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
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
|
//
// Copyright (C) 2007-2013 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 AtomPairs.h
A few quick notes about fingerprint size and the way chirality is handled in
these functions.
By default the atom-pair and topologic-torsion fingerprints do not include any
information about
chirality; the atom invariants only include information about the atomic
number,
number of pi electrons, and degree.
When chirality is included, two additional bits are added to the atom
invariants to flag R/S/no
chirality. These additional bits change the size of the atom invariants and
either the size
of the final fingerprint (atom pairs) or the maximum allowed path length
(torsions). This means
that even fingerprints for achiral molecules are different when
includeChirality is true.
*/
#include <RDGeneral/export.h>
#ifndef __RD_ATOMPAIRS_H__
#define __RD_ATOMPAIRS_H__
#include <DataStructs/SparseIntVect.h>
#include <DataStructs/BitVects.h>
#include <boost/cstdint.hpp>
#include <GraphMol/Fingerprints/FingerprintUtil.h>
namespace RDKit {
class Atom;
namespace AtomPairs {
const std::string atomPairsVersion = "1.1.0";
//! returns the atom-pair fingerprint for a molecule
/*!
The algorithm used is described here:
R.E. Carhart, D.H. Smith, R. Venkataraghavan; "Atom Pairs as
Molecular Features in Structure-Activity Studies: Definition
and Applications" JCICS 25, 64-73 (1985).
\param mol: the molecule to be fingerprinted
\param minLength: minimum distance between atoms to be
considered in a pair. Default is 1 bond.
\param maxLength: maximum distance between atoms to be
considered in a pair.
Default is maxPathLen-1 bonds.
\param fromAtoms: if provided, only atom pairs that involve
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any atom pairs that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param includeChirality: if set, chirality will be used in the atom invariants
(note: this is ignored if atomInvariants are
provided)
\param use2D: if set, the 2D (topological) distance matrix is used.
\param confId: the conformation to use if 3D distances are being used
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int32_t> *getAtomPairFingerprint(
const ROMol &mol, unsigned int minLength, unsigned int maxLength,
const std::vector<boost::uint32_t> *fromAtoms = 0,
const std::vector<boost::uint32_t> *ignoreAtoms = 0,
const std::vector<boost::uint32_t> *atomInvariants = 0,
bool includeChirality = false, bool use2D = true, int confId = -1);
//! \overload
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int32_t> *getAtomPairFingerprint(
const ROMol &mol, const std::vector<boost::uint32_t> *fromAtoms = 0,
const std::vector<boost::uint32_t> *ignoreAtoms = 0,
const std::vector<boost::uint32_t> *atomInvariants = 0,
bool includeChirality = false, bool use2D = true, int confId = -1);
//! returns the hashed atom-pair fingerprint for a molecule
/*!
\param mol: the molecule to be fingerprinted
\param nBits: the length of the fingerprint to generate
\param minLength: minimum distance between atoms to be
considered in a pair. Default is 1 bond.
\param maxLength: maximum distance between atoms to be
considered in a pair.
Default is maxPathLen-1 bonds.
\param fromAtoms: if provided, only atom pairs that involve
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any atom pairs that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param includeChirality: if set, chirality will be used in the atom invariants
(note: this is ignored if atomInvariants are
provided)
\param use2D: if set, the 2D (topological) distance matrix is used.
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int32_t>
*getHashedAtomPairFingerprint(
const ROMol &mol, unsigned int nBits = 2048, unsigned int minLength = 1,
unsigned int maxLength = maxPathLen - 1,
const std::vector<boost::uint32_t> *fromAtoms = 0,
const std::vector<boost::uint32_t> *ignoreAtoms = 0,
const std::vector<boost::uint32_t> *atomInvariants = 0,
bool includeChirality = false, bool use2D = true, int confId = -1);
//! returns the hashed atom-pair fingerprint for a molecule as a bit vector
/*!
\param mol: the molecule to be fingerprinted
\param nBits: the length of the fingerprint to generate
\param minLength: minimum distance between atoms to be
considered in a pair. Default is 1 bond.
