MMFF/AngleBend.h
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//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ 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_MMFFANGLEBEND_H__
#define __RD_MMFFANGLEBEND_H__
#include <ForceField/ForceField.h>
#include <ForceField/Contrib.h>
namespace ForceFields {
namespace MMFF {
class MMFFBond;
class MMFFAngle;
class MMFFProp;
//! The angle-bend term for MMFF
class RDKIT_FORCEFIELD_EXPORT AngleBendContrib : public ForceFieldContrib {
public:
AngleBendContrib() {}
//! Constructor
/*!
The angle is between atom1 - atom2 - atom3
\param owner pointer to the owning ForceField
\param idx1 index of atom1 in the ForceField's positions
\param idx2 index of atom2 in the ForceField's positions
\param idx3 index of atom3 in the ForceField's positions
\param angleType MMFF type of the angle (as an unsigned int)
*/
AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2,
unsigned int idx3, const MMFFAngle *mmffAngleParams,
const MMFFProp *mmffPropParamsCentralAtom);
double getEnergy(double *pos) const override;
void getGrad(double *pos, double *grad) const override;
AngleBendContrib *copy() const override {
return new AngleBendContrib(*this);
}
private:
bool d_isLinear;
int d_at1Idx{-1}, d_at2Idx{-1}, d_at3Idx{-1};
double d_ka, d_theta0;
};
namespace Utils {
//! returns the MMFF rest value for an angle
RDKIT_FORCEFIELD_EXPORT double calcAngleRestValue(
const MMFFAngle *mmffAngleParams);
//! returns the MMFF force constant for an angle
RDKIT_FORCEFIELD_EXPORT double calcAngleForceConstant(
const MMFFAngle *mmffAngleParams);
//! calculates and returns the cosine of the angle between points p1, p2, p3
RDKIT_FORCEFIELD_EXPORT double calcCosTheta(RDGeom::Point3D p1,
RDGeom::Point3D p2,
RDGeom::Point3D p3, double dist1,
double dist2);
//! calculates and returns the angle bending MMFF energy
RDKIT_FORCEFIELD_EXPORT double calcAngleBendEnergy(const double theta0,
const double ka,
bool isLinear,
const double cosTheta);
RDKIT_FORCEFIELD_EXPORT void calcAngleBendGrad(RDGeom::Point3D *r, double *dist,
double **g, double &dE_dTheta,
double &cosTheta,
double &sinTheta);
} // namespace Utils
} // namespace MMFF
} // namespace ForceFields
#endif
Contrib.h
ForceField.h
ForceFields::ForceFieldContrib
abstract base class for contributions to ForceFields
Definition: Contrib.h:18
ForceFields::ForceField
A class to store forcefields and handle minimization.
Definition: ForceField.h:79
ForceFields::MMFF::AngleBendContrib
The angle-bend term for MMFF.
Definition: MMFF/AngleBend.h:26
ForceFields::MMFF::AngleBendContrib::getGrad
void getGrad(double *pos, double *grad) const override
calculates our contribution to the gradients of a position
ForceFields::MMFF::AngleBendContrib::copy
AngleBendContrib * copy() const override
return a copy
Definition: MMFF/AngleBend.h:45
ForceFields::MMFF::AngleBendContrib::AngleBendContrib
AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom)
Constructor.
ForceFields::MMFF::AngleBendContrib::AngleBendContrib
AngleBendContrib()
Definition: MMFF/AngleBend.h:28
ForceFields::MMFF::AngleBendContrib::getEnergy
double getEnergy(double *pos) const override
returns our contribution to the energy of a position
ForceFields::MMFF::MMFFAngle
class to store MMFF parameters for angle bending
Definition: MMFF/Params.h:112
ForceFields::MMFF::MMFFBond
class to store MMFF parameters for bond stretching
Definition: MMFF/Params.h:88
ForceFields::MMFF::MMFFProp
class to store MMFF Properties
Definition: MMFF/Params.h:61
RDGeom::Point3D
Definition: point.h:54
export.h
RDKIT_FORCEFIELD_EXPORT
#define RDKIT_FORCEFIELD_EXPORT
Definition: export.h:177
ForceFields::MMFF::Utils::calcAngleForceConstant
RDKIT_FORCEFIELD_EXPORT double calcAngleForceConstant(const MMFFAngle *mmffAngleParams)
returns the MMFF force constant for an angle
ForceFields::MMFF::Utils::calcCosTheta
RDKIT_FORCEFIELD_EXPORT double calcCosTheta(RDGeom::Point3D p1, RDGeom::Point3D p2, RDGeom::Point3D p3, double dist1, double dist2)
calculates and returns the cosine of the angle between points p1, p2, p3
ForceFields::MMFF::Utils::calcAngleRestValue
RDKIT_FORCEFIELD_EXPORT double calcAngleRestValue(const MMFFAngle *mmffAngleParams)
returns the MMFF rest value for an angle
ForceFields::MMFF::Utils::calcAngleBendEnergy
RDKIT_FORCEFIELD_EXPORT double calcAngleBendEnergy(const double theta0, const double ka, bool isLinear, const double cosTheta)
calculates and returns the angle bending MMFF energy
ForceFields::MMFF::Utils::calcAngleBendGrad
RDKIT_FORCEFIELD_EXPORT void calcAngleBendGrad(RDGeom::Point3D *r, double *dist, double **g, double &dE_dTheta, double &cosTheta, double &sinTheta)
ForceFields
Definition: TorsionAngleM6.h:24