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RDKit
Open-source cheminformatics and machine learning.
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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 | |
RDKIT_DESCRIPTORS_EXPORT void | AUTOCORR2D (const ROMol &, std::vector< double > &res, const std::string &customAtomPropName="") |
RDKIT_DESCRIPTORS_EXPORT double | calcChi0v (const ROMol &mol, bool force=false) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcChi1v (const ROMol &mol, bool force=false) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcChi2v (const ROMol &mol, bool force=false) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcChi3v (const ROMol &mol, bool force=false) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcChi4v (const ROMol &mol, bool force=false) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) More... | |
RDKIT_DESCRIPTORS_EXPORT 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... | |
RDKIT_DESCRIPTORS_EXPORT double | calcChi0n (const ROMol &mol, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT double | calcChi1n (const ROMol &mol, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT double | calcChi2n (const ROMol &mol, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT double | calcChi3n (const ROMol &mol, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT double | calcChi4n (const ROMol &mol, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT double | calcChiNn (const ROMol &mol, unsigned int n, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT double | calcHallKierAlpha (const ROMol &mol, std::vector< double > *atomContribs=0) |
RDKIT_DESCRIPTORS_EXPORT double | calcKappa1 (const ROMol &mol) |
RDKIT_DESCRIPTORS_EXPORT double | calcKappa2 (const ROMol &mol) |
RDKIT_DESCRIPTORS_EXPORT double | calcKappa3 (const ROMol &mol) |
RDKIT_DESCRIPTORS_EXPORT 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) |
RDKIT_DESCRIPTORS_EXPORT 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... | |
RDKIT_DESCRIPTORS_EXPORT double | calcClogP (const ROMol &mol) |
calculate the default Wildman-Crippen LogP for a molecule More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcMR (const ROMol &mol) |
calculate the default Wildman-Crippen MR Estimate for a molecule More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcLipinskiHBA (const ROMol &mol) |
calculates the standard Lipinski HBA definition (number of Ns and Os) More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcLipinskiHBD (const ROMol &mol) |
calculates the standard Lipinski HBA definition (number of N-H and O-H More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumRotatableBonds (const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) |
calculates the number of rotatable bonds More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumRotatableBonds (const ROMol &mol, bool strict) |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumHBD (const ROMol &mol) |
calculates the number of H-bond donors More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumHBA (const ROMol &mol) |
calculates the number of H-bond acceptors More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumHeteroatoms (const ROMol &mol) |
calculates the number of heteroatoms More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumAmideBonds (const ROMol &mol) |
calculates the number of amide bonds More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcFractionCSP3 (const ROMol &mol) |
calculates the fraction of carbons that are SP3 hybridized More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumRings (const ROMol &mol) |
calculates the number of SSSR rings More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumAromaticRings (const ROMol &mol) |
calculates the number of aromatic SSSR rings More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumAliphaticRings (const ROMol &mol) |
calculates the number of aliphatic (at least one non-aromatic bond) SSSR More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumSaturatedRings (const ROMol &mol) |
calculates the number of saturated SSSR rings More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumHeterocycles (const ROMol &mol) |
calculates the number of SSSR heterocycles More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumAromaticHeterocycles (const ROMol &mol) |
calculates the number of aromatic SSSR heterocycles More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumAromaticCarbocycles (const ROMol &mol) |
