RDKit
Open-source cheminformatics and machine learning.
MolSurf.h
Go to the documentation of this file.
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 MolSurf.h
12 
13  \brief Use MolDescriptors.h in client code.
14 
15 */
16 #include <RDGeneral/export.h>
17 #ifndef __RD_MOLSURF_H__
18 #define __RD_MOLSURF_H__
19 
20 #include <vector>
21 
22 namespace RDKit {
23 class ROMol;
24 namespace Descriptors {
25 const std::string labuteASAVersion = "1.0.2";
26 
27 //! calculates atomic contributions to Labute's Approximate Surface Area
28 /*!
29  Definition from P. Labute's article in the Journal of the
30  Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477
31  (2000)
32 
33  \param mol the molecule of interest
34  \param Vi used to return the explict atom contribs
35  \param hContrib used to return the H contributions (if calculated)
36  \param includeHs (optional) if this is true (the default),
37  the contribution of H atoms to the ASA will be included.
38  \param force (optional) calculate the values even if they are cached.
39 
40  \return the sum of the atomic contributions
41 
42 */
44  std::vector<double> &Vi,
45  double &hContrib,
46  bool includeHs = true,
47  bool force = false);
48 
49 //! calculates Labute's Approximate Surface Area (ASA from MOE)
50 /*!
51  Definition from P. Labute's article in the Journal of the
52  Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477
53  (2000)
54 
55  \param mol the molecule of interest
56  \param includeHs (optional) if this is true (the default),
57  the contribution of H atoms to the ASA will be included.
58  \param force (optional) calculate the value even if it's cached.
59 
60 */
62  bool includeHs = true,
63  bool force = false);
64 
65 const std::string tpsaVersion = "2.0.0";
66 //! calculates atomic contributions to the TPSA value
67 /*!
68  The TPSA definition is from:
69  P. Ertl, B. Rohde, P. Selzer
70  Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based
71  Contributions and Its Application to the Prediction of Drug Transport
72  Properties, J.Med.Chem. 43, 3714-3717, 2000
73  By default the calculation does not include contributions from S or P atoms,
74  this can be be changed with the includeSandP argument.
75 
76  \param mol the molecule of interest
77  \param Vi used to return the atom contribs
78  \param force (optional) calculate the values even if they are cached.
79  \param includeSandP (optional) include contributions from S and P atoms
80 
81  \return the sum of the atomic contributions
82 
83 */
85  std::vector<double> &Vi,
86  bool force = false,
87  bool includeSandP = false);
88 
89 //! calculates the TPSA value for a molecule
90 /*!
91  The TPSA definition is from:
92  P. Ertl, B. Rohde, P. Selzer
93  Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based
94  Contributions and Its Application to the Prediction of Drug Transport
95  Properties, J.Med.Chem. 43, 3714-3717, 2000
96  By default the calculation does not include contributions from S or P atoms,
97  this can be be changed with the includeSandP argument.
98 
99  \param mol the molecule of interest
100  \param force (optional) calculate the value even if it's cached.
101  \param includeSandP (optional) include contributions from S and P atoms
102 
103 */
104 RDKIT_DESCRIPTORS_EXPORT double calcTPSA(const ROMol &mol, bool force = false,
105  bool includeSandP = false);
106 
107 RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcSlogP_VSA(
108  const ROMol &mol, std::vector<double> *bins = 0, bool force = false);
109 RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcSMR_VSA(
110  const ROMol &mol, std::vector<double> *bins = 0, bool force = false);
111 RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcPEOE_VSA(
112  const ROMol &mol, std::vector<double> *bins = 0, bool force = false);
113 RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcCustomProp_VSA(
114  const ROMol &mol, const std::string &customPropName,
115  const std::vector<double> &bins, bool force = false);
116 
117 } // end of namespace Descriptors
118 } // end of namespace RDKit
119 
120 #endif
RDKit::Descriptors::calcTPSA
RDKIT_DESCRIPTORS_EXPORT double calcTPSA(const ROMol &mol, bool force=false, bool includeSandP=false)
calculates the TPSA value for a molecule
RDKit::Descriptors::getLabuteAtomContribs
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
RDKIT_DESCRIPTORS_EXPORT
#define RDKIT_DESCRIPTORS_EXPORT
Definition: export.h:138
RDKit::Descriptors::calcLabuteASA
RDKIT_DESCRIPTORS_EXPORT double calcLabuteASA(const ROMol &mol, bool includeHs=true, bool force=false)
calculates Labute's Approximate Surface Area (ASA from MOE)
RDKit::Descriptors::calcCustomProp_VSA
RDKIT_DESCRIPTORS_EXPORT std::vector< double > calcCustomProp_VSA(const ROMol &mol, const std::string &customPropName, const std::vector< double > &bins, bool force=false)
RDKit::ROMol
Definition: ROMol.h:171
RDKit::Descriptors::calcPEOE_VSA
RDKIT_DESCRIPTORS_EXPORT std::vector< double > calcPEOE_VSA(const ROMol &mol, std::vector< double > *bins=0, bool force=false)
RDKit::Descriptors::labuteASAVersion
const std::string labuteASAVersion
Definition: MolSurf.h:25
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::Descriptors::calcSMR_VSA
RDKIT_DESCRIPTORS_EXPORT std::vector< double > calcSMR_VSA(const ROMol &mol, std::vector< double > *bins=0, bool force=false)
RDKit::Descriptors::calcSlogP_VSA
RDKIT_DESCRIPTORS_EXPORT std::vector< double > calcSlogP_VSA(const ROMol &mol, std::vector< double > *bins=0, bool force=false)
RDKit::Descriptors::getTPSAAtomContribs
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
RDKit::Descriptors::tpsaVersion
const std::string tpsaVersion
Definition: MolSurf.h:65
export.h