RDMIF::Coulomb Class Reference

class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric) More...

#include <MIFDescriptors.h>

Public Member Functions
	Coulomb ()=default
	~Coulomb ()=default
	Coulomb (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)
	constructs Coulomb object from vectors of charges and positions
	Coulomb (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)
	constructs Coulomb object from a molecule object
double	operator() (double x, double y, double z, double thres) const
	calculated the electrostatic interaction at point pt in the molecules field in [kJ mol^-1]

Detailed Description

class for calculation of electrostatic interaction (Coulomb energy) between probe and molecule in vacuum (no dielectric)

Definition at line 110 of file MIFDescriptors.h.

Constructor & Destructor Documentation

Coulomb() [1/3]

RDMIF::Coulomb::Coulomb ( )

default

~Coulomb()

RDMIF::Coulomb::~Coulomb ( )

default

Coulomb() [2/3]

RDMIF::Coulomb::Coulomb	(	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 )

constructs Coulomb 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)

Coulomb() [3/3]

RDMIF::Coulomb::Coulomb	(	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 )

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)
absVal	if true, absolute values of interactions are calculated (default: false)
probeCharge	charge of probe [e] (default: 1.0)
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)

Member Function Documentation

operator()()

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

calculated the electrostatic interaction at point pt in the molecules field in [kJ mol^-1]

Parameters

x,y,z	coordinates at which the interaction is calculated
thres	squared max distance until interactions are calc.

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