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MMFF/Nonbonded.h
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// Copyright (C) 2013-2025 Paolo Tosco and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_MMFFNONBONDED_H__
#define __RD_MMFFNONBONDED_H__
#include <ForceField/Contrib.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
namespace ForceFields {
namespace MMFF {
class MMFFVdWCollection;
class MMFFVdW;
//! combined vdW and charge terms for MMFF
class RDKIT_FORCEFIELD_EXPORT NonbondedContrib : public ForceFieldContrib {
public:
NonbondedContrib() {}
NonbondedContrib(ForceField *owner);
//! Track a new VdW pair
void addTerm(unsigned int idx1, unsigned int idx2,
const MMFFVdWRijstarEps *mmffVdWConstants, bool includeCharge,
double chargeTerm, std::uint8_t dielModel, bool is1_4);
double getEnergy(double *pos) const override;
void getGrad(double *pos, double *grad) const override;
NonbondedContrib *copy() const override {
return new NonbondedContrib(*this);
}
private:
enum ContribType {
VDW = 1 << 0, //!< van der Waals contribution
ELECTROSTATIC = 1 << 1 //!< electrostatic contribution
};
std::vector<int16_t> d_at1Idxs;
std::vector<int16_t> d_at2Idxs;
std::vector<std::uint8_t>
d_contribTypes; //!< bit field 0x1: vdW, 0x2: electrostatic
std::vector<double> d_R_ij_stars; //!< the preferred length of the contact
std::vector<double>
d_wellDepths; //!< the vdW well depth (strength of the interaction)
std::vector<double> d_chargeTerms;
std::vector<std::uint8_t> d_is_1_4s;
std::vector<std::uint8_t>
d_dielModels; //!< dielectric model (1: constant; 2: distance-dependent)
};
//! the van der Waals term for MMFF
class RDKIT_FORCEFIELD_EXPORT VdWContrib : public ForceFieldContrib {
public:
VdWContrib() {}
VdWContrib(ForceField *owner);
//! Track a new VdW pair
void addTerm(unsigned int idx1, unsigned int idx2,
const MMFFVdWRijstarEps *mmffVdWConstants);
double getEnergy(double *pos) const override;
void getGrad(double *pos, double *grad) const override;
VdWContrib *copy() const override { return new VdWContrib(*this); }
private:
std::vector<int16_t> d_at1Idxs;
std::vector<int16_t> d_at2Idxs;
std::vector<double> d_R_ij_stars; //!< the preferred length of the contact
std::vector<double>
d_wellDepths; //!< the vdW well depth (strength of the interaction)
};
//! the electrostatic term for MMFF
class RDKIT_FORCEFIELD_EXPORT EleContrib : public ForceFieldContrib {
public:
EleContrib() {}
//! Constructor
/*!
\param owner pointer to the owning ForceField
\param idx1 index of end1 in the ForceField's positions
\param idx2 index of end2 in the ForceField's positions
*/
EleContrib(ForceField *owner);
void addTerm(unsigned int idx1, unsigned int idx2, double chargeTerm,
std::uint8_t dielModel, bool is1_4);
double getEnergy(double *pos) const override;
void getGrad(double *pos, double *grad) const override;
EleContrib *copy() const override { return new EleContrib(*this); }
private:
std::vector<int16_t> d_at1Idxs;
std::vector<int16_t> d_at2Idxs;
std::vector<double> d_chargeTerms;
std::vector<std::uint8_t> d_is_1_4s;
std::vector<std::uint8_t>
d_dielModels; //!< dielectric model (1: constant; 2: distance-dependent)
};
namespace Utils {
//! calculates and returns the unscaled minimum distance (R*ij) for a MMFF VdW
/// contact
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWMinimum(
const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1,
const MMFFVdW *mmffVdWParamsAtom2);
//! calculates and returns the unscaled well depth (epsilon) for a MMFF VdW
/// contact
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWWellDepth(
double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom,
const MMFFVdW *mmffVdWParamsJAtom);
//! scales the VdW parameters
RDKIT_FORCEFIELD_EXPORT void scaleVdWParams(double &R_star_ij,
double &wellDepth,
const MMFFVdWCollection *mmffVdW,
const MMFFVdW *mmffVdWParamsIAtom,
const MMFFVdW *mmffVdWParamsJAtom);
//! calculates and returns the Van der Waals MMFF energy
RDKIT_FORCEFIELD_EXPORT double calcVdWEnergy(const double dist,
const double R_star_ij,
const double wellDepth);
//! calculates and returns the electrostatic MMFF energy
// FIX: idx1 and idx2 are not used
RDKIT_FORCEFIELD_EXPORT double calcEleEnergy(unsigned int idx1,
unsigned int idx2, double dist,
double chargeTerm,
std::uint8_t dielModel,
bool is1_4);
} // namespace Utils
} // namespace MMFF
} // namespace ForceFields
#endif
Contrib.h
AtomTyper.h
RDKitBase.h
pulls in the core RDKit functionality
ForceFields::ForceFieldContrib::ForceField
friend class ForceField
Definition Contrib.h:20
ForceFields::ForceFieldContrib::ForceFieldContrib
ForceFieldContrib()
Definition Contrib.h:22
ForceFields::MMFF::EleContrib::copy
EleContrib * copy() const override
return a copy
Definition MMFF/Nonbonded.h:92
ForceFields::MMFF::EleContrib::EleContrib
EleContrib()
Definition MMFF/Nonbonded.h:77
ForceFields::MMFF::EleContrib::getEnergy
double getEnergy(double *pos) const override
returns our contribution to the energy of a position
ForceFields::MMFF::EleContrib::getGrad
void getGrad(double *pos, double *grad) const override
calculates our contribution to the gradients of a position
ForceFields::MMFF::EleContrib::EleContrib
EleContrib(ForceField *owner)
Constructor.
