ForceFields::MMFF::Utils Namespace Reference

Functions
RDKIT_FORCEFIELD_EXPORT double	calcAngleRestValue (const MMFFAngle *mmffAngleParams)
	returns the MMFF rest value for an angle
RDKIT_FORCEFIELD_EXPORT double	calcAngleForceConstant (const MMFFAngle *mmffAngleParams)
	returns the MMFF force constant for an angle
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
RDKIT_FORCEFIELD_EXPORT double	calcAngleBendEnergy (const double theta0, const double ka, bool isLinear, const double cosTheta)
	calculates and returns the angle bending MMFF energy
RDKIT_FORCEFIELD_EXPORT void	calcAngleBendGrad (RDGeom::Point3D *r, double *dist, double **g, double &dE_dTheta, double &cosTheta, double &sinTheta)
RDKIT_FORCEFIELD_EXPORT double	calcBondRestLength (const MMFFBond *mmffBondParams)
	returns the MMFF rest length for a bond
RDKIT_FORCEFIELD_EXPORT double	calcBondForceConstant (const MMFFBond *mmffBondParams)
	returns the MMFF force constant for a bond
RDKIT_FORCEFIELD_EXPORT double	calcBondStretchEnergy (const double r0, const double kb, const double distance)
	calculates and returns the bond stretching MMFF energy
RDKIT_FORCEFIELD_EXPORT double	calcUnscaledVdWMinimum (const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1, const MMFFVdW *mmffVdWParamsAtom2)
RDKIT_FORCEFIELD_EXPORT double	calcUnscaledVdWWellDepth (double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
RDKIT_FORCEFIELD_EXPORT void	scaleVdWParams (double &R_star_ij, double &wellDepth, const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom)
	scales the VdW parameters
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
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
RDKIT_FORCEFIELD_EXPORT double	calcOopChi (const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint)
	calculates and returns the Wilson angle (in degrees)
RDKIT_FORCEFIELD_EXPORT double	calcOopBendForceConstant (const MMFFOop *mmffOopParams)
	returns the out-of-plane force constant koop
RDKIT_FORCEFIELD_EXPORT double	calcOopBendEnergy (const double chi, const double koop)
	calculates and returns the out-of-plane MMFF energy
RDKIT_FORCEFIELD_EXPORT std::pair< double, double >	calcStbnForceConstants (const MMFFStbn *mmffStbnParams)
	returns the std::pair of stretch-bend force constants for an angle
RDKIT_FORCEFIELD_EXPORT std::pair< double, double >	calcStretchBendEnergy (const double deltaDist1, const double deltaDist2, const double deltaTheta, const std::pair< double, double > forceConstants)
	calculates and returns the stretch-bending MMFF energy
RDKIT_FORCEFIELD_EXPORT double	calcTorsionCosPhi (const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint)
	calculates and returns the cosine of a torsion angle
RDKIT_FORCEFIELD_EXPORT std::tuple< double, double, double >	calcTorsionForceConstant (const MMFFTor *mmffTorParams)
	returns the 3-tuple of a torsion angle force constants
RDKIT_FORCEFIELD_EXPORT double	calcTorsionEnergy (const double V1, const double V2, const double V3, const double cosPhi)
	calculates and returns the torsional MMFF energy
RDKIT_FORCEFIELD_EXPORT void	calcTorsionGrad (RDGeom::Point3D *r, RDGeom::Point3D *t, double *d, double **g, double &sinTerm, double &cosPhi)

Function Documentation

calcAngleBendEnergy()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcAngleBendEnergy	(	const double	theta0,
		const double	ka,
		bool	isLinear,
		const double	cosTheta )

calculates and returns the angle bending MMFF energy

calcAngleBendGrad()

RDKIT_FORCEFIELD_EXPORT void ForceFields::MMFF::Utils::calcAngleBendGrad	(	RDGeom::Point3D *	r,
		double *	dist,
		double **	g,
		double &	dE_dTheta,
		double &	cosTheta,
		double &	sinTheta )

calcAngleForceConstant()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcAngleForceConstant

(

const MMFFAngle *

mmffAngleParams

)

returns the MMFF force constant for an angle

calcAngleRestValue()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcAngleRestValue

