RDKit: ConnectivityDescriptors.h Source File

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ConnectivityDescriptors.h
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1 //
2 // Copyright (C) 2012 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 ConnectivityDescriptors.h
12
13 \brief Use MolDescriptors.h in client code.
14
15 */
16 #ifndef __RD_CONNECTIVITYDESCRIPTORS_H__
17 #define __RD_CONNECTIVITYDESCRIPTORS_H__
18
19 #include <string>
20 #include <vector>
21 #include <boost/smart_ptr.hpp>
22
23 namespace RDKit {
24 class ROMol;
25 namespace Descriptors {
26
27 //! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
28 /*!
29 \param mol the molecule of interest
30 \param force forces the value to be recalculated instead
31 of pulled from the cache
32 */
33 double calcChi0v(const ROMol &mol, bool force = false);
34 const std::string chi0vVersion = "1.2.0";
35 //! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
36 /*!
37 \param mol the molecule of interest
38 \param force forces the value to be recalculated instead
39 of pulled from the cache
40 */
41 double calcChi1v(const ROMol &mol, bool force = false);
42 const std::string chi1vVersion = "1.2.0";
43 //! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
44 /*!
45 \param mol the molecule of interest
46 \param force forces the value to be recalculated instead
47 of pulled from the cache
48 */
49 double calcChi2v(const ROMol &mol, bool force = false);
50 const std::string chi2vVersion = "1.2.0";
51 //! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
52 /*!
53 \param mol the molecule of interest
54 \param force forces the value to be recalculated instead
55 of pulled from the cache
56 */
57 double calcChi3v(const ROMol &mol, bool force = false);
58 const std::string chi3vVersion = "1.2.0";
59 //! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
60 /*!
61 \param mol the molecule of interest
62 \param force forces the value to be recalculated instead
63 of pulled from the cache
64 */
65 double calcChi4v(const ROMol &mol, bool force = false);
66 const std::string chi4vVersion = "1.2.0";
67 //! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
68 /*!
69 \param mol the molecule of interest
70 \param n the order of the connectivity index
71 \param force forces the value to be recalculated instead
72 of pulled from the cache
73 */
74 double calcChiNv(const ROMol &mol, unsigned int n, bool force = false);
75 const std::string chiNvVersion = "1.2.0";
76
77 //! Similar to Hall Kier ChiXv, but uses nVal instead of valence
78 //! This makes a big difference after we get out of the first row.
79 /*!
80 \param mol the molecule of interest
81 \param force forces the value to be recalculated instead
82 of pulled from the cache
83 */
84 double calcChi0n(const ROMol &mol, bool force = false);
85 const std::string chi0nVersion = "1.2.0";
86 //! Similar to Hall Kier ChiXv, but uses nVal instead of valence
87 //! This makes a big difference after we get out of the first row.
88 /*!
89 \param mol the molecule of interest
90 \param force forces the value to be recalculated instead
91 of pulled from the cache
92 */
93 double calcChi1n(const ROMol &mol, bool force = false);
94 const std::string chi1nVersion = "1.2.0";
95 //! Similar to Hall Kier ChiXv, but uses nVal instead of valence
96 //! This makes a big difference after we get out of the first row.
97 /*!
98 \param mol the molecule of interest
99 \param force forces the value to be recalculated instead
100 of pulled from the cache
101 */
102 double calcChi2n(const ROMol &mol, bool force = false);
103 const std::string chi2nVersion = "1.2.0";
104 //! Similar to Hall Kier ChiXv, but uses nVal instead of valence
105 //! This makes a big difference after we get out of the first row.
106 /*!
107 \param mol the molecule of interest
108 \param force forces the value to be recalculated instead
109 of pulled from the cache
110 */
111 double calcChi3n(const ROMol &mol, bool force = false);
112 const std::string chi3nVersion = "1.2.0";
113 //! Similar to Hall Kier ChiXv, but uses nVal instead of valence
114 //! This makes a big difference after we get out of the first row.
115 /*!
116 \param mol the molecule of interest
117 \param force forces the value to be recalculated instead
118 of pulled from the cache
119 */
120 double calcChi4n(const ROMol &mol, bool force = false);
121 const std::string chi4nVersion = "1.2.0";
122 //! Similar to Hall Kier ChiXv, but uses nVal instead of valence
123 //! This makes a big difference after we get out of the first row.
124 /*!
125 \param mol the molecule of interest
126 \param n the order of the connectivity index
127 \param force forces the value to be recalculated instead
128 of pulled from the cache
129 */
130 double calcChiNn(const ROMol &mol, unsigned int n, bool force = false);
131 const std::string chiNnVersion = "1.2.0";
132
133 //! calculate the Hall-Kier alpha value for a molecule
134 //! From equation (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)
135 /*!
136 \param mol the molecule of interest
137 \param atomContribs if provided, this will be used to return the
138 contributions
139 of the individual atoms to the value. These do not
140 neccessarily sum to the full value.
