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

Namespaces

 detail
 

Classes

class  CrippenParamCollection
 singleton class for retrieving Crippen parameters More...
 
class  CrippenParams
 a class used to store Crippen parameters More...
 
class  Properties
 Holds a collection of properties for computation purposes. More...
 
struct  PropertyFunctor
 

Typedefs

typedef Queries::Query< bool, const ROMol &, true > PROP_BOOL_QUERY
 
typedef Queries::AndQuery< int, const ROMol &, true > PROP_AND_QUERY
 
typedef Queries::OrQuery< int, const ROMol &, true > PROP_OR_QUERY
 
typedef Queries::XOrQuery< int, const ROMol &, true > PROP_XOR_QUERY
 
typedef Queries::EqualityQuery< double, const ROMol &, true > PROP_EQUALS_QUERY
 
typedef Queries::GreaterQuery< double, const ROMol &, true > PROP_GREATER_QUERY
 
typedef Queries::GreaterEqualQuery< double, const ROMol &, true > PROP_GREATEREQUAL_QUERY
 
typedef Queries::LessQuery< double, const ROMol &, true > PROP_LESS_QUERY
 
typedef Queries::LessEqualQuery< double, const ROMol &, true > PROP_LESSEQUAL_QUERY
 
typedef Queries::RangeQuery< double, const ROMol &, true > PROP_RANGE_QUERY
 

Enumerations

enum  NumRotatableBondsOptions { Default = -1, NonStrict = 0, Strict = 1, StrictLinkages = 2 }
 

Functions

double calcChi0v (const ROMol &mol, bool force=false)
 From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More...
 
double calcChi1v (const ROMol &mol, bool force=false)
 From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More...
 
double calcChi2v (const ROMol &mol, bool force=false)
 From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More...
 
double calcChi3v (const ROMol &mol, bool force=false)
 From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More...
 
double calcChi4v (const ROMol &mol, bool force=false)
 From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More...
 
double calcChiNv (const ROMol &mol, unsigned int n, bool force=false)
 From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More...
 
double calcChi0n (const ROMol &mol, bool force=false)
 
double calcChi1n (const ROMol &mol, bool force=false)
 
double calcChi2n (const ROMol &mol, bool force=false)
 
double calcChi3n (const ROMol &mol, bool force=false)
 
double calcChi4n (const ROMol &mol, bool force=false)
 
double calcChiNn (const ROMol &mol, unsigned int n, bool force=false)
 
double calcHallKierAlpha (const ROMol &mol, std::vector< double > *atomContribs=0)
 
double calcKappa1 (const ROMol &mol)
 
double calcKappa2 (const ROMol &mol)
 
double calcKappa3 (const ROMol &mol)
 
void getCrippenAtomContribs (const ROMol &mol, std::vector< double > &logpContribs, std::vector< double > &mrContribs, bool force=false, std::vector< unsigned int > *atomTypes=0, std::vector< std::string > *atomTypeLabels=0)
 
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 More...
 
double calcClogP (const ROMol &mol)
 calculate the default Wildman-Crippen LogP for a molecule More...
 
double calcMR (const ROMol &mol)
 calculate the default Wildman-Crippen MR Estimate for a molecule More...
 
unsigned int calcLipinskiHBA (const ROMol &mol)
 calculates the standard Lipinski HBA definition (number of Ns and Os) More...
 
unsigned int calcLipinskiHBD (const ROMol &mol)
 calculates the standard Lipinski HBA definition (number of N-H and O-H More...
 
unsigned int calcNumRotatableBonds (const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default)
 calculates the number of rotatable bonds More...
 
unsigned int calcNumRotatableBonds (const ROMol &mol, bool strict)
 
unsigned int calcNumHBD (const ROMol &mol)
 calculates the number of H-bond donors More...
 
unsigned int calcNumHBA (const ROMol &mol)
 calculates the number of H-bond acceptors More...
 
unsigned int calcNumHeteroatoms (const ROMol &mol)
 calculates the number of heteroatoms More...
 
unsigned int calcNumAmideBonds (const ROMol &mol)
 calculates the number of amide bonds More...
 
double calcFractionCSP3 (const ROMol &mol)
 calculates the fraction of carbons that are SP3 hybridized More...
 
unsigned int calcNumRings (const ROMol &mol)
 calculates the number of SSSR rings More...
 
unsigned int calcNumAromaticRings (const ROMol &mol)
 calculates the number of aromatic SSSR rings More...
 
