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
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
|
//
// Copyright (C) 2002-2022 Greg Landrum and other RDKit contributors
//
// @@ 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.
//
#include <RDGeneral/export.h>
#ifndef RD_FILEPARSERS_H
#define RD_FILEPARSERS_H
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include "CDXMLParser.h"
#include <string>
#include <string_view>
#include <iostream>
#include <vector>
#include <exception>
#include <boost/shared_ptr.hpp>
namespace RDKit {
const int MOLFILE_MAXLINE = 256;
RDKIT_FILEPARSERS_EXPORT std::string strip(const std::string &orig);
class RDKIT_FILEPARSERS_EXPORT MolFileUnhandledFeatureException
: public std::exception {
public:
//! construct with an error message
explicit MolFileUnhandledFeatureException(const char *msg) : _msg(msg) {}
//! construct with an error message
explicit MolFileUnhandledFeatureException(const std::string msg)
: _msg(msg) {}
//! get the error message
const char *what() const noexcept override { return _msg.c_str(); }
~MolFileUnhandledFeatureException() noexcept override = default;
private:
std::string _msg;
};
//-----
// mol files
//-----
typedef std::vector<RWMOL_SPTR> RWMOL_SPTR_VECT;
// \brief construct a molecule from MDL mol data in a stream
/*!
* \param inStream - stream containing the data
* \param line - current line number (used for error reporting)
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param line - current line number (used for error reporting)
* \param strictParsing - if set to false, the parser is more lax about
* correctness of the contents.
*
*/
RDKIT_FILEPARSERS_EXPORT RWMol *MolDataStreamToMol(std::istream *inStream,
unsigned int &line,
bool sanitize = true,
bool removeHs = true,
bool strictParsing = true);
// \overload
RDKIT_FILEPARSERS_EXPORT RWMol *MolDataStreamToMol(std::istream &inStream,
unsigned int &line,
bool sanitize = true,
bool removeHs = true,
bool strictParsing = true);
// \brief construct a molecule from an MDL mol block
/*!
* \param molBlock - string containing the mol block
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param strictParsing - if set to false, the parser is more lax about
* correctness of the contents.
*/
RDKIT_FILEPARSERS_EXPORT RWMol *MolBlockToMol(const std::string &molBlock,
bool sanitize = true,
bool removeHs = true,
bool strictParsing = true);
// \brief construct a molecule from an MDL mol file
/*!
* \param fName - string containing the file name
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param strictParsing - if set to false, the parser is more lax about
* correctness of the contents.
*/
RDKIT_FILEPARSERS_EXPORT RWMol *MolFileToMol(const std::string &fName,
bool sanitize = true,
bool removeHs = true,
bool strictParsing = true);
// \brief generates an MDL mol block for a molecule
/*!
* \param mol - the molecule in question
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is
* written
* \param forceV3000 - force generation a V3000 mol block (happens
* automatically with
* more than 999 atoms or bonds)
*/
RDKIT_FILEPARSERS_EXPORT std::string MolToMolBlock(const ROMol &mol,
bool includeStereo = true,
int confId = -1,
bool kekulize = true,
bool forceV3000 = false);
// \brief generates an MDL v3000 mol block for a molecule
/*!
* \param mol - the molecule in question
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is
* written
*/
inline std::string MolToV3KMolBlock(const ROMol &mol, bool includeStereo = true,
int confId = -1, bool kekulize = true) {
return MolToMolBlock(mol, includeStereo, confId, kekulize, true);
}
// \brief Writes a molecule to an MDL mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is
* written
* \param forceV3000 - force generation a V3000 mol block (happens
* automatically with
* more than 999 atoms or bonds)
*/
RDKIT_FILEPARSERS_EXPORT void MolToMolFile(
const ROMol &mol, const std::string &fName, bool includeStereo = true,
int confId = -1, bool kekulize = true, bool forceV3000 = false);
// \brief Writes a molecule to an MDL V3000 mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is
* written
*/
inline void MolToV3KMolFile(const ROMol &mol, const std::string &fName,
bool includeStereo = true, int confId = -1,
bool kekulize = true) {
MolToMolFile(mol, fName, includeStereo, confId, kekulize, true);
}
RDKIT_FILEPARSERS_EXPORT std::string MolToCMLBlock(const ROMol &mol,
int confId = -1,
bool kekulize = true);
RDKIT_FILEPARSERS_EXPORT void MolToCMLFile(const ROMol &mol,
const std::string &fName,
int confId = -1,
bool kekulize = true);
RDKIT_FILEPARSERS_EXPORT std::string MolToXYZBlock(const ROMol &mol,
int confId = -1);
RDKIT_FILEPARSERS_EXPORT void MolToXYZFile(const ROMol &mol,
const std::string &fName,
int confId = -1);
//-----
// TPL handling:
//-----
//! \brief translate TPL data (BioCad format) into a multi-conf molecule
/*!
