Classes
class	CrippenParams
	a class used to store Crippen parameters More...
class	CrippenParamCollection
	singleton class for retrieving Crippen parameters More...
Functions
void	getCrippenAtomContribs (const ROMol &mol, std::vector< double > &logpContribs, std::vector< double > &mrContribs, bool force=false)
void	calcCrippenDescriptors (const ROMol &mol, double &logp, double &mr, bool includeHs=true, bool force=false)
	generate Wildman-Crippen LogP and MR estimates for a molecule
unsigned int	calcLipinskiHBA (const ROMol &mol)
	calculates the standard Lipinski HBA definition
unsigned int	calcLipinskiHBD (const ROMol &mol)
	calculates the standard Lipinski HBA definition
unsigned int	calcNumRotatableBonds (const ROMol &mol)
unsigned int	calcNumHBD (const ROMol &mol)
unsigned int	calcNumHBA (const ROMol &mol)
unsigned int	calcNumHeteroatoms (const ROMol &mol)
unsigned int	calcNumAmideBonds (const ROMol &mol)
unsigned int	calcNumRings (const ROMol &mol)
double	calcAMW (const ROMol &mol, bool onlyHeavy=false)
double	calcExactMW (const ROMol &mol, bool onlyHeavy=false)
std::string	calcMolFormula (const ROMol &mol)
double	getLabuteAtomContribs (const ROMol &mol, std::vector< double > &Vi, double &hContrib, bool includeHs=true, bool force=false)
	calculates atomic contributions to Labute's Approximate Surface Area
double	calcLabuteASA (const ROMol &mol, bool includeHs=true, bool force=false)
	calculates Labute's Approximate Surface Area (ASA from MOE)
double	getTPSAAtomContribs (const ROMol &mol, std::vector< double > &Vi, bool force=false)
	calculates atomic contributions to the TPSA value
double	calcTPSA (const ROMol &mol, bool force=false)
	calculates the TPSA value for a molecule
std::vector< double >	calcSlogP_VSA (const ROMol &mol, std::vector< double > *bins=0, bool force=false)
std::vector< double >	calcSMR_VSA (const ROMol &mol, std::vector< double > *bins=0, bool force=false)
std::vector< double >	calcPEOE_VSA (const ROMol &mol, std::vector< double > *bins=0, bool force=false)
Variables
const std::string	crippenVersion = "1.2.0"
const std::string	lipinskiHBAVersion = "1.0.0"
const std::string	lipinskiHBDVersion = "2.0.0"
const std::string	NumRotatableBondsVersion
const std::string	NumHBDVersion
const std::string	NumHBAVersion
const std::string	NumHeteroatomsVersion
const std::string	NumAmideBondsVersion
const std::string	NumRingsVersion
const std::string	labuteASAVersion = "1.0.2"
const std::string	tpsaVersion = "1.1.0"

Function Documentation

double RDKit::Descriptors::calcAMW	(	const ROMol &	mol,
		bool	onlyHeavy = `false`
	)

Calculates a molecule's average molecular weight

Parameters:

	mol	the molecule of interest
	onlyHeavy	(optional) if this is true (the default is false), only heavy atoms will be included in the MW calculation

Returns:: the AMW

void RDKit::Descriptors::calcCrippenDescriptors	(	const ROMol &	mol,
		double &	logp,
		double &	mr,
		bool	includeHs = `true`,
		bool	force = `false`
	)

generate Wildman-Crippen LogP and MR estimates for a molecule

Uses an atom-based scheme based on the values in the paper: S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)

Parameters:

	mol	the molecule of interest
	logp	used to return the logp estimate
	mr	used to return the MR estimate
	includeHs	(optional) if this is true (the default), a copy of `mol` is made and Hs are added to it. If false, Hs that are not explicitly present in the graph will not be included.
	force	forces the value to be recalculated instead of pulled from the cache

double RDKit::Descriptors::calcExactMW	(	const ROMol &	mol,
		bool	onlyHeavy = `false`
	)

Calculates a molecule's exact molecular weight

Parameters:

	mol	the molecule of interest
	onlyHeavy	(optional) if this is true (the default is false), only heavy atoms will be included in the MW calculation

Returns:: the exact MW

double RDKit::Descriptors::calcLabuteASA	(	const ROMol &	mol,
		bool	includeHs = `true`,
		bool	force = `false`
	)

calculates Labute's Approximate Surface Area (ASA from MOE)