unsigned int calcNumAliphaticRings (const ROMol &mol)
 calculates the number of aliphatic (at least one non-aromatic bond) SSSR More...
 
unsigned int calcNumSaturatedRings (const ROMol &mol)
 calculates the number of saturated SSSR rings More...
 
unsigned int calcNumHeterocycles (const ROMol &mol)
 calculates the number of SSSR heterocycles More...
 
unsigned int calcNumAromaticHeterocycles (const ROMol &mol)
 calculates the number of aromatic SSSR heterocycles More...
 
unsigned int calcNumAromaticCarbocycles (const ROMol &mol)
 calculates the number of aromatic SSSR carbocycles More...
 
unsigned int calcNumSaturatedHeterocycles (const ROMol &mol)
 calculates the number of saturated SSSR heterocycles More...
 
unsigned int calcNumSaturatedCarbocycles (const ROMol &mol)
 calculates the number of saturated SSSR carbocycles More...
 
unsigned int calcNumAliphaticHeterocycles (const ROMol &mol)
 calculates the number of aliphatic (at least one non-aromatic bond) SSSR More...
 
unsigned int calcNumAliphaticCarbocycles (const ROMol &mol)
 calculates the number of aliphatic (at least one non-aromatic bond) SSSR More...
 
unsigned int calcNumSpiroAtoms (const ROMol &mol, std::vector< unsigned int > *atoms=NULL)
 calculates the number of spiro atoms (atoms shared between rings that share More...
 
unsigned int calcNumBridgeheadAtoms (const ROMol &mol, std::vector< unsigned int > *atoms=NULL)
 calculates the number of bridgehead atoms (atoms shared between rings that More...
 
unsigned numAtomStereoCenters (const ROMol &mol)
 calculates the number of stereo atom stereo centers More...
 
unsigned numUnspecifiedAtomStereoCenters (const ROMol &mol)
 
void registerDescriptors ()
 Helper function to register the descriptors with the descriptor service. More...
 
double calcAMW (const ROMol &mol, bool onlyHeavy=false)
 
double calcExactMW (const ROMol &mol, bool onlyHeavy=false)
 
std::string calcMolFormula (const ROMol &mol, bool separateIsotopes=false, bool abbreviateHIsotopes=true)
 
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 More...
 
double calcLabuteASA (const ROMol &mol, bool includeHs=true, bool force=false)
 calculates Labute's Approximate Surface Area (ASA from MOE) More...
 
double getTPSAAtomContribs (const ROMol &mol, std::vector< double > &Vi, bool force=false)
 calculates atomic contributions to the TPSA value More...
 
double calcTPSA (const ROMol &mol, bool force=false)
 calculates the TPSA value for a molecule More...
 
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)
 
std::vector< unsigned int > calcMQNs (const ROMol &mol, bool force=false)
 calculates MQN descriptors More...
 
template<class T >
T * makePropertyQuery (const std::string &name, double what)
 
PROP_RANGE_QUERYmakePropertyRangeQuery (const std::string &name, double min, double max)
 

Variables

const std::string chi0vVersion = "1.2.0"
 
const std::string chi1vVersion = "1.2.0"
 
const std::string chi2vVersion = "1.2.0"
 
const std::string chi3vVersion = "1.2.0"
 
const std::string chi4vVersion = "1.2.0"
 
const std::string chiNvVersion = "1.2.0"
 
const std::string chi0nVersion = "1.2.0"
 
const std::string chi1nVersion = "1.2.0"
 
const std::string chi2nVersion = "1.2.0"
 
const std::string chi3nVersion = "1.2.0"
 
const std::string chi4nVersion = "1.2.0"
 
const std::string chiNnVersion = "1.2.0"
 
const std::string hallKierAlphaVersion = "1.2.0"
 
const std::string kappa1Version = "1.1.0"
 
const std::string kappa2Version = "1.1.0"
 
const std::string kappa3Version = "1.1.0"
 
const std::string crippenVersion = "1.2.0"
 
const std::string CrippenClogPVersion = crippenVersion
 
const std::string CrippenMRVersion = crippenVersion
 
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 FractionCSP3Version
 
const std::string NumRingsVersion
 
const std::string NumAromaticRingsVersion
 
const std::string NumAliphaticRingsVersion
 
const std::string NumSaturatedRingsVersion
 
const std::string NumHeterocyclesVersion
 
const std::string NumAromaticHeterocyclesVersion
 
const std::string NumAromaticCarbocyclesVersion
 
const std::string NumSaturatedHeterocyclesVersion
 
const std::string NumSaturatedCarbocyclesVersion
 
const std::string NumAliphaticHeterocyclesVersion
 
const std::string NumAliphaticCarbocyclesVersion
 
const std::string NumSpiroAtomsVersion
 
const std::string NumBridgeheadAtomsVersion
 
const std::string NumAtomStereoCentersVersion
 
const std::string NumUnspecifiedAtomStereoCentersVersion
 calculates the number of unspecified stereo atom stereo centers More...
 
