RDKit::Descriptors::DoubleCubicLatticeVolume Class Reference

#include <DCLV.h>

Public Member Functions
	DoubleCubicLatticeVolume (const ROMol &mol, bool isProtein=true, bool includeLigand=false, double probeRadius=1.4, int depth=2, int dotDensity=0)
double	getSurfaceArea ()
double	getVolume ()
double	getVDWVolume ()
double	getCompactness ()
double	getPackingDensity ()

Detailed Description

Definition at line 29 of file DCLV.h.

Constructor & Destructor Documentation

DoubleCubicLatticeVolume()

RDKit::Descriptors::DoubleCubicLatticeVolume::DoubleCubicLatticeVolume	(	const ROMol &	mol,
		bool	isProtein = true,
		bool	includeLigand = false,
		double	probeRadius = 1.4,
		int	depth = 2,
		int	dotDensity = 0 )

Parameters

mol	input molecule or protein
isProtein	flag to identify input as protein vs unbound ligand (default=true, Protein as input) NOTE that the results for isProtein=false are currently not correct
includeLigand	flag to trigger inclusion of bound ligand in surface area and volume calculations where molecule is a protein [default false]
probeRadius	radius of the sphere representing the probe solvent atom
depth	controls the number of dots per atom
dotDensity	controls density of dots per atom

Member Function Documentation

getCompactness()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getCompactness ( )

inline

Returns

Compactness of the protein

Definition at line 74 of file DCLV.h.

getPackingDensity()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getPackingDensity ( )

inline

Returns

Packing Density of the protein

Definition at line 79 of file DCLV.h.

getSurfaceArea()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getSurfaceArea ( )

inline

Class for calculation of the Shrake and Rupley surface area and volume using the Double Cubic Lattice Method.

Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander and Michael Scharf, "The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", Journal of Computational Chemistry, Vol. 16, No. 3, pp. 273-284, 1995.

Returns

Solvent Accessible Surface Area

Definition at line 60 of file DCLV.h.

getVDWVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getVDWVolume ( )

inline

Returns

van der Waals Volume

Definition at line 70 of file DCLV.h.

getVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getVolume ( )

inline

Returns

Volume bound by probe sphere

Definition at line 65 of file DCLV.h.

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

• DCLV.h