calculates the number of aromatic SSSR carbocycles More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumSaturatedHeterocycles (const ROMol &mol) |
calculates the number of saturated SSSR heterocycles More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumSaturatedCarbocycles (const ROMol &mol) |
calculates the number of saturated SSSR carbocycles More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumAliphaticHeterocycles (const ROMol &mol) |
calculates the number of aliphatic (at least one non-aromatic bond) SSSR More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumAliphaticCarbocycles (const ROMol &mol) |
calculates the number of aliphatic (at least one non-aromatic bond) SSSR More... | |
RDKIT_DESCRIPTORS_EXPORT 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... | |
RDKIT_DESCRIPTORS_EXPORT unsigned int | calcNumBridgeheadAtoms (const ROMol &mol, std::vector< unsigned int > *atoms=NULL) |
calculates the number of bridgehead atoms (atoms shared between rings that More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned | numAtomStereoCenters (const ROMol &mol) |
calculates the total number of atom stereo centers More... | |
RDKIT_DESCRIPTORS_EXPORT unsigned | numUnspecifiedAtomStereoCenters (const ROMol &mol) |
RDKIT_DESCRIPTORS_EXPORT void | registerDescriptors () |
Helper function to register the descriptors with the descriptor service. More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcAMW (const ROMol &mol, bool onlyHeavy=false) |
RDKIT_DESCRIPTORS_EXPORT double | calcExactMW (const ROMol &mol, bool onlyHeavy=false) |
RDKIT_DESCRIPTORS_EXPORT std::string | calcMolFormula (const ROMol &mol, bool separateIsotopes=false, bool abbreviateHIsotopes=true) |
RDKIT_DESCRIPTORS_EXPORT 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... | |
RDKIT_DESCRIPTORS_EXPORT double | calcLabuteASA (const ROMol &mol, bool includeHs=true, bool force=false) |
calculates Labute's Approximate Surface Area (ASA from MOE) More... | |
RDKIT_DESCRIPTORS_EXPORT double | getTPSAAtomContribs (const ROMol &mol, std::vector< double > &Vi, bool force=false, bool includeSandP=false) |
calculates atomic contributions to the TPSA value More... | |
RDKIT_DESCRIPTORS_EXPORT double | calcTPSA (const ROMol &mol, bool force=false, bool includeSandP=false) |
calculates the TPSA value for a molecule More... | |
RDKIT_DESCRIPTORS_EXPORT std::vector< double > | calcSlogP_VSA (const ROMol &mol, std::vector< double > *bins=0, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT std::vector< double > | calcSMR_VSA (const ROMol &mol, std::vector< double > *bins=0, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT std::vector< double > | calcPEOE_VSA (const ROMol &mol, std::vector< double > *bins=0, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT std::vector< double > | calcCustomProp_VSA (const ROMol &mol, const std::string &customPropName, const std::vector< double > &bins, bool force=false) |
RDKIT_DESCRIPTORS_EXPORT 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) |
RDKIT_DESCRIPTORS_EXPORT PROP_RANGE_QUERY * | makePropertyRangeQuery (const std::string &name, double min, double max) |
RDKIT_DESCRIPTORS_EXPORT void | USR (const ROMol &mol, std::vector< double > &descriptor, int confId=-1) |
RDKIT_DESCRIPTORS_EXPORT void | USRCAT (const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int >> &atomIds, int confId=-1) |
RDKIT_DESCRIPTORS_EXPORT void | calcUSRDistributions (const RDGeom::Point3DConstPtrVect &coords, std::vector< std::vector< double >> &dist, std::vector< RDGeom::Point3D > &points) |
RDKIT_DESCRIPTORS_EXPORT void | calcUSRDistributionsFromPoints (const RDGeom::Point3DConstPtrVect &coords, const std::vector< RDGeom::Point3D > &points, std::vector< std::vector< double >> &dist) |
RDKIT_DESCRIPTORS_EXPORT void | calcUSRFromDistributions (const std::vector< std::vector< double >> &dist, std::vector< double > &descriptor) |
RDKIT_DESCRIPTORS_EXPORT double | calcUSRScore (const std::vector< double > &d1, const std::vector< double > &d2, const std::vector< double > &weights) |
typedef Queries::AndQuery<int, const ROMol &, true> RDKit::Descriptors::PROP_AND_QUERY |
Definition at line 94 of file Property.h.
typedef Queries::Query<bool, const ROMol &, true> RDKit::Descriptors::PROP_BOOL_QUERY |
Definition at line 93 of file Property.h.
typedef Queries::EqualityQuery<double, const ROMol &, true> RDKit::Descriptors::PROP_EQUALS_QUERY |
Definition at line 98 of file Property.h.