\param inStream: the stream from which to read
\param line: used to track the line number of errors
\param sanitize: toggles sanitization and stereochemistry
perception of the molecule
\param skipFirstConf: according to the TPL format description, the atomic
coords in the atom-information block describe the first
conformation and the first conf block describes second
conformation. The CombiCode, on the other hand, writes
the first conformation data both to the atom-information
block and to the first conf block. We want to be able to
read CombiCode-style tpls, so we'll allow this
mis-feature
to be parsed when this flag is set.
*/
RDKIT_FILEPARSERS_EXPORT RWMol *TPLDataStreamToMol(std::istream *inStream,
unsigned int &line,
bool sanitize = true,
bool skipFirstConf = false);
//! \brief construct a multi-conf molecule from a TPL (BioCad format) file
/*!
\param fName: the name of the file from which to read
\param sanitize: toggles sanitization and stereochemistry
perception of the molecule
\param skipFirstConf: according to the TPL format description, the atomic
coords in the atom-information block describe the first
conformation and the first conf block describes second
conformation. The CombiCode, on the other hand, writes
the first conformation data both to the atom-information
block and to the first conf block. We want to be able to
read CombiCode-style tpls, so we'll allow this
mis-feature
to be parsed when this flag is set.
*/
RDKIT_FILEPARSERS_EXPORT RWMol *TPLFileToMol(const std::string &fName,
bool sanitize = true,
bool skipFirstConf = false);
RDKIT_FILEPARSERS_EXPORT std::string MolToTPLText(
const ROMol &mol, const std::string &partialChargeProp = "_GasteigerCharge",
bool writeFirstConfTwice = false);
RDKIT_FILEPARSERS_EXPORT void MolToTPLFile(
const ROMol &mol, const std::string &fName,
const std::string &partialChargeProp = "_GasteigerCharge",
bool writeFirstConfTwice = false);
//-----
// MOL2 handling
//-----
typedef enum {
CORINA = 0 //!< supports output from Corina and some dbtranslate output
} Mol2Type;
// \brief construct a molecule from a Tripos mol2 file
/*!
*
* \param fName - string containing the file name
* \param sanitize - toggles sanitization of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param variant - the atom type definitions to use
* \param cleanupSubstructures - toggles recognition and cleanup of common
* substructures
*/
RDKIT_FILEPARSERS_EXPORT RWMol *Mol2FileToMol(const std::string &fName,
bool sanitize = true,
bool removeHs = true,
Mol2Type variant = CORINA,
bool cleanupSubstructures = true);
// \brief construct a molecule from Tripos mol2 data in a stream
/*!
* \param inStream - stream containing the data
* \param sanitize - toggles sanitization of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param variant - the atom type definitions to use
* \param cleanupSubstructures - toggles recognition and cleanup of common
* substructures
*/
RDKIT_FILEPARSERS_EXPORT RWMol *Mol2DataStreamToMol(
std::istream *inStream, bool sanitize = true, bool removeHs = true,
Mol2Type variant = CORINA, bool cleanupSubstructures = true);
// \overload
RDKIT_FILEPARSERS_EXPORT RWMol *Mol2DataStreamToMol(
std::istream &inStream, bool sanitize = true, bool removeHs = true,
Mol2Type variant = CORINA, bool cleanupSubstructures = true);
// \brief construct a molecule from a Tripos mol2 block
/*!
* \param molBlock - string containing the mol block
* \param sanitize - toggles sanitization of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param variant - the atom type definitions to use
* \param cleanupSubstructures - toggles recognition and cleanup of common
* substructures
*/
RDKIT_FILEPARSERS_EXPORT RWMol *Mol2BlockToMol(
const std::string &molBlock, bool sanitize = true, bool removeHs = true,
Mol2Type variant = CORINA, bool cleanupSubstructures = true);
RDKIT_FILEPARSERS_EXPORT RWMol *XYZDataStreamToMol(std::istream &inStream);
// \brief construct a molecule from an xyz block
/*!
