RDMIF::CoulombDielectric Class Reference

class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule by taking a distance-dependent dielectric into account: More...

#include <MIFDescriptors.h>

Public Member Functions
	CoulombDielectric ()
	CoulombDielectric (const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0)
	constructs CoulombDielectric object from vectors of charges and positions
	CoulombDielectric (const RDKit::ROMol &mol, int confId=-1, double probeCharge=1.0, bool absVal=false, const std::string &prop="_GasteigerCharge", double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0)
	constructs Coulomb object from a molecule object
double	operator() (double x, double y, double z, double thres) const
	returns the electrostatic interaction at point pt in the molecule's field in [kJ mol^-1]

Detailed Description

class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule by taking a distance-dependent dielectric into account:

Same energy term as used in GRID References: J. Med. Chem. 1985, 28, 849. J. Comp. Chem. 1983, 4, 187.

Definition at line 203 of file MIFDescriptors.h.

Constructor & Destructor Documentation

CoulombDielectric() [1/3]

RDMIF::CoulombDielectric::CoulombDielectric ( )

inline

Definition at line 205 of file MIFDescriptors.h.

CoulombDielectric() [2/3]

RDMIF::CoulombDielectric::CoulombDielectric	(	const std::vector< double > &	charges,
		const std::vector< RDGeom::Point3D > &	positions,
		double	probeCharge = 1.0,
		bool	absVal = false,
		double	alpha = 0.0,
		double	cutoff = 1.0,
		double	epsilon = 80.0,
		double	xi = 4.0
	)

constructs CoulombDielectric object from vectors of charges and positions

Parameters

charges	vector of charges [e]
pos	vector of postions [A]
probeCharge	charge of probe [e] (default: 1.0)
absVal	if true, negative (favored) values of interactions are calculated (default: false)
alpha	softcore interaction parameter [A^2]; if zero, a minimum cutoff distance is used (default: 0.0)
cutoff	minimum cutoff distance [A] (default: 1.0)
epsilon	relative permittivity of solvent (default: 80.0)
xi	relative permittivity of solute (default: 4.0)

CoulombDielectric() [3/3]

RDMIF::CoulombDielectric::CoulombDielectric	(	const RDKit::ROMol &	mol,
		int	confId = -1,
		double	probeCharge = 1.0,
		bool	absVal = false,
		const std::string &	prop = "_GasteigerCharge",
		double	alpha = 0.0,
		double	cutoff = 1.0,
		double	epsilon = 80.0,
		double	xi = 4.0
	)

constructs Coulomb object from a molecule object

The molecule mol needs to have partial charges set as property of atoms.

Parameters

mol	molecule object
confId	conformation id which is used to get positions of atoms (default=-1)
probeCharge	charge of probe [e] (default: 1.0)
absVal	if true, negative (favored) values of interactions are calculated (default: false)
prop	property key for retrieving partial charges of atoms (default: "_GasteigerCharge")
alpha	softcore interaction parameter [A^2], if zero, a minimum cutoff distance is used (default: 0.0)
cutoff	minimum cutoff distance [A] (default: 1.0)
epsilon	relative permittivity of solvent (default: 80.0)
xi	relative permittivity of solute (default: 4.0)

Member Function Documentation

operator()()

double RDMIF::CoulombDielectric::operator()	(	double	x,
		double	y,
		double	z,
		double	thres
	)		const

returns the electrostatic interaction at point pt in the molecule's field in [kJ mol^-1]

Parameters

x,y,z	coordinates at which the interaction is calculated
thres	squared threshold distance

Returns

electrostatic interaction energy in [kJ mol^-1]

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The documentation for this class was generated from the following file:

• MIFDescriptors.h