typedef Queries::GreaterQuery<double, const ROMol &, true> RDKit::Descriptors::PROP_GREATER_QUERY |
Definition at line 100 of file Property.h.
typedef Queries::GreaterEqualQuery<double, const ROMol &, true> RDKit::Descriptors::PROP_GREATEREQUAL_QUERY |
Definition at line 103 of file Property.h.
typedef Queries::LessQuery<double, const ROMol &, true> RDKit::Descriptors::PROP_LESS_QUERY |
Definition at line 106 of file Property.h.
typedef Queries::LessEqualQuery<double, const ROMol &, true> RDKit::Descriptors::PROP_LESSEQUAL_QUERY |
Definition at line 108 of file Property.h.
typedef Queries::OrQuery<int, const ROMol &, true> RDKit::Descriptors::PROP_OR_QUERY |
Definition at line 95 of file Property.h.
typedef Queries::RangeQuery<double, const ROMol &, true> RDKit::Descriptors::PROP_RANGE_QUERY |
Definition at line 110 of file Property.h.
typedef Queries::XOrQuery<int, const ROMol &, true> RDKit::Descriptors::PROP_XOR_QUERY |
Definition at line 96 of file Property.h.
Enumerator | |
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Default | |
NonStrict | |
Strict | |
StrictLinkages |
Definition at line 35 of file Lipinski.h.
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::AUTOCORR2D | ( | const ROMol & | , |
std::vector< double > & | res, | ||
const std::string & | customAtomPropName = "" |
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) |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcAMW | ( | const ROMol & | mol, |
bool | onlyHeavy = false |
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RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi0n | ( | const ROMol & | mol, |
bool | force = false |
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) |
Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi0v | ( | const ROMol & | mol, |
bool | force = false |
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) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi1n | ( | const ROMol & | mol, |
bool | force = false |
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) |
Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi1v | ( | const ROMol & | mol, |
bool | force = false |
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) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi2n | ( | const ROMol & | mol, |
bool | force = false |
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) |
Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi2v | ( | const ROMol & | mol, |
bool | force = false |
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) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi3n | ( | const ROMol & | mol, |
bool | force = false |
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) |
Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi3v | ( | const ROMol & | mol, |
bool | force = false |
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) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi4n | ( | const ROMol & | mol, |
bool | force = false |
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) |
Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChi4v | ( | const ROMol & | mol, |
bool | force = false |
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) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
mol | the molecule of interest |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChiNn | ( | const ROMol & | mol, |
unsigned int | n, | ||
bool | force = false |
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) |
Similar to Hall Kier ChiXv, but uses nVal instead of valence This makes a big difference after we get out of the first row.
mol | the molecule of interest |
n | the order of the connectivity index |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcChiNv | ( | const ROMol & | mol, |
unsigned int | n, | ||
bool | force = false |
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) |
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
mol | the molecule of interest |
n | the order of the connectivity index |
force | forces the value to be recalculated instead of pulled from the cache |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcClogP | ( | const ROMol & | mol | ) |
calculate the default Wildman-Crippen LogP for a molecule
See calcCrippenDescriptors
mol | the molecule of interest |
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::calcCrippenDescriptors | ( | const ROMol & | mol, |
double & | logp, | ||
double & | mr, | ||
bool | includeHs = true , |
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bool | force = false |
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) |
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)
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 |
RDKIT_DESCRIPTORS_EXPORT std::vector<double> RDKit::Descriptors::calcCustomProp_VSA | ( | const ROMol & | mol, |
const std::string & | customPropName, | ||
const std::vector< double > & | bins, | ||
bool | force = false |
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RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcExactMW | ( | const ROMol & | mol, |
bool | onlyHeavy = false |
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RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcFractionCSP3 | ( | const ROMol & | mol | ) |
calculates the fraction of carbons that are SP3 hybridized
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcHallKierAlpha | ( | const ROMol & | mol, |
std::vector< double > * | atomContribs = 0 |
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calculate the Hall-Kier alpha value for a molecule From equation (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)
mol | the molecule of interest |
atomContribs | if 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. |
RDKIT_DESCRIPTORS_EXPORT 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)
mol | the molecule of interest |
RDKIT_DESCRIPTORS_EXPORT 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)
mol | the molecule of interest |
