__
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#include <ForceField/Contrib.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
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namespace ForceFields {
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namespace MMFF {
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class MMFFVdWCollection;
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class MMFFVdW;
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//! the van der Waals term for MMFF
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class RDKIT_FORCEFIELD_EXPORT VdWContrib : public ForceFieldContrib {
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public:
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VdWContrib() {}
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//! Constructor
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/*!
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\param owner pointer to the owning ForceField
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\param idx1 index of end1 in the ForceField's positions
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\param idx2 index of end2 in the ForceField's positions
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*/
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VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
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const MMFFVdWRijstarEps *mmffVdWConstants);
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double getEnergy(double *pos) const;
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void getGrad(double *pos, double *grad) const;
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virtual VdWContrib *copy() const { return new VdWContrib(*this); }
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private:
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int d_at1Idx{-1}, d_at2Idx{-1};
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double d_R_ij_star; //!< the preferred length of the contact
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double d_wellDepth; //!< the vdW well depth (strength of the interaction)
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};
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//! the electrostatic term for MMFF
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class RDKIT_FORCEFIELD_EXPORT EleContrib : public ForceFieldContrib {
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public:
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EleContrib() {}
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//! Constructor
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/*!
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\param owner pointer to the owning ForceField
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\param idx1 index of end1 in the ForceField's positions
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\param idx2 index of end2 in the ForceField's positions
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*/
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EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
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double chargeTerm, std::uint8_t dielModel, bool is1_4);
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double getEnergy(double *pos) const;
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void getGrad(double *pos, double *grad) const;
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virtual EleContrib *copy() const { return new EleContrib(*this); }
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private:
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int d_at1Idx{-1}, d_at2Idx{-1};
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double d_chargeTerm; //!< q1 * q2 / D
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std::uint8_t
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d_dielModel; //!< dielectric model (1: constant; 2: distance-dependent)
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bool d_is1_4; //!< flag set for atoms in a 1,4 relationship
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};
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namespace Utils {
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//! calculates and returns the unscaled minimum distance (R*ij) for a MMFF VdW
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// contact
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RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWMinimum(
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const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1,
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const MMFFVdW *mmffVdWParamsAtom2);
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//! calculates and returns the unscaled well depth (epsilon) for a MMFF VdW
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// contact
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RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWWellDepth(
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double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom,
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const MMFFVdW *mmffVdWParamsJAtom);
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//! scales the VdW parameters
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RDKIT_FORCEFIELD_EXPORT void scaleVdWParams(double &R_star_ij,
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double &wellDepth,
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const MMFFVdWCollection *mmffVdW,
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const MMFFVdW *mmffVdWParamsIAtom,
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const MMFFVdW *mmffVdWParamsJAtom);
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//! calculates and returns the Van der Waals MMFF energy
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RDKIT_FORCEFIELD_EXPORT double calcVdWEnergy(const double dist,
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const double R_star_ij,
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const double wellDepth);
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//! calculates and returns the electrostatic MMFF energy
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RDKIT_FORCEFIELD_EXPORT double calcEleEnergy(unsigned int idx1,
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unsigned int idx2, double dist,
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double chargeTerm,
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std::uint8_t dielModel,
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bool is1_4);
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} // namespace Utils
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} // namespace MMFF
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} // namespace ForceFields
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#endif
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