const std::string amwVersion
 
const std::string exactmwVersion
 
const std::string labuteASAVersion = "1.0.2"
 
const std::string tpsaVersion = "1.1.0"
 
const std::string MQNVersion = "1.0.0"
 

Typedef Documentation

Definition at line 93 of file Property.h.

Definition at line 92 of file Property.h.

Definition at line 97 of file Property.h.

Definition at line 99 of file Property.h.

Definition at line 102 of file Property.h.

Definition at line 105 of file Property.h.

Definition at line 107 of file Property.h.

Definition at line 94 of file Property.h.

Definition at line 109 of file Property.h.

Definition at line 95 of file Property.h.

Enumeration Type Documentation

Enumerator
Default 
NonStrict 
Strict 
StrictLinkages 

Definition at line 34 of file Lipinski.h.

Function Documentation

double RDKit::Descriptors::calcAMW ( const ROMol mol,
bool  onlyHeavy = false 
)
double RDKit::Descriptors::calcChi0n ( const ROMol mol,
bool  force = false 
)

Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi0v ( const ROMol mol,
bool  force = false 
)

From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi1n ( const ROMol mol,
bool  force = false 
)

Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi1v ( const ROMol mol,
bool  force = false 
)

From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi2n ( const ROMol mol,
bool  force = false 
)

Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi2v ( const ROMol mol,
bool  force = false 
)

From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi3n ( const ROMol mol,
bool  force = false 
)

Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi3v ( const ROMol mol,
bool  force = false 
)

From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi4n ( const ROMol mol,
bool  force = false 
)

Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChi4v ( const ROMol mol,
bool  force = false 
)

From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChiNn ( const ROMol mol,
unsigned int  n,
bool  force = false 
)

Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.

Parameters
molthe molecule of interest
nthe order of the connectivity index
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcChiNv ( const ROMol mol,
unsigned int  n,
bool  force = false 
)

From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
nthe order of the connectivity index
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcClogP ( const ROMol mol)

calculate the default Wildman-Crippen LogP for a molecule

See calcCrippenDescriptors

Parameters
molthe molecule of interest
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
molthe molecule of interest
logpused to return the logp estimate
mrused 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.
forceforces the value to be recalculated instead of pulled from the cache
double RDKit::Descriptors::calcExactMW ( const ROMol mol,
bool  onlyHeavy = false 
)
double RDKit::Descriptors::calcFractionCSP3 ( const ROMol mol)

calculates the fraction of carbons that are SP3 hybridized

double RDKit::Descriptors::calcHallKierAlpha ( const ROMol mol,
std::vector< double > *  atomContribs = 0 
)

calculate the Hall-Kier alpha value for a molecule From equation (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
atomContribsif provided, this will be used to return the contributions of the individual atoms to the value. These do not neccessarily sum to the full value. Note: this can be a time-consuming calculation.
double RDKit::Descriptors::calcKappa1 ( const ROMol mol)

calculate the Hall-Kier kappa1 value for a molecule From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
double RDKit::Descriptors::calcKappa2 ( const ROMol mol)

calculate the Hall-Kier kappa2 value for a molecule From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367-422, (1991)

Parameters
molthe molecule of interest
double RDKit::Descriptors::calcKappa3 ( const ROMol mol)

calculate the Hall-Kier kappa3 value for a molecule From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367-422,

Parameters
molthe molecule of interest
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
molthe 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 (number of Ns and Os)

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

calculates the standard Lipinski HBA definition (number of N-H and O-H

std::string RDKit::Descriptors::calcMolFormula ( const ROMol mol,
bool  separateIsotopes = false,
bool  abbreviateHIsotopes = true 
)

Calculates a molecule's formula

Parameters
molthe molecule of interest
separateIsotopesif true, isotopes will show up separately in the formula. So C[13CH2]O will give the formula: C[13C]H6O
abbreviateHIsotopesif true, 2H and 3H will be represented as D and T instead of [2H] and [3H]. This only applies if separateIsotopes is true
Returns
the formula as a string
std::vector<unsigned int> RDKit::Descriptors::calcMQNs ( const ROMol mol,
bool  force = false 
)

calculates MQN descriptors

Definition from Nguyen, K. T., Blum, L. C., Van Deursen, R. & Reymond, J.-L. "Classification of Organic Molecules by Molecular Quantum Numbers." ChemMedChem 4, 1803–1805 (2009).

