RDKit
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Lipinski.h
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1 //
2 // Copyright (C) 2007-2011 Greg Landrum
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 
11 /*! \file Lipinski.h
12 
13  \brief Contains Lipinski and Lipinski-like descriptors. Use MolDescriptors.h
14  in client code.
15 
16 */
17 #include <RDGeneral/export.h>
18 #ifndef __RD_LIPINSKI_H__
19 #define __RD_LIPINSKI_H__
20 #include "RegisterDescriptor.h"
21 
22 namespace RDKit {
23 class ROMol;
24 namespace Descriptors {
25 
26 const std::string lipinskiHBAVersion = "1.0.0";
27 //! calculates the standard Lipinski HBA definition (number of Ns and Os)
28 RDKIT_DESCRIPTORS_EXPORT unsigned int calcLipinskiHBA(const ROMol &mol);
29 
30 const std::string lipinskiHBDVersion = "2.0.0";
31 //! calculates the standard Lipinski HBA definition (number of N-H and O-H
32 // bonds)
33 RDKIT_DESCRIPTORS_EXPORT unsigned int calcLipinskiHBD(const ROMol &mol);
34 
36  Default = -1,
37  NonStrict = 0,
38  Strict = 1,
40 };
41 
42 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumRotatableBondsVersion;
43 //! calculates the number of rotatable bonds
44 /*!
45  \param mol the molecule of interest
46  \param strict if Strict, a stricter definition of rotable bonds is used
47  this excludes amides, esters, etc.
48  if StrictLinkages, a much stricter definition that
49  handles rotatable bonds between rings as well.
50  if Default - uses the default choice (normally Strict)
51 */
53  const ROMol &mol, NumRotatableBondsOptions useStrictDefinition = Default);
54 
55 //! calculates the number of rotatable bonds ( backwards compatibility function,
56 //! deprecated, please use calcNumRotatableBonds(const ROMol&, int)
57 /*!
58  \param mol the molecule of interest
59  \param strict if Strict == true, uses NumRotatableBondsOptions::Strict
60 */
62  bool strict);
63 
64 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumHBDVersion;
65 //! calculates the number of H-bond donors
66 RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHBD(const ROMol &mol);
67 
68 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumHBAVersion;
69 //! calculates the number of H-bond acceptors
70 RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHBA(const ROMol &mol);
71 
72 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumHeteroatomsVersion;
73 //! calculates the number of heteroatoms
74 RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHeteroatoms(const ROMol &mol);
75 
76 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumAmideBondsVersion;
77 //! calculates the number of amide bonds
78 RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAmideBonds(const ROMol &mol);
79 
80 RDKIT_DESCRIPTORS_EXPORT extern const std::string FractionCSP3Version;
81 //! calculates the fraction of carbons that are SP3 hybridized
83 
84 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumRingsVersion;
85 //! calculates the number of SSSR rings
86 RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumRings(const ROMol &mol);
87 
88 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumAromaticRingsVersion;
89 //! calculates the number of aromatic SSSR rings
90 RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAromaticRings(const ROMol &mol);
91 
92 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumAliphaticRingsVersion;
93 //! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
94 // rings
96 
97 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumSaturatedRingsVersion;
98 //! calculates the number of saturated SSSR rings
100 
101 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumHeterocyclesVersion;
102 //! calculates the number of SSSR heterocycles
103 RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHeterocycles(const ROMol &mol);
104 
105 RDKIT_DESCRIPTORS_EXPORT extern const std::string
107 //! calculates the number of aromatic SSSR heterocycles
109  const ROMol &mol);
110 
112 //! calculates the number of aromatic SSSR carbocycles
114  const ROMol &mol);
115 
116 RDKIT_DESCRIPTORS_EXPORT extern const std::string
118 //! calculates the number of saturated SSSR heterocycles
120  const ROMol &mol);
121 
122 RDKIT_DESCRIPTORS_EXPORT extern const std::string
124 //! calculates the number of saturated SSSR carbocycles
126  const ROMol &mol);
127 
128 RDKIT_DESCRIPTORS_EXPORT extern const std::string
130 //! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
131 // heterocycles
133  const ROMol &mol);
134 
135 RDKIT_DESCRIPTORS_EXPORT extern const std::string
137 //! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
138 // carbocycles
140  const ROMol &mol);
141 