Definition from P. Labute's article in the Journal of the Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477 (2000)

Parameters:

	mol	the molecule of interest
	includeHs	(optional) if this is true (the default), the contribution of H atoms to the ASA will be included.
	force	(optional) calculate the value even if it's cached.

unsigned int RDKit::Descriptors::calcLipinskiHBA ( const ROMol & mol )

calculates the standard Lipinski HBA definition

Parameters:

mol

the molecule of interest

Returns:: the number of Ns and Os in the molecule

unsigned int RDKit::Descriptors::calcLipinskiHBD ( const ROMol & mol )

calculates the standard Lipinski HBA definition

Parameters:

mol

the molecule of interest

Returns:: the number of N-H and O-H bonds in the molecule

std::string RDKit::Descriptors::calcMolFormula ( const ROMol & mol )

Calculates a molecule's formula

Parameters:

mol

the molecule of interest

Returns:: the formula as a string

unsigned int RDKit::Descriptors::calcNumAmideBonds ( const ROMol & mol )

unsigned int RDKit::Descriptors::calcNumHBA ( const ROMol & mol )

unsigned int RDKit::Descriptors::calcNumHBD ( const ROMol & mol )

unsigned int RDKit::Descriptors::calcNumHeteroatoms ( const ROMol & mol )

unsigned int RDKit::Descriptors::calcNumRings ( const ROMol & mol )

unsigned int RDKit::Descriptors::calcNumRotatableBonds ( const ROMol & mol )

std::vector<double> RDKit::Descriptors::calcPEOE_VSA	(	const ROMol &	mol,
		std::vector< double > *	bins = `0`,
		bool	force = `false`
	)

std::vector<double> RDKit::Descriptors::calcSlogP_VSA	(	const ROMol &	mol,
		std::vector< double > *	bins = `0`,
		bool	force = `false`
	)

std::vector<double> RDKit::Descriptors::calcSMR_VSA	(	const ROMol &	mol,
		std::vector< double > *	bins = `0`,
		bool	force = `false`
	)

double RDKit::Descriptors::calcTPSA	(	const ROMol &	mol,
		bool	force = `false`
	)

calculates the TPSA value for a molecule

The TPSA definition is from: P. Ertl, B. Rohde, P. Selzer Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based Contributions and Its Application to the Prediction of Drug Transport Properties, J.Med.Chem. 43, 3714-3717, 2000

Parameters:

	mol	the molecule of interest
	force	(optional) calculate the value even if it's cached.

void RDKit::Descriptors::getCrippenAtomContribs	(	const ROMol &	mol,
		std::vector< double > &	logpContribs,
		std::vector< double > &	mrContribs,
		bool	force = `false`
	)

generate atomic contributions to the Wildman-Crippen LogP and MR estimates for a molecule

Uses an atom-based scheme based on the values in the paper: S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999)

Parameters:

	mol	the molecule of interest
	logpContribs	used to return the logp contributions, must be equal in length to the number of atoms
	mrContribs	used to return the MR contributions, must be equal in length to the number of atoms
	force	forces the value to be recalculated instead of pulled from the cache

double RDKit::Descriptors::getLabuteAtomContribs	(	const ROMol &	mol,
		std::vector< double > &	Vi,
		double &	hContrib,
		bool	includeHs = `true`,
		bool	force = `false`
	)

calculates atomic contributions to Labute's Approximate Surface Area

Definition from P. Labute's article in the Journal of the Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477 (2000)

Parameters:

	mol	the molecule of interest
	Vi	used to return the explict atom contribs
	hContrib	used to return the H contributions (if calculated)
	includeHs	(optional) if this is true (the default), the contribution of H atoms to the ASA will be included.
	force	(optional) calculate the values even if they are cached.

Returns:: the sum of the atomic contributions

double RDKit::Descriptors::getTPSAAtomContribs	(	const ROMol &	mol,
		std::vector< double > &	Vi,
		bool	force = `false`
	)

calculates atomic contributions to the TPSA value

The TPSA definition is from: P. Ertl, B. Rohde, P. Selzer Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based Contributions and Its Application to the Prediction of Drug Transport Properties, J.Med.Chem. 43, 3714-3717, 2000

Parameters: