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
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
|
using System;
using System.Runtime.InteropServices;
namespace com.epam.indigo
{
/// <summary>
/// Bingo instance corresponds to a single chemical database
/// </summary>
[StructLayout(LayoutKind.Sequential, CharSet = CharSet.Auto)]
public unsafe class Bingo : IDisposable
{
private readonly Indigo _indigo;
private int _id;
private Bingo(Indigo indigo, int id)
{
_indigo = indigo;
_id = id;
version(); // Preloads native library
}
/// <summary>
/// Destructor
/// </summary>
~Bingo()
{
Dispose();
}
/// <summary>
/// Dispose method that closes the database
/// </summary>
public void Dispose()
{
if (_id >= 0)
{
_indigo.setSessionID();
Bingo.checkResult(BingoLib.bingoCloseDatabase(_id));
_id = -1;
}
}
/// <summary>
/// Method to close a database
/// </summary>
public void close()
{
Dispose();
}
internal static int checkResult(int result)
{
if (result < 0)
{
throw new BingoException(new string(IndigoLib.indigoGetLastError()));
}
return result;
}
internal static float checkResult(float result)
{
if (result < 0.0)
{
throw new BingoException(new string(IndigoLib.indigoGetLastError()));
}
return result;
}
internal static string checkResult(string result)
{
if (result == null)
{
throw new BingoException(new string(IndigoLib.indigoGetLastError()));
}
return result;
}
public static string checkResult(sbyte* result)
{
if (result == null)
{
throw new BingoException(new string(IndigoLib.indigoGetLastError()));
}
return new string(result);
}
/// <summary>
/// Creates a chemical storage of a specifed type in a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <param name="type">"molecule" or "reaction"</param>
/// <param name="options">Additional options separated with a semicolon. See the Bingo documentation for more details.</param>
/// <returns>Bingo database instance</returns>
public static Bingo createDatabaseFile(Indigo indigo, string location, string type, string options)
{
indigo.setSessionID();
if (options == null)
{
options = "";
}
int databaseID = checkResult(BingoLib.bingoCreateDatabaseFile(location, type, options));
return new Bingo(indigo, databaseID);
}
/// <summary>
/// Creates a chemical storage of a specifed type in a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <param name="type">"molecule" or "reaction"</param>
/// <returns>Bingo database instance</returns>
public static Bingo createDatabaseFile(Indigo indigo, string location, string type)
{
return createDatabaseFile(indigo, location, type, null);
}
/// <summary>
/// Loads a chemical storage of a specifed type from a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <param name="options">Additional options separated with a semicolon. See the Bingo documentation for more details.</param>
/// <returns>Bingo database instance</returns>
public static Bingo loadDatabaseFile(Indigo indigo, string location, string options)
{
if (options == null)
{
options = "";
}
indigo.setSessionID();
int databaseID = checkResult(BingoLib.bingoLoadDatabaseFile(location, options));
return new Bingo(indigo, databaseID);
}
/// <summary>
/// Loads a chemical storage of a specifed type from a specified location
/// </summary>
/// <param name="indigo">Indigo instance</param>
/// <param name="location">Directory with the files location</param>
/// <returns>Bingo database instance</returns>
public static Bingo loadDatabaseFile(Indigo indigo, string location)
{
return loadDatabaseFile(indigo, location, null);
}
/// <summary>
/// Insert a structure into the database and returns id of this structure
/// </summary>
/// <param name="record">Indigo object with a chemical structure (molecule or reaction)</param>
/// <returns>record id</returns>
public int insert(IndigoObject record)
{
_indigo.setSessionID();
return checkResult(BingoLib.bingoInsertRecordObj(_id, record.self));
}
/// <summary>
/// Inserts a structure under a specified id
/// </summary>
/// <param name="record">Indigo object with a chemical structure (molecule or reaction)</param>
/// <param name="id">record id</param>
/// <returns> inserted record id</returns>
public int insert(IndigoObject record, int id)
{
_indigo.setSessionID();
return checkResult(BingoLib.bingoInsertRecordObjWithId(_id, record.self, id));
}
/// <summary>
/// Insert a structure into the database and returns id of this structure
/// </summary>
/// <param name="record">Indigo object with a chemical structure (molecule or reaction)</param>
/// <param name="ext_fp">Indigo object with a external similarity fingerprint</param>
/// <returns>record id</returns>
public int insertWithExtFP(IndigoObject record, IndigoObject ext_fp)
{
_indigo.setSessionID();
return checkResult(BingoLib.bingoInsertRecordObjWithExtFP(_id, record.self, ext_fp.self));
}
/// <summary>
/// Inserts a structure under a specified id
/// </summary>
/// <param name="record">Indigo object with a chemical structure (molecule or reaction)</param>
/// <param name="ext_fp">Indigo object with a external similarity fingerprint</param>
/// <param name="id">record id</param>
/// <returns> inserted record id</returns>
public int insertWithExtFP(IndigoObject record, IndigoObject ext_fp, int id)
{
_indigo.setSessionID();
return checkResult(BingoLib.bingoInsertRecordObjWithIdAndExtFP(_id, record.self, id, ext_fp.self));
}
/// <summary>
/// Delete a record by id
/// </summary>
/// <param name="id">Record id</param>
public void delete(int id)
{
_indigo.setSessionID();
checkResult(BingoLib.bingoDeleteRecord(_id, id));
}
/// <summary>
/// Execute substructure search operation
/// </summary>
/// <param name="query">Indigo query object (molecule or reaction)</param>
/// <param name="options">Search options</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSub(IndigoObject query, string options)
{
if (options == null)
{
options = "";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoSearchSub(_id, query.self, options)), _indigo);
}
/// <summary>
/// Execute substructure search operation
/// </summary>
/// <param name="query">Indigo query object (molecule or reaction)</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSub(IndigoObject query)
{
return searchSub(query, null);
}
/// <summary>
