1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
|
//
// Copyright (C) 2012-2021 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
/*! \file ConnectivityDescriptors.h
\brief Use MolDescriptors.h in client code.
*/
#include <RDGeneral/export.h>
#ifndef __RD_CONNECTIVITYDESCRIPTORS_H__
#define __RD_CONNECTIVITYDESCRIPTORS_H__
#include <string>
#include <vector>
#include <boost/smart_ptr.hpp>
namespace RDKit {
class ROMol;
namespace Descriptors {
//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi0v(const ROMol &mol, bool force = false);
const std::string chi0vVersion = "1.2.0";
//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi1v(const ROMol &mol, bool force = false);
const std::string chi1vVersion = "1.2.0";
//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi2v(const ROMol &mol, bool force = false);
const std::string chi2vVersion = "1.2.0";
//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi3v(const ROMol &mol, bool force = false);
const std::string chi3vVersion = "1.2.0";
//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi4v(const ROMol &mol, bool force = false);
const std::string chi4vVersion = "1.2.0";
//! From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
/*!
\param mol the molecule of interest
\param n the order of the connectivity index
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChiNv(const ROMol &mol, unsigned int n,
bool force = false);
const std::string chiNvVersion = "1.2.0";
//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
//! This makes a big difference after we get out of the first row.
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi0n(const ROMol &mol, bool force = false);
const std::string chi0nVersion = "1.2.0";
//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
//! This makes a big difference after we get out of the first row.
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi1n(const ROMol &mol, bool force = false);
const std::string chi1nVersion = "1.2.0";
//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
//! This makes a big difference after we get out of the first row.
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi2n(const ROMol &mol, bool force = false);
const std::string chi2nVersion = "1.2.0";
//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
//! This makes a big difference after we get out of the first row.
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi3n(const ROMol &mol, bool force = false);
const std::string chi3nVersion = "1.2.0";
//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
//! This makes a big difference after we get out of the first row.
/*!
\param mol the molecule of interest
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChi4n(const ROMol &mol, bool force = false);
const std::string chi4nVersion = "1.2.0";
//! Similar to Hall Kier ChiXv, but uses nVal instead of valence
//! This makes a big difference after we get out of the first row.
/*!
\param mol the molecule of interest
\param n the order of the connectivity index
\param force forces the value to be recalculated instead
of pulled from the cache
*/
RDKIT_DESCRIPTORS_EXPORT double calcChiNn(const ROMol &mol, unsigned int n,
bool force = false);
const std::string chiNnVersion = "1.2.0";
//! calculate the Hall-Kier alpha value for a molecule
//! From equation (58) of Rev. Comp. Chem. vol 2, 367-422, (1991)
//!
//! \note Because hybridization is used to calculate this, results may differ
//! from other implementations which have different conventions for assigning
//! hybridization
/*!
\param mol the molecule of interest
\param atomContribs if provided, this will be used to return the
contributions
of the individual atoms to the value. These do not
necessarily sum to the full value.
Note: this can be a time-consuming calculation.
*/
RDKIT_DESCRIPTORS_EXPORT double calcHallKierAlpha(
const ROMol &mol, std::vector<double> *atomContribs = nullptr);
const std::string hallKierAlphaVersion = "1.2.0";
//! calculate the Hall-Kier kappa1 value for a molecule
//! From equations (58) and (59) of Rev. Comp. Chem. vol 2, 367-422, (1991)
//!
//! \note Because hybridization is used to calculate this, results may differ
//! from other implementations which have different conventions for assigning
//! hybridization
/*!
\param mol the molecule of interest
*/
RDKIT_DESCRIPTORS_EXPORT double calcKappa1(const ROMol &mol);
const std::string kappa1Version = "1.1.0";
//! calculate the Hall-Kier kappa2 value for a molecule
//! From equations (58) and (60) of Rev. Comp. Chem. vol 2, 367-422, (1991)
//!
//! \note Because hybridization is used to calculate this results may differ
//! from other implementations which have different conventions for assigning
//! hybridization
/*!
\param mol the molecule of interest
*/
RDKIT_DESCRIPTORS_EXPORT double calcKappa2(const ROMol &mol);
const std::string kappa2Version = "1.1.0";
//! calculate the Hall-Kier kappa3 value for a molecule
//! From equations (58), (61) and (62) of Rev. Comp. Chem. vol 2, 367-422,
/// 1991)
//!
//! \note Because hybridization is used to calculate this results may differ
//! from other implementations which have different conventions for assigning
//! hybridization
/*!
\param mol the molecule of interest
*/
RDKIT_DESCRIPTORS_EXPORT double calcKappa3(const ROMol &mol);
const std::string kappa3Version = "1.1.0";
//! calculate the Kier Phi value for a molecule
//! From Quantitative Structure-Activity Relationships 8, 221–224 (1989).
//!
//! \note Because hybridization is used to calculate this results may differ
//! from other implementations which have different conventions for assigning
//! hybridization
/*!
\param mol the molecule of interest
*/
RDKIT_DESCRIPTORS_EXPORT double calcPhi(const ROMol &mol);
const std::string PhiVersion = "1.0.0";
namespace detail {
RDKIT_DESCRIPTORS_EXPORT void hkDeltas(const ROMol &mol,
std::vector<double> &deltas, bool force);
}
} // end of namespace Descriptors
} // namespace RDKit
#endif
|
