RDKit: MolSurf.h Source File

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MolSurf.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 MolSurf.h
12
13 \brief Use MolDescriptors.h in client code.
14
15 */
16 #ifndef __RD_MOLSURF_H__
17 #define __RD_MOLSURF_H__
18
19 #include <vector>
20
21 namespace RDKit {
22 class ROMol;
23 namespace Descriptors {
24 const std::string labuteASAVersion = "1.0.2";
25
26 //! calculates atomic contributions to Labute's Approximate Surface Area
27 /*!
28 Definition from P. Labute's article in the Journal of the
29 Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477
30 (2000)
31
32 \param mol the molecule of interest
33 \param Vi used to return the explict atom contribs
34 \param hContrib used to return the H contributions (if calculated)
35 \param includeHs (optional) if this is true (the default),
36 the contribution of H atoms to the ASA will be included.
37 \param force (optional) calculate the values even if they are cached.
38
39 \return the sum of the atomic contributions
40
41 */
42 double getLabuteAtomContribs(const ROMol &mol, std::vector<double> &Vi,
43 double &hContrib, bool includeHs = true,
44 bool force = false);
45
46 //! calculates Labute's Approximate Surface Area (ASA from MOE)
47 /*!
48 Definition from P. Labute's article in the Journal of the
49 Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477
50 (2000)
51
52 \param mol the molecule of interest
53 \param includeHs (optional) if this is true (the default),
54 the contribution of H atoms to the ASA will be included.
55 \param force (optional) calculate the value even if it's cached.
56
57 */
58 double calcLabuteASA(const ROMol &mol, bool includeHs = true,
59 bool force = false);
60
61 const std::string tpsaVersion = "1.1.0";
62 //! calculates atomic contributions to the TPSA value
63 /*!
64 The TPSA definition is from:
65 P. Ertl, B. Rohde, P. Selzer
66 Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based
67 Contributions and Its Application to the Prediction of Drug Transport
68 Properties, J.Med.Chem. 43, 3714-3717, 2000
69
70 \param mol the molecule of interest
71 \param Vi used to return the atom contribs
72 \param force (optional) calculate the values even if they are cached.
73
74 \return the sum of the atomic contributions
75
76 */
77 double getTPSAAtomContribs(const ROMol &mol, std::vector<double> &Vi,
78 bool force = false);
79
80 //! calculates the TPSA value for a molecule
81 /*!
82 The TPSA definition is from:
83 P. Ertl, B. Rohde, P. Selzer
84 Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based
85 Contributions and Its Application to the Prediction of Drug Transport
86 Properties, J.Med.Chem. 43, 3714-3717, 2000
87
88 \param mol the molecule of interest
89 \param force (optional) calculate the value even if it's cached.
90
91 */
92 double calcTPSA(const ROMol &mol, bool force = false);
93
94 std::vector<double> calcSlogP_VSA(const ROMol &mol,
95 std::vector<double> *bins = 0,
96 bool force = false);
97 std::vector<double> calcSMR_VSA(const ROMol &mol, std::vector<double> *bins = 0,
98 bool force = false);
99 std::vector<double> calcPEOE_VSA(const ROMol &mol,
100 std::vector<double> *bins = 0,
101 bool force = false);
102
103 } // end of namespace Descriptors
104 } // end of namespace RDKit
105
106 #endif
RDKit::Descriptors::getTPSAAtomContribs
double getTPSAAtomContribs(const ROMol &mol, std::vector< double > &Vi, bool force=false)
calculates atomic contributions to the TPSA value
RDKit::Descriptors::calcPEOE_VSA
std::vector< double > calcPEOE_VSA(const ROMol &mol, std::vector< double > *bins=0, bool force=false)
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:102
RDKit::Descriptors::calcTPSA
double calcTPSA(const ROMol &mol, bool force=false)
calculates the TPSA value for a molecule
RDKit::Descriptors::calcSMR_VSA
std::vector< double > calcSMR_VSA(const ROMol &mol, std::vector< double > *bins=0, bool force=false)
RDKit::Descriptors::labuteASAVersion
const std::string labuteASAVersion
Definition: MolSurf.h:24
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::Descriptors::getLabuteAtomContribs
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::calcSlogP_VSA
std::vector< double > calcSlogP_VSA(const ROMol &mol, std::vector< double > *bins=0, bool force=false)
RDKit::Descriptors::calcLabuteASA
double calcLabuteASA(const ROMol &mol, bool includeHs=true, bool force=false)
calculates Labute's Approximate Surface Area (ASA from MOE)
RDKit::Descriptors::tpsaVersion
const std::string tpsaVersion
Definition: MolSurf.h:61