ForceFields::UFF::Utils Namespace Reference

Functions
double	calcAngleForceConstant (double theta0, double bondOrder12, double bondOrder23, const AtomicParams *at1Params, const AtomicParams *at2Params, const AtomicParams *at3Params)
	Calculate the force constant for an angle bend.
double	calcBondRestLength (double bondOrder, const AtomicParams *end1Params, const AtomicParams *end2Params)
	calculates and returns the UFF rest length for a bond
double	calcBondForceConstant (double restLength, const AtomicParams *end1Params, const AtomicParams *end2Params)
	calculates and returns the UFF force constant for a bond
double	calcNonbondedMinimum (const AtomicParams *at1Params, const AtomicParams *at2Params)
	calculates and returns the UFF minimum position for a vdW contact
double	calcNonbondedDepth (const AtomicParams *at1Params, const AtomicParams *at2Params)
	calculates and returns the UFF well depth for a vdW contact
double	calculateCosTorsion (const RDGeom::Point3D &p1, const RDGeom::Point3D &p2, const RDGeom::Point3D &p3, const RDGeom::Point3D &p4)
	calculates and returns the cosine of a torsion angle

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Function Documentation

double ForceFields::UFF::Utils::calcAngleForceConstant	(	double	theta0,
		double	bondOrder12,
		double	bondOrder23,
		const AtomicParams *	at1Params,
		const AtomicParams *	at2Params,
		const AtomicParams *	at3Params
	)

Calculate the force constant for an angle bend.

The angle is between atom1 - atom2 - atom3

Parameters:

	theta0	the preferred value of the angle (in radians)
	bondOrder12	order of the bond between atoms 1 and 2 (as a double)
	bondOrder23	order of the bond between atoms 2 and 3 (as a double)
	at1Params	pointer to the parameters for atom 1
	at2Params	pointer to the parameters for atom 2
	at3Params	pointer to the parameters for atom 3

double ForceFields::UFF::Utils::calcBondForceConstant	(	double	restLength,
		const AtomicParams *	end1Params,
		const AtomicParams *	end2Params
	)

calculates and returns the UFF force constant for a bond

Parameters:

	restLength	the rest length of the bond
	end1Params	pointer to the parameters for end1
	end2Params	pointer to the parameters for end2

Returns:

the force constant

double ForceFields::UFF::Utils::calcBondRestLength	(	double	bondOrder,
		const AtomicParams *	end1Params,
		const AtomicParams *	end2Params
	)

calculates and returns the UFF rest length for a bond

Parameters:

	bondOrder	the order of the bond (as a double)
	end1Params	pointer to the parameters for end1
	end2Params	pointer to the parameters for end2

Returns:

the rest length

double ForceFields::UFF::Utils::calcNonbondedDepth	(	const AtomicParams *	at1Params,
		const AtomicParams *	at2Params
	)

calculates and returns the UFF well depth for a vdW contact

Parameters:

	at1Params	pointer to the parameters for end1
	at2Params	pointer to the parameters for end2

Returns:

the depth of the well

double ForceFields::UFF::Utils::calcNonbondedMinimum	(	const AtomicParams *	at1Params,
		const AtomicParams *	at2Params
	)

calculates and returns the UFF minimum position for a vdW contact

Parameters:

	at1Params	pointer to the parameters for end1
	at2Params	pointer to the parameters for end2

Returns:

the position of the minimum

double ForceFields::UFF::Utils::calculateCosTorsion	(	const RDGeom::Point3D &	p1,
		const RDGeom::Point3D &	p2,
		const RDGeom::Point3D &	p3,
		const RDGeom::Point3D &	p4
	)

calculates and returns the cosine of a torsion angle