ForceFields::MMFF::EleContrib::addTerm
void addTerm(unsigned int idx1, unsigned int idx2, double chargeTerm, std::uint8_t dielModel, bool is1_4)
ForceFields::MMFF::MMFFVdWCollection
Definition MMFF/Params.h:961
ForceFields::MMFF::MMFFVdWRijstarEps
Definition MMFF/Params.h:143
ForceFields::MMFF::MMFFVdW
class to store MMFF parameters for non-bonded Van der Waals
Definition MMFF/Params.h:133
ForceFields::MMFF::NonbondedContrib::NonbondedContrib
NonbondedContrib()
Definition MMFF/Nonbonded.h:24
ForceFields::MMFF::NonbondedContrib::NonbondedContrib
NonbondedContrib(ForceField *owner)
ForceFields::MMFF::NonbondedContrib::copy
NonbondedContrib * copy() const override
return a copy
Definition MMFF/Nonbonded.h:32
ForceFields::MMFF::NonbondedContrib::getGrad
void getGrad(double *pos, double *grad) const override
calculates our contribution to the gradients of a position
ForceFields::MMFF::NonbondedContrib::getEnergy
double getEnergy(double *pos) const override
returns our contribution to the energy of a position
ForceFields::MMFF::NonbondedContrib::addTerm
void addTerm(unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants, bool includeCharge, double chargeTerm, std::uint8_t dielModel, bool is1_4)
Track a new VdW pair.
ForceFields::MMFF::VdWContrib::addTerm
void addTerm(unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants)
Track a new VdW pair.
ForceFields::MMFF::VdWContrib::VdWContrib
VdWContrib()
Definition MMFF/Nonbonded.h:57
ForceFields::MMFF::VdWContrib::getEnergy
double getEnergy(double *pos) const override
returns our contribution to the energy of a position
ForceFields::MMFF::VdWContrib::copy
VdWContrib * copy() const override
return a copy
Definition MMFF/Nonbonded.h:64
ForceFields::MMFF::VdWContrib::VdWContrib
VdWContrib(ForceField *owner)
ForceFields::MMFF::VdWContrib::getGrad
void getGrad(double *pos, double *grad) const override
calculates our contribution to the gradients of a position
export.h
RDKIT_FORCEFIELD_EXPORT
#define RDKIT_FORCEFIELD_EXPORT
Definition export.h:201
ForceFields::MMFF::Utils::calcUnscaledVdWMinimum
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWMinimum(const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1, const MMFFVdW *mmffVdWParamsAtom2)
ForceFields::MMFF::Utils::calcVdWEnergy
RDKIT_FORCEFIELD_EXPORT double calcVdWEnergy(const double dist, const double R_star_ij, const double wellDepth)
calculates and returns the Van der Waals MMFF energy
ForceFields::MMFF::Utils::scaleVdWParams
RDKIT_FORCEFIELD_EXPORT void scaleVdWParams(double &R_star_ij, double &wellDepth, const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
scales the VdW parameters
ForceFields::MMFF::Utils::calcUnscaledVdWWellDepth
RDKIT_FORCEFIELD_EXPORT double calcUnscaledVdWWellDepth(double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
ForceFields::MMFF::Utils::calcEleEnergy
RDKIT_FORCEFIELD_EXPORT double calcEleEnergy(unsigned int idx1, unsigned int idx2, double dist, double chargeTerm, std::uint8_t dielModel, bool is1_4)
calculates and returns the electrostatic MMFF energy
ForceFields::MMFF
Definition MMFF/AngleBend.h:17
ForceFields
Definition TorsionAngleContribs.h:21