RDKit: Lipinski.h Source File

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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 #ifndef __RD_LIPINSKI_H__
18 #define __RD_LIPINSKI_H__
19 #include "RegisterDescriptor.h"
20
21 namespace RDKit {
22 class ROMol;
23 namespace Descriptors {
24
25 const std::string lipinskiHBAVersion = "1.0.0";
26 //! calculates the standard Lipinski HBA definition (number of Ns and Os)
27 unsigned int calcLipinskiHBA(const ROMol &mol);
28
29 const std::string lipinskiHBDVersion = "2.0.0";
30 //! calculates the standard Lipinski HBA definition (number of N-H and O-H
31 // bonds)
32 unsigned int calcLipinskiHBD(const ROMol &mol);
33
34 enum NumRotatableBondsOptions {
35 Default = -1,
36 NonStrict = 0,
37 Strict = 1,
38 StrictLinkages = 2,
39 };
40
41 extern const std::string NumRotatableBondsVersion;
42 //! calculates the number of rotatable bonds
43 /*!
44 \param mol the molecule of interest
45 \param strict if Strict, a stricter definition of rotable bonds is used
46 this excludes amides, esters, etc.
47 if StrictLinkages, a much stricter definition that
48 handles rotatable bonds between rings as well.
49 if Default - uses the default choice (normally Strict)
50 */
51 unsigned int calcNumRotatableBonds(const ROMol &mol,
52 NumRotatableBondsOptions useStrictDefinition=Default);
53
54 //! calculates the number of rotatable bonds ( backwards compatibility function,
55 //! deprecated, please use calcNumRotatableBonds(const ROMol&, int)
56 /*!
57 \param mol the molecule of interest
58 \param strict if Strict == true, uses NumRotatableBondsOptions::Strict
59 */
60 unsigned int calcNumRotatableBonds(const ROMol &mol, bool strict);
61
62 extern const std::string NumHBDVersion;
63 //! calculates the number of H-bond donors
64 unsigned int calcNumHBD(const ROMol &mol);
65
66 extern const std::string NumHBAVersion;
67 //! calculates the number of H-bond acceptors
68 unsigned int calcNumHBA(const ROMol &mol);
69
70 extern const std::string NumHeteroatomsVersion;
71 //! calculates the number of heteroatoms
72 unsigned int calcNumHeteroatoms(const ROMol &mol);
73
74 extern const std::string NumAmideBondsVersion;
75 //! calculates the number of amide bonds
76 unsigned int calcNumAmideBonds(const ROMol &mol);
77
78 extern const std::string FractionCSP3Version;
79 //! calculates the fraction of carbons that are SP3 hybridized
80 double calcFractionCSP3(const ROMol &mol);
81
82 extern const std::string NumRingsVersion;
83 //! calculates the number of SSSR rings
84 unsigned int calcNumRings(const ROMol &mol);
85
86 extern const std::string NumAromaticRingsVersion;
87 //! calculates the number of aromatic SSSR rings
88 unsigned int calcNumAromaticRings(const ROMol &mol);
89
90 extern const std::string NumAliphaticRingsVersion;
91 //! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
92 // rings
93 unsigned int calcNumAliphaticRings(const ROMol &mol);
94
95 extern const std::string NumSaturatedRingsVersion;
96 //! calculates the number of saturated SSSR rings
97 unsigned int calcNumSaturatedRings(const ROMol &mol);
98
99 extern const std::string NumHeterocyclesVersion;
100 //! calculates the number of SSSR heterocycles
101 unsigned int calcNumHeterocycles(const ROMol &mol);
102
103 extern const std::string NumAromaticHeterocyclesVersion;
104 //! calculates the number of aromatic SSSR heterocycles
105 unsigned int calcNumAromaticHeterocycles(const ROMol &mol);
106
107 extern const std::string NumAromaticCarbocyclesVersion;
108 //! calculates the number of aromatic SSSR carbocycles
109 unsigned int calcNumAromaticCarbocycles(const ROMol &mol);
110
111 extern const std::string NumSaturatedHeterocyclesVersion;
112 //! calculates the number of saturated SSSR heterocycles
113 unsigned int calcNumSaturatedHeterocycles(const ROMol &mol);
114
115 extern const std::string NumSaturatedCarbocyclesVersion;
116 //! calculates the number of saturated SSSR carbocycles
117 unsigned int calcNumSaturatedCarbocycles(const ROMol &mol);
118
119 extern const std::string NumAliphaticHeterocyclesVersion;
120 //! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
121 // heterocycles
122 unsigned int calcNumAliphaticHeterocycles(const ROMol &mol);
123
124 extern const std::string NumAliphaticCarbocyclesVersion;
125 //! calculates the number of aliphatic (at least one non-aromatic bond) SSSR
126 // carbocycles
127 unsigned int calcNumAliphaticCarbocycles(const ROMol &mol);
128
129 extern const std::string NumSpiroAtomsVersion;
130 //! calculates the number of spiro atoms (atoms shared between rings that share
131 // exactly one atom)
132 unsigned int calcNumSpiroAtoms(const ROMol &mol,
133 std::vector<unsigned int> *atoms = NULL);
134
135 extern const std::string NumBridgeheadAtomsVersion;
136 //! calculates the number of bridgehead atoms (atoms shared between rings that
137 // share at least two bonds)
138 unsigned int calcNumBridgeheadAtoms(const ROMol &mol,
139 std::vector<unsigned int> *atoms = NULL);
140
141 extern const std::string NumAtomStereoCentersVersion;
142 //! calculates the total number of atom stereo centers
143 unsigned numAtomStereoCenters(const ROMol &mol);
144
145 //! calculates the number of unspecified stereo atom stereo centers
146 extern const std::string NumUnspecifiedAtomStereoCentersVersion;
147 unsigned numUnspecifiedAtomStereoCenters(const ROMol &mol);
148
149 //! Helper function to register the descriptors with the descriptor service
150 void registerDescriptors();
151 } // end of namespace Descriptors
152 } // end of namespace RDKit
153
154 #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:35
RDKit::Descriptors::NumAtomStereoCentersVersion
const std::string NumAtomStereoCentersVersion
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:37
RDKit::Descriptors::NumAliphaticHeterocyclesVersion
const std::string NumAliphaticHeterocyclesVersion
RDKit::Descriptors::StrictLinkages
Definition: Lipinski.h:38
RDKit::Descriptors::NumSaturatedHeterocyclesVersion
const std::string NumSaturatedHeterocyclesVersion
RDKit::Descriptors::registerDescriptors
void registerDescriptors()
Helper function to register the descriptors with the descriptor service.
RDKit::Descriptors::NumUnspecifiedAtomStereoCentersVersion
const std::string NumUnspecifiedAtomStereoCentersVersion
calculates the number of unspecified stereo atom stereo centers
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:36
RDKit::Descriptors::numUnspecifiedAtomStereoCenters
unsigned numUnspecifiedAtomStereoCenters(const ROMol &mol)
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:103
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:34
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
Std stuff.
Definition: Atom.h:29
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::numAtomStereoCenters
unsigned numAtomStereoCenters(const ROMol &mol)
calculates the total number of atom stereo centers
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:29
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
RegisterDescriptor.h
RDKit::Descriptors::lipinskiHBAVersion
const std::string lipinskiHBAVersion
Definition: Lipinski.h:25
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