Lipinski.h
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//
// Copyright (C) 2007-2011 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
/*! \file Lipinski.h
\brief Contains Lipinski and Lipinski-like descriptors. Use MolDescriptors.h
in client code.
*/
#ifndef __RD_LIPINSKI_H__
#define __RD_LIPINSKI_H__
namespace RDKit {
class ROMol;
namespace Descriptors {
const std::string lipinskiHBAVersion = "1.0.0";
//! calculates the standard Lipinski HBA definition (number of Ns and Os)
unsigned int calcLipinskiHBA(const ROMol &mol);
const std::string lipinskiHBDVersion = "2.0.0";
//! calculates the standard Lipinski HBA definition (number of N-H and O-H
// bonds)
unsigned int calcLipinskiHBD(const ROMol &mol);
enum NumRotatableBondsOptions {
Default = -1,
NonStrict = 0,
Strict = 1,
StrictLinkages = 2,
};
extern const std::string NumRotatableBondsVersion;
//! calculates the number of rotatable bonds
/*!
\param mol the molecule of interest
\param 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)
*/
unsigned int calcNumRotatableBonds(const ROMol &mol,
NumRotatableBondsOptions useStrictDefinition=Default);
//! calculates the number of rotatable bonds ( backwards compatibility function,
//! deprecated, please use calcNumRotatableBonds(const ROMol&, int)
/*!
\param mol the molecule of interest
\param strict if Strict == true, uses NumRotatableBondsOptions::Strict
*/
unsigned int calcNumRotatableBonds(const ROMol &mol, bool strict);
extern const std::string NumHBDVersion;
//! calculates the number of H-bond donors
unsigned int calcNumHBD(const ROMol &mol);
extern const std::string NumHBAVersion;
//! calculates the number of H-bond acceptors
unsigned int calcNumHBA(const ROMol &mol);
extern const std::string NumHeteroatomsVersion;
//! calculates the number of heteroatoms
unsigned int calcNumHeteroatoms(const ROMol &mol);
extern const std::string NumAmideBondsVersion;
//! calculates the number of amide bonds
unsigned int calcNumAmideBonds(const ROMol &mol);
extern const std::string FractionCSP3Version;
//! calculates the fraction of carbons that are SP3 hybridized
double calcFractionCSP3(const ROMol &mol);
extern const std::string NumRingsVersion;
//! calculates the number of SSSR rings
unsigned int calcNumRings(const ROMol &mol);
extern const std::string NumAromaticRingsVersion;
//! calculates the number of aromatic SSSR rings
unsigned int calcNumAromaticRings(const ROMol &mol);
extern const std::string NumAliphaticRingsVersion;
//! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
// rings
unsigned int calcNumAliphaticRings(const ROMol &mol);
extern const std::string NumSaturatedRingsVersion;
//! calculates the number of saturated SSSR rings
unsigned int calcNumSaturatedRings(const ROMol &mol);
extern const std::string NumHeterocyclesVersion;
//! calculates the number of SSSR heterocycles
unsigned int calcNumHeterocycles(const ROMol &mol);
extern const std::string NumAromaticHeterocyclesVersion;
//! calculates the number of aromatic SSSR heterocycles
unsigned int calcNumAromaticHeterocycles(const ROMol &mol);
extern const std::string NumAromaticCarbocyclesVersion;
//! calculates the number of aromatic SSSR carbocycles
unsigned int calcNumAromaticCarbocycles(const ROMol &mol);
extern const std::string NumSaturatedHeterocyclesVersion;
//! calculates the number of saturated SSSR heterocycles
unsigned int calcNumSaturatedHeterocycles(const ROMol &mol);
extern const std::string NumSaturatedCarbocyclesVersion;
//! calculates the number of saturated SSSR carbocycles
unsigned int calcNumSaturatedCarbocycles(const ROMol &mol);
extern const std::string NumAliphaticHeterocyclesVersion;
//! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
// heterocycles
unsigned int calcNumAliphaticHeterocycles(const ROMol &mol);
extern const std::string NumAliphaticCarbocyclesVersion;
//! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
// carbocycles
unsigned int calcNumAliphaticCarbocycles(const ROMol &mol);
extern const std::string NumSpiroAtomsVersion;
//! calculates the number of spiro atoms (atoms shared between rings that share
// exactly one atom)
unsigned int calcNumSpiroAtoms(const ROMol &mol,
std::vector<unsigned int> *atoms = NULL);
extern const std::string NumBridgeheadAtomsVersion;
//! calculates the number of bridgehead atoms (atoms shared between rings that
// share at least two bonds)
unsigned int calcNumBridgeheadAtoms(const ROMol &mol,
std::vector<unsigned int> *atoms = NULL);
} // end of namespace Descriptors
} // end of namespace RDKit
#endif
RDKit::Descriptors::calcNumSpiroAtoms
unsigned int calcNumSpiroAtoms(const ROMol &mol, std::vector< unsigned int > *atoms=NULL)
calculates the number of spiro atoms (atoms shared between rings that share
RDKit::Descriptors::Default
Definition: Lipinski.h:33
RDKit::Descriptors::NumAliphaticCarbocyclesVersion
const std::string NumAliphaticCarbocyclesVersion
RDKit::Descriptors::NumRotatableBondsVersion
const std::string NumRotatableBondsVersion