Parameters
molthe molecule of interest
force(optional) calculate the values even if they are cached.
Returns
a vector with the MQNs
double RDKit::Descriptors::calcMR ( const ROMol mol)

calculate the default Wildman-Crippen MR Estimate for a molecule

See calcCrippenDescriptors

Parameters
molthe molecule of interest
unsigned int RDKit::Descriptors::calcNumAliphaticCarbocycles ( const ROMol mol)

calculates the number of aliphatic (at least one non-aromatic bond) SSSR

unsigned int RDKit::Descriptors::calcNumAliphaticHeterocycles ( const ROMol mol)

calculates the number of aliphatic (at least one non-aromatic bond) SSSR

unsigned int RDKit::Descriptors::calcNumAliphaticRings ( const ROMol mol)

calculates the number of aliphatic (at least one non-aromatic bond) SSSR

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

calculates the number of amide bonds

unsigned int RDKit::Descriptors::calcNumAromaticCarbocycles ( const ROMol mol)

calculates the number of aromatic SSSR carbocycles

unsigned int RDKit::Descriptors::calcNumAromaticHeterocycles ( const ROMol mol)

calculates the number of aromatic SSSR heterocycles

unsigned int RDKit::Descriptors::calcNumAromaticRings ( const ROMol mol)

calculates the number of aromatic SSSR rings

unsigned int RDKit::Descriptors::calcNumBridgeheadAtoms ( const ROMol mol,
std::vector< unsigned int > *  atoms = NULL 
)

calculates the number of bridgehead atoms (atoms shared between rings that

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

calculates the number of H-bond acceptors

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

calculates the number of H-bond donors

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

calculates the number of heteroatoms

unsigned int RDKit::Descriptors::calcNumHeterocycles ( const ROMol mol)

calculates the number of SSSR heterocycles

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

calculates the number of SSSR rings

unsigned int RDKit::Descriptors::calcNumRotatableBonds ( const ROMol mol,
NumRotatableBondsOptions  useStrictDefinition = Default 
)

calculates the number of rotatable bonds

Parameters
molthe molecule of interest
strictif Strict, a stricter definition of rotable bonds is used this excludes amides, esters, etc. if StrictLinkages, a much stricter definition that handles rotatable bonds between rings as well. if Default - uses the default choice (normally Strict)
unsigned int RDKit::Descriptors::calcNumRotatableBonds ( const ROMol mol,
bool  strict 
)

calculates the number of rotatable bonds ( backwards compatibility function, deprecated, please use calcNumRotatableBonds(const ROMol&, int)

Parameters
molthe molecule of interest
strictif Strict == true, uses NumRotatableBondsOptions::Strict
unsigned int RDKit::Descriptors::calcNumSaturatedCarbocycles ( const ROMol mol)

calculates the number of saturated SSSR carbocycles

unsigned int RDKit::Descriptors::calcNumSaturatedHeterocycles ( const ROMol mol)

calculates the number of saturated SSSR heterocycles

unsigned int RDKit::Descriptors::calcNumSaturatedRings ( const ROMol mol)

calculates the number of saturated SSSR rings

unsigned int RDKit::Descriptors::calcNumSpiroAtoms ( const ROMol mol,
std::vector< unsigned int > *  atoms = NULL 
)

calculates the number of spiro atoms (atoms shared between rings that share

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
molthe 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,
std::vector< unsigned int > *  atomTypes = 0,
std::vector< std::string > *  atomTypeLabels = 0 
)

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
molthe molecule of interest
logpContribsused to return the logp contributions, must be equal in length to the number of atoms
mrContribsused to return the MR contributions, must be equal in length to the number of atoms
forceforces the value to be recalculated instead of pulled from the cache
atomTypesif provided will be used to return the indices of the atom types, should be as long as the number of atoms
atomTypeLabelsif provided will be used to return the labels of the atom types, should be as long as the number of atoms
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
molthe molecule of interest
Viused to return the explict atom contribs
hContribused 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
molthe molecule of interest
Viused to return the atom contribs
force(optional) calculate the values even if they are cached.
Returns
the sum of the atomic contributions
template<class T >
T* RDKit::Descriptors::makePropertyQuery ( const std::string &  name,
double  what 
)
PROP_RANGE_QUERY* RDKit::Descriptors::makePropertyRangeQuery ( const std::string &  name,
double  min,
double  max 
)

Referenced by makePropertyQuery().

unsigned RDKit::Descriptors::numAtomStereoCenters ( const ROMol mol)

calculates the number of stereo atom stereo centers

unsigned RDKit::Descriptors::numUnspecifiedAtomStereoCenters ( const ROMol mol)
void RDKit::Descriptors::registerDescriptors ( )

Helper function to register the descriptors with the descriptor service.

