RDKit::Descriptors::DoubleCubicLatticeVolume Class Reference

#include <DCLV.h>

Public Member Functions
	DoubleCubicLatticeVolume (const ROMol &mol, std::vector< double > radii, bool isProtein=false, bool includeLigand=true, double probeRadius=1.4, int confId=-1)
	DoubleCubicLatticeVolume (const ROMol &mol, bool isProtein=false, bool includeLigand=true, double probeRadius=1.4, int confId=-1)
double	getSurfaceArea ()
double	getPolarSurfaceArea (bool includeSandP, bool includeHs)
double	getPartialSurfaceArea (const boost::dynamic_bitset<> &incAtoms)
double	getAtomSurfaceArea (unsigned int atomIdx)
std::map< unsigned int, std::vector< RDGeom::Point3D > > &	getSurfacePoints ()
double	getVolume ()
double	getVDWVolume ()
double	getPolarVolume (bool includeSandP, bool includeHs)
double	getPartialVolume (const boost::dynamic_bitset<> &incAtoms)
double	getAtomVolume (unsigned int atomIdx, double solventRadius)
double	getCompactness ()
double	getPackingDensity ()

Public Attributes
const ROMol &	mol
std::vector< double >	radii_
bool	isProtein = false
bool	includeLigand = true
double	probeRadius = 1.4
int	confId = -1
double	maxRadius = 1.7

Detailed Description

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.

Definition at line 37 of file DCLV.h.

Constructor & Destructor Documentation

DoubleCubicLatticeVolume() [1/2]

RDKit::Descriptors::DoubleCubicLatticeVolume::DoubleCubicLatticeVolume	(	const ROMol &	mol,
		std::vector< double >	radii,
		bool	isProtein = false,
		bool	includeLigand = true,
		double	probeRadius = 1.4,
		int	confId = -1 )

Parameters

mol	input molecule or protein
radii	radii for atoms of input mol, empty for default values
isProtein	flag to calculate burried surface area of a protein ligand complex [default=false, free ligand]
includeLigand	flag to trigger inclusion of bound ligand in surface area and volume calculations where molecule is a protein [default=true]
probeRadius	radius of the sphere representing the probe solvent atom [default=1.4]
confId	conformer ID to consider [default=-1]

References confId, includeLigand, isProtein, mol, and probeRadius.

Referenced by DoubleCubicLatticeVolume().

DoubleCubicLatticeVolume() [2/2]

RDKit::Descriptors::DoubleCubicLatticeVolume::DoubleCubicLatticeVolume ( const ROMol & mol, bool isProtein = false, bool includeLigand = true, double probeRadius = 1.4, int confId = -1 )

inline

Definition at line 67 of file DCLV.h.

References confId, DoubleCubicLatticeVolume(), includeLigand, isProtein, mol, and probeRadius.

Member Function Documentation

getAtomSurfaceArea()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getAtomSurfaceArea

(

unsigned int

atomIdx

)

Returns

Solvent Accessible Surface Area for specified atom

getAtomVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getAtomVolume	(	unsigned int	atomIdx,
		double	solventRadius )

Returns

Volume for specified atom

getCompactness()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getCompactness

(

)

Returns

Compactness of the protein

getPackingDensity()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getPackingDensity

(

)

Returns

Packing Density of the protein

getPartialSurfaceArea()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getPartialSurfaceArea

(

const boost::dynamic_bitset<> &

incAtoms

)

Returns

Surface Area from specified atoms

getPartialVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getPartialVolume

(

const boost::dynamic_bitset<> &

incAtoms

)

Returns

Volume from specified atoms

getPolarSurfaceArea()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getPolarSurfaceArea	(	bool	includeSandP,
		bool	includeHs )

Returns

Polar Surface Area

getPolarVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getPolarVolume	(	bool	includeSandP,
		bool	includeHs )

Returns

Polar Volume

getSurfaceArea()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getSurfaceArea

(

)

Returns

Solvent Accessible Surface Area

getSurfacePoints()

std::map< unsigned int, std::vector< RDGeom::Point3D > > & RDKit::Descriptors::DoubleCubicLatticeVolume::getSurfacePoints

(

)

Returns

Set of Points representing the surface

getVDWVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getVDWVolume

(

)

Returns

van der Waals Volume

getVolume()

double RDKit::Descriptors::DoubleCubicLatticeVolume::getVolume

(

)

Returns

Volume bound by probe sphere

Member Data Documentation

confId

int RDKit::Descriptors::DoubleCubicLatticeVolume::confId = -1

Definition at line 45 of file DCLV.h.

Referenced by DoubleCubicLatticeVolume(), and DoubleCubicLatticeVolume().

includeLigand

bool RDKit::Descriptors::DoubleCubicLatticeVolume::includeLigand = true

Definition at line 43 of file DCLV.h.

Referenced by DoubleCubicLatticeVolume(), and DoubleCubicLatticeVolume().

isProtein

bool RDKit::Descriptors::DoubleCubicLatticeVolume::isProtein = false

Definition at line 42 of file DCLV.h.

Referenced by DoubleCubicLatticeVolume(), and DoubleCubicLatticeVolume().

maxRadius

double RDKit::Descriptors::DoubleCubicLatticeVolume::maxRadius = 1.7

Definition at line 46 of file DCLV.h.

mol

const ROMol& RDKit::Descriptors::DoubleCubicLatticeVolume::mol

Definition at line 40 of file DCLV.h.

Referenced by DoubleCubicLatticeVolume(), and DoubleCubicLatticeVolume().

probeRadius

double RDKit::Descriptors::DoubleCubicLatticeVolume::probeRadius = 1.4

Definition at line 44 of file DCLV.h.

Referenced by DoubleCubicLatticeVolume(), and DoubleCubicLatticeVolume().

radii_

std::vector<double> RDKit::Descriptors::DoubleCubicLatticeVolume::radii_

Definition at line 41 of file DCLV.h.

---

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

• DCLV.h