RDKIT_DESCRIPTORS_EXPORT 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,
mol | the molecule of interest |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcLabuteASA | ( | const ROMol & | mol, |
bool | includeHs = true , |
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bool | force = false |
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) |
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)
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. |
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcLipinskiHBA | ( | const ROMol & | mol | ) |
calculates the standard Lipinski HBA definition (number of Ns and Os)
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcLipinskiHBD | ( | const ROMol & | mol | ) |
calculates the standard Lipinski HBA definition (number of N-H and O-H
RDKIT_DESCRIPTORS_EXPORT std::string RDKit::Descriptors::calcMolFormula | ( | const ROMol & | mol, |
bool | separateIsotopes = false , |
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bool | abbreviateHIsotopes = true |
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) |
Calculates a molecule's formula
mol | the molecule of interest |
separateIsotopes | if true, isotopes will show up separately in the formula. So C[13CH2]O will give the formula: C[13C]H6O |
abbreviateHIsotopes | if true, 2H and 3H will be represented as D and T instead of [2H] and [3H]. This only applies if separateIsotopes is true |
RDKIT_DESCRIPTORS_EXPORT std::vector<unsigned int> RDKit::Descriptors::calcMQNs | ( | const ROMol & | mol, |
bool | force = false |
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) |
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).
mol | the molecule of interest |
force | (optional) calculate the values even if they are cached. |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcMR | ( | const ROMol & | mol | ) |
calculate the default Wildman-Crippen MR Estimate for a molecule
See calcCrippenDescriptors
mol | the molecule of interest |
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumAliphaticCarbocycles | ( | const ROMol & | mol | ) |
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumAliphaticHeterocycles | ( | const ROMol & | mol | ) |
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumAliphaticRings | ( | const ROMol & | mol | ) |
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumAmideBonds | ( | const ROMol & | mol | ) |
calculates the number of amide bonds
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumAromaticCarbocycles | ( | const ROMol & | mol | ) |
calculates the number of aromatic SSSR carbocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumAromaticHeterocycles | ( | const ROMol & | mol | ) |
calculates the number of aromatic SSSR heterocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumAromaticRings | ( | const ROMol & | mol | ) |
calculates the number of aromatic SSSR rings
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumBridgeheadAtoms | ( | const ROMol & | mol, |
std::vector< unsigned int > * | atoms = NULL |
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) |
calculates the number of bridgehead atoms (atoms shared between rings that
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumHBA | ( | const ROMol & | mol | ) |
calculates the number of H-bond acceptors
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumHBD | ( | const ROMol & | mol | ) |
calculates the number of H-bond donors
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumHeteroatoms | ( | const ROMol & | mol | ) |
calculates the number of heteroatoms
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumHeterocycles | ( | const ROMol & | mol | ) |
calculates the number of SSSR heterocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumRings | ( | const ROMol & | mol | ) |
calculates the number of SSSR rings
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumRotatableBonds | ( | const ROMol & | mol, |
NumRotatableBondsOptions | useStrictDefinition = Default |
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calculates the number of rotatable bonds
mol | the molecule of interest |
strict | if 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) |
RDKIT_DESCRIPTORS_EXPORT 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)
mol | the molecule of interest |
strict | if Strict == true, uses NumRotatableBondsOptions::Strict |
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumSaturatedCarbocycles | ( | const ROMol & | mol | ) |
calculates the number of saturated SSSR carbocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumSaturatedHeterocycles | ( | const ROMol & | mol | ) |
calculates the number of saturated SSSR heterocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int RDKit::Descriptors::calcNumSaturatedRings | ( | const ROMol & | mol | ) |
calculates the number of saturated SSSR rings
RDKIT_DESCRIPTORS_EXPORT 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
RDKIT_DESCRIPTORS_EXPORT std::vector<double> RDKit::Descriptors::calcPEOE_VSA | ( | const ROMol & | mol, |
std::vector< double > * | bins = 0 , |
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bool | force = false |
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) |
RDKIT_DESCRIPTORS_EXPORT std::vector<double> RDKit::Descriptors::calcSlogP_VSA | ( | const ROMol & | mol, |
std::vector< double > * | bins = 0 , |
||
bool | force = false |
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) |
RDKIT_DESCRIPTORS_EXPORT std::vector<double> RDKit::Descriptors::calcSMR_VSA | ( | const ROMol & | mol, |
std::vector< double > * | bins = 0 , |
||
bool | force = false |
||
) |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcTPSA | ( | const ROMol & | mol, |
bool | force = false , |
||
bool | includeSandP = 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 By default the calculation does not include contributions from S or P atoms, this can be be changed with the includeSandP argument.