142 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumSpiroAtomsVersion;
143 //! calculates the number of spiro atoms (atoms shared between rings that share
144 // exactly one atom)
146  const ROMol &mol, std::vector<unsigned int> *atoms = NULL);
147 
148 RDKIT_DESCRIPTORS_EXPORT extern const std::string NumBridgeheadAtomsVersion;
149 //! calculates the number of bridgehead atoms (atoms shared between rings that
150 // share at least two bonds)
152  const ROMol &mol, std::vector<unsigned int> *atoms = NULL);
153 
155 //! calculates the total number of atom stereo centers
157 
158 //! calculates the number of unspecified stereo atom stereo centers
159 RDKIT_DESCRIPTORS_EXPORT extern const std::string
162  const ROMol &mol);
163 
164 //! Helper function to register the descriptors with the descriptor service
166 } // end of namespace Descriptors
167 } // end of namespace RDKit
168 
169 #endif
RDKit::Descriptors::calcLipinskiHBD
RDKIT_DESCRIPTORS_EXPORT unsigned int calcLipinskiHBD(const ROMol &mol)
calculates the standard Lipinski HBA definition (number of N-H and O-H
RDKit::Descriptors::NumAliphaticCarbocyclesVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAliphaticCarbocyclesVersion
RDKit::Descriptors::calcNumBridgeheadAtoms
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
RDKit::Descriptors::NumAliphaticHeterocyclesVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAliphaticHeterocyclesVersion
RDKit::Descriptors::numAtomStereoCenters
RDKIT_DESCRIPTORS_EXPORT unsigned numAtomStereoCenters(const ROMol &mol)
calculates the total number of atom stereo centers
RDKit::Descriptors::NumHeteroatomsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumHeteroatomsVersion
RDKit::Descriptors::calcNumSpiroAtoms
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
RDKit::Descriptors::NumHBAVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumHBAVersion
RDKit::Descriptors::NumSaturatedCarbocyclesVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumSaturatedCarbocyclesVersion
RDKit::Descriptors::calcNumHBA
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHBA(const ROMol &mol)
calculates the number of H-bond acceptors
RDKIT_DESCRIPTORS_EXPORT
#define RDKIT_DESCRIPTORS_EXPORT
Definition: export.h:138
RDKit::Descriptors::NumBridgeheadAtomsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumBridgeheadAtomsVersion
RDKit::Descriptors::NumSaturatedRingsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumSaturatedRingsVersion
RDKit::Descriptors::calcNumAliphaticRings
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAliphaticRings(const ROMol &mol)
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKit::Descriptors::NumAliphaticRingsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAliphaticRingsVersion
RDKit::Descriptors::calcNumAmideBonds
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAmideBonds(const ROMol &mol)
calculates the number of amide bonds
RDKit::Descriptors::calcNumHeteroatoms
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHeteroatoms(const ROMol &mol)
calculates the number of heteroatoms
RDKit::Descriptors::NumAromaticCarbocyclesVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAromaticCarbocyclesVersion
RDKit::Descriptors::numUnspecifiedAtomStereoCenters
RDKIT_DESCRIPTORS_EXPORT unsigned numUnspecifiedAtomStereoCenters(const ROMol &mol)
RDKit::Descriptors::NumHBDVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumHBDVersion
RDKit::Descriptors::calcLipinskiHBA
RDKIT_DESCRIPTORS_EXPORT unsigned int calcLipinskiHBA(const ROMol &mol)
calculates the standard Lipinski HBA definition (number of Ns and Os)
RDKit::Descriptors::calcNumAromaticCarbocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAromaticCarbocycles(const ROMol &mol)
calculates the number of aromatic SSSR carbocycles
RDKit::Descriptors::NumAromaticRingsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAromaticRingsVersion
RDKit::ROMol
Definition: ROMol.h:171
RDKit::Descriptors::calcNumAromaticRings
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAromaticRings(const ROMol &mol)
calculates the number of aromatic SSSR rings
RDKit::Descriptors::NumRotatableBondsOptions
NumRotatableBondsOptions
Definition: Lipinski.h:35
RDKit::Descriptors::NumRotatableBondsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumRotatableBondsVersion
RDKit::Descriptors::NumUnspecifiedAtomStereoCentersVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumUnspecifiedAtomStereoCentersVersion
calculates the number of unspecified stereo atom stereo centers
RDKit::Descriptors::registerDescriptors
RDKIT_DESCRIPTORS_EXPORT void registerDescriptors()
Helper function to register the descriptors with the descriptor service.