* \param xyzBlock - string containing the xyz block
*/
RDKIT_FILEPARSERS_EXPORT RWMol *XYZBlockToMol(const std::string &xyzBlock);
// \brief construct a molecule from an xyz file
/*!
* \param fName - string containing the file name
*/
RDKIT_FILEPARSERS_EXPORT RWMol *XYZFileToMol(const std::string &fName);
RDKIT_FILEPARSERS_EXPORT RWMol *PDBBlockToMol(const char *str,
bool sanitize = true,
bool removeHs = true,
unsigned int flavor = 0,
bool proximityBonding = true);
RDKIT_FILEPARSERS_EXPORT RWMol *PDBBlockToMol(const std::string &str,
bool sanitize = true,
bool removeHs = true,
unsigned int flavor = 0,
bool proximityBonding = true);
RDKIT_FILEPARSERS_EXPORT RWMol *PDBDataStreamToMol(
std::istream *inStream, bool sanitize = true, bool removeHs = true,
unsigned int flavor = 0, bool proximityBonding = true);
RDKIT_FILEPARSERS_EXPORT RWMol *PDBDataStreamToMol(
std::istream &inStream, bool sanitize = true, bool removeHs = true,
unsigned int flavor = 0, bool proximityBonding = true);
RDKIT_FILEPARSERS_EXPORT RWMol *PDBFileToMol(const std::string &fname,
bool sanitize = true,
bool removeHs = true,
unsigned int flavor = 0,
bool proximityBonding = true);
// \brief generates an PDB block for a molecule
/*!
* \param mol - the molecule in question
* \param confId - selects the conformer to be used
* \param flavor - controls what gets written:
* flavor & 1 : Write MODEL/ENDMDL lines around each record
* flavor & 2 : Don't write single CONECT records
* flavor & 4 : Write CONECT records in both directions
* flavor & 8 : Don't use multiple CONECTs to encode bond order
* flavor & 16 : Write MASTER record
* flavor & 32 : Write TER record
*/
RDKIT_FILEPARSERS_EXPORT std::string MolToPDBBlock(const ROMol &mol,
int confId = -1,
unsigned int flavor = 0);
// \brief Writes a molecule to an MDL mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param confId - selects the conformer to be used
* \param flavor - controls what gets written:
* flavor & 1 : Write MODEL/ENDMDL lines around each record
* flavor & 2 : Don't write single CONECT records
* flavor & 4 : Write CONECT records in both directions
* flavor & 8 : Don't use multiple CONECTs to encode bond order
* flavor & 16 : Write MASTER record
* flavor & 32 : Write TER record
*/
RDKIT_FILEPARSERS_EXPORT void MolToPDBFile(const ROMol &mol,
const std::string &fname,
int confId = -1,
unsigned int flavor = 0);
// \brief reads a molecule from the metadata in an RDKit-generated SVG file
/*!
* \param svg - string containing the SVG
* \param sanitize - toggles sanitization of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
*
* **NOTE** This functionality should be considered beta.
*/
RDKIT_FILEPARSERS_EXPORT RWMol *RDKitSVGToMol(const std::string &svg,
bool sanitize = true,
bool removeHs = true);
/*! \overload
*/
RDKIT_FILEPARSERS_EXPORT RWMol *RDKitSVGToMol(std::istream *instream,
bool sanitize = true,
bool removeHs = true);
inline std::unique_ptr<RDKit::RWMol> operator"" _ctab(const char *text,
size_t len) {
std::string data(text, len);
RWMol *ptr = nullptr;
try {
ptr = MolBlockToMol(data);
} catch (const RDKit::MolSanitizeException &) {
ptr = nullptr;
}
return std::unique_ptr<RWMol>(ptr);
}
inline std::unique_ptr<RDKit::RWMol> operator"" _mol2(const char *text,
size_t len) {
std::string data(text, len);
RWMol *ptr = nullptr;
try {
ptr = Mol2BlockToMol(data);
} catch (const RDKit::MolSanitizeException &) {
ptr = nullptr;
}
return std::unique_ptr<RWMol>(ptr);
}
inline std::unique_ptr<RDKit::RWMol> operator"" _pdb(const char *text,
size_t len) {
std::string data(text, len);
RWMol *ptr = nullptr;
try {
ptr = PDBBlockToMol(data);
} catch (const RDKit::MolSanitizeException &) {
ptr = nullptr;
}
return std::unique_ptr<RWMol>(ptr);
}
} // namespace RDKit
#endif
|