\param maxLength: maximum distance between atoms to be
considered in a pair.
Default is maxPathLen-1 bonds.
\param fromAtoms: if provided, only atom pairs that involve
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any atom pairs that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param nBitsPerEntry: number of bits to use in simulating counts
\param includeChirality: if set, chirality will be used in the atom invariants
(note: this is ignored if atomInvariants are
provided)
\param use2D: if set, the 2D (topological) distance matrix is used.
\param confId: the conformation to use if 3D distances are being used
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *
getHashedAtomPairFingerprintAsBitVect(
const ROMol &mol, unsigned int nBits = 2048, unsigned int minLength = 1,
unsigned int maxLength = maxPathLen - 1,
const std::vector<boost::uint32_t> *fromAtoms = 0,
const std::vector<boost::uint32_t> *ignoreAtoms = 0,
const std::vector<boost::uint32_t> *atomInvariants = 0,
unsigned int nBitsPerEntry = 4, bool includeChirality = false,
bool use2D = true, int confId = -1);
//! returns the topological-torsion fingerprint for a molecule
/*!
The algorithm used is described here:
R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan;
"Topological Torsion: A New Molecular Descriptor for SAR Applications.
Comparison with Other Descriptors" JCICS 27, 82-85 (1987).
\param mol: the molecule to be fingerprinted
\param targetSize: the number of atoms to include in the "torsions"
\param fromAtoms: if provided, only torsions that start or end at
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any torsions that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param includeChirality: if set, chirality will be used in the atom invariants
(note: this is ignored if atomInvariants are
provided)
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int64_t>
*getTopologicalTorsionFingerprint(
const ROMol &mol, unsigned int targetSize = 4,
const std::vector<boost::uint32_t> *fromAtoms = 0,
const std::vector<boost::uint32_t> *ignoreAtoms = 0,
const std::vector<boost::uint32_t> *atomInvariants = 0,
bool includeChirality = false);
//! returns a hashed topological-torsion fingerprint for a molecule
/*!
The algorithm used is described here:
R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan;
"Topological Torsion: A New Molecular Descriptor for SAR Applications.
Comparison with Other Descriptors" JCICS 27, 82-85 (1987).
\param mol: the molecule to be fingerprinted
\param nBits: number of bits to include in the fingerprint
\param targetSize: the number of atoms to include in the "torsions"
\param fromAtoms: if provided, only torsions that start or end at
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any torsions that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param includeChirality: if set, chirality will be used in the atom invariants
(note: this is ignored if atomInvariants are
provided)
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int64_t> *
getHashedTopologicalTorsionFingerprint(
const ROMol &mol, unsigned int nBits = 2048, unsigned int targetSize = 4,
const std::vector<boost::uint32_t> *fromAtoms = 0,
const std::vector<boost::uint32_t> *ignoreAtoms = 0,
const std::vector<boost::uint32_t> *atomInvariants = 0,
bool includeChirality = false);
//! returns a hashed topological-torsion fingerprint for a molecule as a bit
// vector
/*!
\param mol: the molecule to be fingerprinted
\param nBits: number of bits to include in the fingerprint
\param targetSize: the number of atoms to include in the "torsions"
\param fromAtoms: if provided, only torsions that start or end at
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any torsions that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param nBitsPerEntry: number of bits to use in simulating counts
\param includeChirality: if set, chirality will be used in the atom invariants
(note: this is ignored if atomInvariants are
provided)
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *
getHashedTopologicalTorsionFingerprintAsBitVect(
const ROMol &mol, unsigned int nBits = 2048, unsigned int targetSize = 4,
const std::vector<boost::uint32_t> *fromAtoms = 0,
const std::vector<boost::uint32_t> *ignoreAtoms = 0,
const std::vector<boost::uint32_t> *atomInvariants = 0,
unsigned int nBitsPerEntry = 4, bool includeChirality = false);
} // namespace AtomPairs
} // namespace RDKit
#endif
|