RDKit::Descriptors::NumAtomStereoCentersVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAtomStereoCentersVersion
RDKit::Descriptors::calcNumRotatableBonds
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default)
calculates the number of rotatable bonds
RDKit::Descriptors::NumRingsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumRingsVersion
RDKit::Descriptors::calcFractionCSP3
RDKIT_DESCRIPTORS_EXPORT double calcFractionCSP3(const ROMol &mol)
calculates the fraction of carbons that are SP3 hybridized
RDKit::Descriptors::calcNumAliphaticHeterocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAliphaticHeterocycles(const ROMol &mol)
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RegisterDescriptor.h
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::Descriptors::calcNumHBD
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHBD(const ROMol &mol)
calculates the number of H-bond donors
RDKit::Descriptors::NumAmideBondsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAmideBondsVersion
RDKit::Descriptors::StrictLinkages
@ StrictLinkages
Definition: Lipinski.h:39
RDKit::Descriptors::calcNumSaturatedCarbocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumSaturatedCarbocycles(const ROMol &mol)
calculates the number of saturated SSSR carbocycles
RDKit::Descriptors::NumSaturatedHeterocyclesVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumSaturatedHeterocyclesVersion
RDKit::Descriptors::NumAromaticHeterocyclesVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumAromaticHeterocyclesVersion
RDKit::Descriptors::NumSpiroAtomsVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumSpiroAtomsVersion
RDKit::Descriptors::calcNumSaturatedRings
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumSaturatedRings(const ROMol &mol)
calculates the number of saturated SSSR rings
RDKit::Descriptors::calcNumAliphaticCarbocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAliphaticCarbocycles(const ROMol &mol)
calculates the number of aliphatic (at least one non-aromatic bond) SSSR
RDKit::Descriptors::lipinskiHBAVersion
const std::string lipinskiHBAVersion
Definition: Lipinski.h:26
RDKit::Descriptors::FractionCSP3Version
const RDKIT_DESCRIPTORS_EXPORT std::string FractionCSP3Version
RDKit::Descriptors::calcNumRings
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumRings(const ROMol &mol)
calculates the number of SSSR rings
RDKit::Descriptors::NonStrict
@ NonStrict
Definition: Lipinski.h:37
RDKit::Descriptors::calcNumAromaticHeterocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumAromaticHeterocycles(const ROMol &mol)
calculates the number of aromatic SSSR heterocycles
RDKit::Descriptors::NumHeterocyclesVersion
const RDKIT_DESCRIPTORS_EXPORT std::string NumHeterocyclesVersion
RDKit::Descriptors::calcNumHeterocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumHeterocycles(const ROMol &mol)
calculates the number of SSSR heterocycles
RDKit::Descriptors::Default
@ Default
Definition: Lipinski.h:36
RDKit::Descriptors::calcNumSaturatedHeterocycles
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumSaturatedHeterocycles(const ROMol &mol)
calculates the number of saturated SSSR heterocycles
RDKit::Descriptors::Strict
@ Strict
Definition: Lipinski.h:38
export.h
RDKit::Descriptors::lipinskiHBDVersion
const std::string lipinskiHBDVersion
Definition: Lipinski.h:30