Variable Documentation

const std::string RDKit::Descriptors::amwVersion

Calculates a molecule's average molecular weight

Parameters
molthe 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
const std::string RDKit::Descriptors::chi0nVersion = "1.2.0"

Definition at line 85 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi0vVersion = "1.2.0"

Definition at line 34 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi1nVersion = "1.2.0"

Definition at line 94 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi1vVersion = "1.2.0"

Definition at line 42 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi2nVersion = "1.2.0"

Definition at line 103 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi2vVersion = "1.2.0"

Definition at line 50 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi3nVersion = "1.2.0"

Definition at line 112 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi3vVersion = "1.2.0"

Definition at line 58 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi4nVersion = "1.2.0"

Definition at line 121 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chi4vVersion = "1.2.0"

Definition at line 66 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chiNnVersion = "1.2.0"

Definition at line 131 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::chiNvVersion = "1.2.0"

Definition at line 75 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::CrippenClogPVersion = crippenVersion

Definition at line 85 of file Crippen.h.

const std::string RDKit::Descriptors::CrippenMRVersion = crippenVersion

Definition at line 93 of file Crippen.h.

const std::string RDKit::Descriptors::crippenVersion = "1.2.0"

Definition at line 26 of file Crippen.h.

const std::string RDKit::Descriptors::exactmwVersion

Calculates a molecule's exact molecular weight

Parameters
molthe 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
const std::string RDKit::Descriptors::FractionCSP3Version
const std::string RDKit::Descriptors::hallKierAlphaVersion = "1.2.0"

Definition at line 145 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::kappa1Version = "1.1.0"

Definition at line 153 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::kappa2Version = "1.1.0"

Definition at line 161 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::kappa3Version = "1.1.0"

Definition at line 170 of file ConnectivityDescriptors.h.

const std::string RDKit::Descriptors::labuteASAVersion = "1.0.2"

Definition at line 24 of file MolSurf.h.

const std::string RDKit::Descriptors::lipinskiHBAVersion = "1.0.0"

Definition at line 25 of file Lipinski.h.

const std::string RDKit::Descriptors::lipinskiHBDVersion = "2.0.0"

Definition at line 29 of file Lipinski.h.

const std::string RDKit::Descriptors::MQNVersion = "1.0.0"

Definition at line 24 of file MQN.h.

const std::string RDKit::Descriptors::NumAliphaticCarbocyclesVersion
const std::string RDKit::Descriptors::NumAliphaticHeterocyclesVersion
const std::string RDKit::Descriptors::NumAliphaticRingsVersion
const std::string RDKit::Descriptors::NumAmideBondsVersion
const std::string RDKit::Descriptors::NumAromaticCarbocyclesVersion
const std::string RDKit::Descriptors::NumAromaticHeterocyclesVersion
const std::string RDKit::Descriptors::NumAromaticRingsVersion
const std::string RDKit::Descriptors::NumAtomStereoCentersVersion
const std::string RDKit::Descriptors::NumBridgeheadAtomsVersion
const std::string RDKit::Descriptors::NumHBAVersion
const std::string RDKit::Descriptors::NumHBDVersion
const std::string RDKit::Descriptors::NumHeteroatomsVersion
const std::string RDKit::Descriptors::NumHeterocyclesVersion
const std::string RDKit::Descriptors::NumRingsVersion
const std::string RDKit::Descriptors::NumRotatableBondsVersion
const std::string RDKit::Descriptors::NumSaturatedCarbocyclesVersion
const std::string RDKit::Descriptors::NumSaturatedHeterocyclesVersion
const std::string RDKit::Descriptors::NumSaturatedRingsVersion
const std::string RDKit::Descriptors::NumSpiroAtomsVersion
const std::string RDKit::Descriptors::NumUnspecifiedAtomStereoCentersVersion

calculates the number of unspecified stereo atom stereo centers

const std::string RDKit::Descriptors::tpsaVersion = "1.1.0"

Definition at line 61 of file MolSurf.h.