mol | the molecule of interest |
force | (optional) calculate the value even if it's cached. |
includeSandP | (optional) include contributions from S and P atoms |
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::calcUSRDistributions | ( | const RDGeom::Point3DConstPtrVect & | coords, |
std::vector< std::vector< double >> & | dist, | ||
std::vector< RDGeom::Point3D > & | points | ||
) |
Calculates the four distance distributions for the USR descriptor
coords | the atom coordinates |
dist | storage for the four distance distributions |
points | storage for the four points |
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::calcUSRDistributionsFromPoints | ( | const RDGeom::Point3DConstPtrVect & | coords, |
const std::vector< RDGeom::Point3D > & | points, | ||
std::vector< std::vector< double >> & | dist | ||
) |
Calculates the four distance distributions for the USR descriptor
coords | the atom coordinates |
points | vector with the points |
dist | storage for the distance distributions |
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::calcUSRFromDistributions | ( | const std::vector< std::vector< double >> & | dist, |
std::vector< double > & | descriptor | ||
) |
Calculates the USR descriptor from the four distance distributions
dist | vector with the four distance distributions |
descriptor | storage for the computed USR descriptor |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::calcUSRScore | ( | const std::vector< double > & | d1, |
const std::vector< double > & | d2, | ||
const std::vector< double > & | weights | ||
) |
Calculates the score between two USRCAT descriptors with weights
d1 | descriptor 1 |
d2 | descriptor 2 |
weights | the weights for each subset of moments |
RDKIT_DESCRIPTORS_EXPORT 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)
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 |
atomTypes | if provided will be used to return the indices of the atom types, should be as long as the number of atoms |
atomTypeLabels | if provided will be used to return the labels of the atom types, should be as long as the number of atoms |
RDKIT_DESCRIPTORS_EXPORT 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)
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. |
RDKIT_DESCRIPTORS_EXPORT double RDKit::Descriptors::getTPSAAtomContribs | ( | const ROMol & | mol, |
std::vector< double > & | Vi, | ||
bool | force = false , |
||
bool | includeSandP = 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 By default the calculation does not include contributions from S or P atoms, this can be be changed with the includeSandP argument.
mol | the molecule of interest |
Vi | used to return the atom contribs |
force | (optional) calculate the values even if they are cached. |
includeSandP | (optional) include contributions from S and P atoms |
T* RDKit::Descriptors::makePropertyQuery | ( | const std::string & | name, |
double | what | ||
) |
Definition at line 114 of file Property.h.
References RDKit::Descriptors::Properties::getProperty(), makePropertyRangeQuery(), and RDKIT_DESCRIPTORS_EXPORT.
RDKIT_DESCRIPTORS_EXPORT PROP_RANGE_QUERY* RDKit::Descriptors::makePropertyRangeQuery | ( | const std::string & | name, |
double | min, | ||
double | max | ||
) |
Referenced by makePropertyQuery().
RDKIT_DESCRIPTORS_EXPORT unsigned RDKit::Descriptors::numAtomStereoCenters | ( | const ROMol & | mol | ) |
calculates the total number of atom stereo centers
RDKIT_DESCRIPTORS_EXPORT unsigned RDKit::Descriptors::numUnspecifiedAtomStereoCenters | ( | const ROMol & | mol | ) |
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::registerDescriptors | ( | ) |
Helper function to register the descriptors with the descriptor service.