141 Note: this can be a time-consuming calculation.
142 */
143 double calcHallKierAlpha(const ROMol &mol,
144 std::vector<double> *atomContribs = 0);
145 const std::string hallKierAlphaVersion = "1.2.0";
146
147 //! calculate the Hall-Kier kappa1 value for a molecule
148 //! From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367-422, (1991)
149 /*!
150 \param mol the molecule of interest
151 */
152 double calcKappa1(const ROMol &mol);
153 const std::string kappa1Version = "1.1.0";
154
155 //! calculate the Hall-Kier kappa2 value for a molecule
156 //! From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367-422, (1991)
157 /*!
158 \param mol the molecule of interest
159 */
160 double calcKappa2(const ROMol &mol);
161 const std::string kappa2Version = "1.1.0";
162
163 //! calculate the Hall-Kier kappa3 value for a molecule
164 //! From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367-422,
165 //(1991)
166 /*!
167 \param mol the molecule of interest
168 */
169 double calcKappa3(const ROMol &mol);
170 const std::string kappa3Version = "1.1.0";
171
172 namespace detail {
173 void hkDeltas(const ROMol &mol, std::vector<double> &deltas, bool force);
174 }
175
176 } // end of namespace Descriptors
177 }
178
179 #endif
RDKit::Descriptors::calcChi2v
double calcChi2v(const ROMol &mol, bool force=false)
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
RDKit::Descriptors::calcKappa2
double calcKappa2(const ROMol &mol)
RDKit::Descriptors::chi4vVersion
const std::string chi4vVersion
Definition: ConnectivityDescriptors.h:66
RDKit::Descriptors::chiNvVersion
const std::string chiNvVersion
Definition: ConnectivityDescriptors.h:75
RDKit::Descriptors::chi2nVersion
const std::string chi2nVersion
Definition: ConnectivityDescriptors.h:103
RDKit::Descriptors::calcKappa1
double calcKappa1(const ROMol &mol)
RDKit::Descriptors::chi1nVersion
const std::string chi1nVersion
Definition: ConnectivityDescriptors.h:94
RDKit::Descriptors::calcChi4v
double calcChi4v(const ROMol &mol, bool force=false)
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
RDKit::Descriptors::kappa1Version
const std::string kappa1Version
Definition: ConnectivityDescriptors.h:153
RDKit::Descriptors::calcChi3n
double calcChi3n(const ROMol &mol, bool force=false)
RDKit::Descriptors::chiNnVersion
const std::string chiNnVersion
Definition: ConnectivityDescriptors.h:131
RDKit::Descriptors::kappa2Version
const std::string kappa2Version
Definition: ConnectivityDescriptors.h:161
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:102
RDKit::Descriptors::calcHallKierAlpha
double calcHallKierAlpha(const ROMol &mol, std::vector< double > *atomContribs=0)
RDKit::Descriptors::calcChi1v
double calcChi1v(const ROMol &mol, bool force=false)
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
RDKit::Descriptors::calcChi3v
double calcChi3v(const ROMol &mol, bool force=false)
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
detail
Definition: types.h:23
RDKit::Descriptors::chi3nVersion
const std::string chi3nVersion
Definition: ConnectivityDescriptors.h:112
RDKit::Descriptors::chi1vVersion
const std::string chi1vVersion
Definition: ConnectivityDescriptors.h:42
RDKit::Descriptors::hallKierAlphaVersion
const std::string hallKierAlphaVersion
Definition: ConnectivityDescriptors.h:145
RDKit::Descriptors::calcChi0n
double calcChi0n(const ROMol &mol, bool force=false)
RDKit::Descriptors::chi3vVersion
const std::string chi3vVersion
Definition: ConnectivityDescriptors.h:58
RDKit::Descriptors::kappa3Version
const std::string kappa3Version
Definition: ConnectivityDescriptors.h:170
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::Descriptors::calcChi4n
double calcChi4n(const ROMol &mol, bool force=false)
RDKit::Descriptors::calcChi0v
double calcChi0v(const ROMol &mol, bool force=false)
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
RDKit::Descriptors::chi2vVersion
const std::string chi2vVersion
Definition: ConnectivityDescriptors.h:50
RDKit::Descriptors::detail::hkDeltas
void hkDeltas(const ROMol &mol, std::vector< double > &deltas, bool force)
RDKit::Descriptors::calcKappa3
double calcKappa3(const ROMol &mol)
RDKit::Descriptors::calcChiNn
double calcChiNn(const ROMol &mol, unsigned int n, bool force=false)
RDKit::Descriptors::chi0nVersion
const std::string chi0nVersion
Definition: ConnectivityDescriptors.h:85
RDKit::Descriptors::chi4nVersion
const std::string chi4nVersion
Definition: ConnectivityDescriptors.h:121
RDKit::Descriptors::calcChiNv
double calcChiNv(const ROMol &mol, unsigned int n, bool force=false)
From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
RDKit::Descriptors::chi0vVersion
const std::string chi0vVersion
Definition: ConnectivityDescriptors.h:34
RDKit::Descriptors::calcChi2n
double calcChi2n(const ROMol &mol, bool force=false)
RDKit::Descriptors::calcChi1n
double calcChi1n(const ROMol &mol, bool force=false)