RDKit::Descriptors::calcNumAromaticHeterocycles
unsigned int calcNumAromaticHeterocycles(const ROMol &mol)
calculates the number of aromatic SSSR heterocycles
RDKit::Descriptors::Strict
Definition: Lipinski.h:35
RDKit::Descriptors::NumAliphaticHeterocyclesVersion
const std::string NumAliphaticHeterocyclesVersion
RDKit::Descriptors::StrictLinkages
Definition: Lipinski.h:36
RDKit::Descriptors::NumSaturatedHeterocyclesVersion
const std::string NumSaturatedHeterocyclesVersion
RDKit::Descriptors::NumAliphaticRingsVersion
const std::string NumAliphaticRingsVersion
RDKit::Descriptors::calcNumSaturatedHeterocycles
unsigned int calcNumSaturatedHeterocycles(const ROMol &mol)
calculates the number of saturated SSSR heterocycles
RDKit::Descriptors::calcNumHBD
unsigned int calcNumHBD(const ROMol &mol)
calculates the number of H-bond donors
RDKit::Descriptors::calcNumSaturatedRings
unsigned int calcNumSaturatedRings(const ROMol &mol)
calculates the number of saturated SSSR rings
RDKit::Descriptors::FractionCSP3Version
const std::string FractionCSP3Version
RDKit::Descriptors::NumAmideBondsVersion
const std::string NumAmideBondsVersion
RDKit::Descriptors::NumAromaticRingsVersion
const std::string NumAromaticRingsVersion
RDKit::Descriptors::calcNumAliphaticRings
unsigned int calcNumAliphaticRings(const ROMol &mol)
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKit::Descriptors::NonStrict
Definition: Lipinski.h:34
RDKit::Descriptors::calcNumBridgeheadAtoms
unsigned int calcNumBridgeheadAtoms(const ROMol &mol, std::vector< unsigned int > *atoms=NULL)
calculates the number of bridgehead atoms (atoms shared between rings that
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:102
RDKit::Descriptors::NumHeterocyclesVersion
const std::string NumHeterocyclesVersion
RDKit::Descriptors::calcNumAromaticRings
unsigned int calcNumAromaticRings(const ROMol &mol)
calculates the number of aromatic SSSR rings
RDKit::Descriptors::NumRotatableBondsOptions
NumRotatableBondsOptions
Definition: Lipinski.h:32
RDKit::Descriptors::calcLipinskiHBA
unsigned int calcLipinskiHBA(const ROMol &mol)
calculates the standard Lipinski HBA definition (number of Ns and Os)
RDKit::Descriptors::calcNumAliphaticCarbocycles
unsigned int calcNumAliphaticCarbocycles(const ROMol &mol)
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKit::Descriptors::calcNumHeterocycles
unsigned int calcNumHeterocycles(const ROMol &mol)
calculates the number of SSSR heterocycles
RDKit::Descriptors::NumRingsVersion
const std::string NumRingsVersion
RDKit::Descriptors::calcNumAmideBonds
unsigned int calcNumAmideBonds(const ROMol &mol)
calculates the number of amide bonds
RDKit::Descriptors::NumSpiroAtomsVersion
const std::string NumSpiroAtomsVersion
RDKit::Descriptors::calcNumRings
unsigned int calcNumRings(const ROMol &mol)
calculates the number of SSSR rings
RDKit::Descriptors::calcLipinskiHBD
unsigned int calcLipinskiHBD(const ROMol &mol)
calculates the standard Lipinski HBA definition (number of N-H and O-H
RDKit::Descriptors::NumSaturatedRingsVersion
const std::string NumSaturatedRingsVersion
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::Descriptors::calcNumHBA
unsigned int calcNumHBA(const ROMol &mol)
calculates the number of H-bond acceptors
RDKit::Descriptors::NumHBAVersion
const std::string NumHBAVersion
RDKit::Descriptors::calcFractionCSP3
double calcFractionCSP3(const ROMol &mol)
calculates the fraction of carbons that are SP3 hybridized
RDKit::Descriptors::NumAromaticHeterocyclesVersion
const std::string NumAromaticHeterocyclesVersion
RDKit::Descriptors::lipinskiHBDVersion
const std::string lipinskiHBDVersion
Definition: Lipinski.h:27
RDKit::Descriptors::calcNumSaturatedCarbocycles
unsigned int calcNumSaturatedCarbocycles(const ROMol &mol)
calculates the number of saturated SSSR carbocycles
RDKit::Descriptors::calcNumAliphaticHeterocycles
unsigned int calcNumAliphaticHeterocycles(const ROMol &mol)
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKit::Descriptors::NumBridgeheadAtomsVersion
const std::string NumBridgeheadAtomsVersion
RDKit::Descriptors::calcNumHeteroatoms
unsigned int calcNumHeteroatoms(const ROMol &mol)
calculates the number of heteroatoms
RDKit::Descriptors::lipinskiHBAVersion
const std::string lipinskiHBAVersion
Definition: Lipinski.h:23
RDKit::Descriptors::NumSaturatedCarbocyclesVersion
const std::string NumSaturatedCarbocyclesVersion
RDKit::Descriptors::calcNumRotatableBonds
unsigned int calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default)
calculates the number of rotatable bonds
RDKit::Descriptors::NumHBDVersion
const std::string NumHBDVersion
RDKit::Descriptors::calcNumAromaticCarbocycles
unsigned int calcNumAromaticCarbocycles(const ROMol &mol)
calculates the number of aromatic SSSR carbocycles
RDKit::Descriptors::NumHeteroatomsVersion
const std::string NumHeteroatomsVersion
RDKit::Descriptors::NumAromaticCarbocyclesVersion
const std::string NumAromaticCarbocyclesVersion