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::USR | ( | const ROMol & | mol, |
std::vector< double > & | descriptor, | ||
int | confId = -1 |
||
) |
Calculates the ultra-fast shape recognition (USR) descriptor
Reference: P. J. Ballester, W. G. Richards, JCC (2007), 28, 1711 - 1723.
Derived from RDKit Python implementation of Jan Domanski who derived his code from Adrian Schreyer's code: http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default
mol | the molecule of interest |
descriptor | storage for the computed USR descriptor |
confId | the conformer Id |
RDKIT_DESCRIPTORS_EXPORT void RDKit::Descriptors::USRCAT | ( | const ROMol & | mol, |
std::vector< double > & | descriptor, | ||
std::vector< std::vector< unsigned int >> & | atomIds, | ||
int | confId = -1 |
||
) |
Calculates the ultra-fast shape recognition with CREDO atom types (USRCAT) descriptor
Reference: A. M. Schreyer, T. Blundell, J. Cheminf. (2012), 4, 27.
Derived from Python implementation Adrian Schreyer: http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default
mol | the molecule of interest |
descriptor | storage for the computed USR descriptor |
confId | the conformer Id |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::amwVersion |
Calculates a molecule's average molecular weight
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 |
const std::string RDKit::Descriptors::AUTOCORR2DVersion = "1.0.0" |
Definition at line 43 of file AUTOCORR2D.h.
const std::string RDKit::Descriptors::chi0nVersion = "1.2.0" |
Definition at line 86 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi0vVersion = "1.2.0" |
Definition at line 35 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi1nVersion = "1.2.0" |
Definition at line 95 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi1vVersion = "1.2.0" |
Definition at line 43 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi2nVersion = "1.2.0" |
Definition at line 104 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi2vVersion = "1.2.0" |
Definition at line 51 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi3nVersion = "1.2.0" |
Definition at line 113 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi3vVersion = "1.2.0" |
Definition at line 59 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi4nVersion = "1.2.0" |
Definition at line 122 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chi4vVersion = "1.2.0" |
Definition at line 67 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chiNnVersion = "1.2.0" |
Definition at line 132 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::chiNvVersion = "1.2.0" |
Definition at line 76 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::CrippenClogPVersion = crippenVersion |
const std::string RDKit::Descriptors::CrippenMRVersion = crippenVersion |
const std::string RDKit::Descriptors::crippenVersion = "1.2.0" |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::exactmwVersion |
Calculates a molecule's exact molecular weight
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 |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::FractionCSP3Version |
const std::string RDKit::Descriptors::hallKierAlphaVersion = "1.2.0" |
Definition at line 146 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::kappa1Version = "1.1.0" |
Definition at line 154 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::kappa2Version = "1.1.0" |
Definition at line 162 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::kappa3Version = "1.1.0" |
Definition at line 171 of file ConnectivityDescriptors.h.
const std::string RDKit::Descriptors::labuteASAVersion = "1.0.2" |
const std::string RDKit::Descriptors::lipinskiHBAVersion = "1.0.0" |
Definition at line 26 of file Lipinski.h.
const std::string RDKit::Descriptors::lipinskiHBDVersion = "2.0.0" |
Definition at line 30 of file Lipinski.h.
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAliphaticCarbocyclesVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAliphaticHeterocyclesVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAliphaticRingsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAmideBondsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAromaticCarbocyclesVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAromaticHeterocyclesVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAromaticRingsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumAtomStereoCentersVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumBridgeheadAtomsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumHBAVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumHBDVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumHeteroatomsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumHeterocyclesVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumRingsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumRotatableBondsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumSaturatedCarbocyclesVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumSaturatedHeterocyclesVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumSaturatedRingsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumSpiroAtomsVersion |
RDKIT_DESCRIPTORS_EXPORT const std::string RDKit::Descriptors::NumUnspecifiedAtomStereoCentersVersion |
calculates the number of unspecified stereo atom stereo centers