(

const MMFFAngle *

mmffAngleParams

)

returns the MMFF rest value for an angle

calcBondForceConstant()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcBondForceConstant

(

const MMFFBond *

mmffBondParams

)

returns the MMFF force constant for a bond

calcBondRestLength()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcBondRestLength

(

const MMFFBond *

mmffBondParams

)

returns the MMFF rest length for a bond

calcBondStretchEnergy()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcBondStretchEnergy	(	const double	r0,
		const double	kb,
		const double	distance )

calculates and returns the bond stretching MMFF energy

calcCosTheta()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::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

calcEleEnergy()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::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

calcOopBendEnergy()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcOopBendEnergy	(	const double	chi,
		const double	koop )

calculates and returns the out-of-plane MMFF energy

calcOopBendForceConstant()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcOopBendForceConstant

(

const MMFFOop *

mmffOopParams

)

returns the out-of-plane force constant koop

calcOopChi()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcOopChi	(	const RDGeom::Point3D &	iPoint,
		const RDGeom::Point3D &	jPoint,
		const RDGeom::Point3D &	kPoint,
		const RDGeom::Point3D &	lPoint )

calculates and returns the Wilson angle (in degrees)

calcStbnForceConstants()

RDKIT_FORCEFIELD_EXPORT std::pair< double, double > ForceFields::MMFF::Utils::calcStbnForceConstants

(

const MMFFStbn *

mmffStbnParams

)

returns the std::pair of stretch-bend force constants for an angle

calcStretchBendEnergy()

RDKIT_FORCEFIELD_EXPORT std::pair< double, double > ForceFields::MMFF::Utils::calcStretchBendEnergy	(	const double	deltaDist1,
		const double	deltaDist2,
		const double	deltaTheta,
		const std::pair< double, double >	forceConstants )

calculates and returns the stretch-bending MMFF energy

calcTorsionCosPhi()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcTorsionCosPhi	(	const RDGeom::Point3D &	iPoint,
		const RDGeom::Point3D &	jPoint,
		const RDGeom::Point3D &	kPoint,
		const RDGeom::Point3D &	lPoint )

calculates and returns the cosine of a torsion angle

calcTorsionEnergy()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcTorsionEnergy	(	const double	V1,
		const double	V2,
		const double	V3,
		const double	cosPhi )

calculates and returns the torsional MMFF energy

calcTorsionForceConstant()

RDKIT_FORCEFIELD_EXPORT std::tuple< double, double, double > ForceFields::MMFF::Utils::calcTorsionForceConstant

(

const MMFFTor *

mmffTorParams

)

returns the 3-tuple of a torsion angle force constants

calcTorsionGrad()

RDKIT_FORCEFIELD_EXPORT void ForceFields::MMFF::Utils::calcTorsionGrad	(	RDGeom::Point3D *	r,
		RDGeom::Point3D *	t,
		double *	d,
		double **	g,
		double &	sinTerm,
		double &	cosPhi )

calcUnscaledVdWMinimum()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcUnscaledVdWMinimum	(	const MMFFVdWCollection *	mmffVdW,
		const MMFFVdW *	mmffVdWParamsAtom1,
		const MMFFVdW *	mmffVdWParamsAtom2 )

calculates and returns the unscaled minimum distance (R*ij) for a MMFF VdW contact

calcUnscaledVdWWellDepth()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcUnscaledVdWWellDepth	(	double	R_star_ij,
		const MMFFVdW *	mmffVdWParamsIAtom,
		const MMFFVdW *	mmffVdWParamsJAtom )

calculates and returns the unscaled well depth (epsilon) for a MMFF VdW contact

calcVdWEnergy()

RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcVdWEnergy	(	const double	dist,
		const double	R_star_ij,
		const double	wellDepth )

calculates and returns the Van der Waals MMFF energy

scaleVdWParams()

RDKIT_FORCEFIELD_EXPORT void ForceFields::MMFF::Utils::scaleVdWParams	(	double &	R_star_ij,
		double &	wellDepth,
		const MMFFVdWCollection *	mmffVdW,
		const MMFFVdW *	mmffVdWParamsIAtom,
		const MMFFVdW *	mmffVdWParamsJAtom )

scales the VdW parameters