RDKit
Open-source cheminformatics and machine learning.
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RDKit::Descriptors::DoubleCubicLatticeVolume Class Reference

#include <DCLV.h>

Public Member Functions

 DoubleCubicLatticeVolume (const ROMol &mol, bool isProtein=false, bool includeLigand=true, double probeRadius=1.2, int depth=4, 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 = false,
bool  includeLigand = true,
double  probeRadius = 1.2,
int  depth = 4,
int  dotDensity = 0 
)
Parameters
molinput molecule or protein
isProteinflag to calculate burried surface area of a protein ligand complex [default=false, free ligand]
includeLigandflag to trigger inclusion of bound ligand in surface area and volume calculations where molecule is a protein [default=true]
probeRadiusradius of the sphere representing the probe solvent atom
depthcontrols the number of dots per atom
dotDensitycontrols density of dots per atom

Member Function Documentation

◆ getCompactness()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getCompactness ( )
inline
Returns
Compactness of the protein

Definition at line 73 of file DCLV.h.

◆ getPackingDensity()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getPackingDensity ( )
inline
Returns
Packing Density of the protein

Definition at line 78 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 59 of file DCLV.h.

◆ getVDWVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getVDWVolume ( )
inline
Returns
van der Waals Volume

Definition at line 69 of file DCLV.h.

◆ getVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getVolume ( )
inline
Returns
Volume bound by probe sphere

Definition at line 64 of file DCLV.h.


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