/// Execute similarity search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <param name="min">Minimum similarity value</param>
/// <param name="max">Maximum similairy value</param>
/// <param name="metric">Default value is "tanimoto"</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSim(IndigoObject query, float min, float max, string metric)
{
if (metric == null)
{
metric = "tanimoto";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoSearchSim(_id, query.self, min, max, metric)), _indigo);
}
/// <summary>
/// Execute similarity search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <param name="min">Minimum similarity value</param>
/// <param name="max">Maximum similairy value</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSim(IndigoObject query, float min, float max)
{
return searchSim(query, min, max, null);
}
/// <summary>
/// Execute similarity search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <param name="min">Minimum similarity value</param>
/// <param name="max">Maximum similairy value</param>
/// <param name="ext_fp">Indigo object with a external similarity fingerprint</param>
/// <param name="metric">Default value is "tanimoto"</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSimWithExtFP(IndigoObject query, float min, float max, IndigoObject ext_fp, string metric)
{
if (metric == null)
{
metric = "tanimoto";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoSearchSimWithExtFP(_id, query.self, min, max, ext_fp.self, metric)), _indigo);
}
/// <summary>
/// Execute similarity search for most similar structures (defined by limit)
/// </summary>
/// <param name="query"> indigo object (molecule or reaction)</param>
/// <param name="limit"> Number of structures</param>
/// <param name="minSim"> Minimum similarity value</param>
/// <param name="metric"> Default value is "tanimoto"</param>
/// <returns> Bingo search object instance</returns>
public BingoObject searchSimTopN(IndigoObject query, int limit, float minSim, string metric)
{
if (metric == null)
{
metric = "tanimoto";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoSearchSimTopN(_id, query.self, limit, minSim, metric)), _indigo);
}
/// <summary>
/// Execute similarity search for most similar structures (defined by limit)
/// </summary>
/// <param name="query"> indigo object (molecule or reaction)</param>
/// <param name="limit"> Number of structures</param>
/// <param name="minSim"> Minimum similarity value</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchSimTopN(IndigoObject query, int limit, float minSim)
{
return searchSimTopN(query, limit, minSim, null);
}
/// <summary>
/// Execute similarity search for most similar structures with external fingerprint
/// </summary>
/// <param name="query"> indigo object (molecule or reaction)</param>
/// <param name="limit"> Number of structures</param>
/// <param name="minSim"> Minimum similarity value</param>
/// <param name="metric"> Default value is "tanimoto"</param>
/// <param name="extFp"> Indigo object with a external similarity fingerprint (molecule or reaction)</param>
/// <returns> Bingo search object instance</returns>
public BingoObject searchSimTopNWithExtFP(IndigoObject query, int limit, float minSim, IndigoObject extFp, string metric)
{
if (metric == null)
{
metric = "tanimoto";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoSearchSimTopNWithExtFP(_id, query.self, limit, minSim, extFp.self, metric)), _indigo);
}
/// <summary>
/// Execute similarity search for most similar structures with external fingerprint
/// </summary>
/// <param name="query"> indigo object (molecule or reaction)</param>
/// <param name="limit"> Number of structures</param>
/// <param name="minSim"> Minimum similarity value</param>
/// <param name="extFp"> Indigo object with a external similarity fingerprint (molecule or reaction)</param>
/// <returns> Bingo search object instance</returns>
public BingoObject searchSimTopNWithExtFP(IndigoObject query, int limit, float minSim, IndigoObject extFp)
{
return searchSimTopNWithExtFP(query, limit, minSim, extFp, null);
}
/// <summary>
/// Execute enumerate id operation
/// </summary>
/// <returns>Bingo enumerate id object instance</returns>
public BingoObject enumerateId()
{
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoEnumerateId(_id)), _indigo);
}
/// <summary>
/// Perform exact search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchExact(IndigoObject query)
{
return searchExact(query, null);
}
/// <summary>
/// Perform exact search operation
/// </summary>
/// <param name="query">indigo object (molecule or reaction)</param>
/// <param name="options">exact search options</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchExact(IndigoObject query, string options)
{
if (options == null)
{
options = "";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoSearchExact(_id, query.self, options)), _indigo);
}
/// <summary>
/// Perform search by molecular formula
/// </summary>
/// <param name="query">string with formula to search. For example, 'C22 H23 N3 O2'.</param>
/// <param name="options">search options</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchMolFormula(string query, string options)
{
if (options == null)
{
options = "";
}
_indigo.setSessionID();
return new BingoObject(Bingo.checkResult(BingoLib.bingoSearchMolFormula(_id, query, options)), _indigo);
}
/// <summary>
/// Perform search by molecular formula
/// </summary>
/// <param name="query">string with formula to search. For example, 'C22 H23 N3 O2'.</param>
/// <returns>Bingo search object instance</returns>
public BingoObject searchMolFormula(string query)
{
return searchMolFormula(query, null);
}
/// <summary>
/// Post-process index optimization
/// </summary>
public void optimize()
{
_indigo.setSessionID();
checkResult(BingoLib.bingoOptimize(_id));
}
/// <summary>
/// Returns an IndigoObject for the record with the specified id
/// </summary>
/// <param name="id">record id</param>
/// <returns>Indigo object</returns>
public IndigoObject getRecordById(int id)
{
_indigo.setSessionID();
return new IndigoObject(_indigo, checkResult(BingoLib.bingoGetRecordObj(_id, id)));
}
/// <summary>
/// Returns Bingo version
/// </summary>
/// <returns>Bingo version</returns>
public string version()
{
_indigo.setSessionID();
return checkResult(BingoLib.bingoVersion());
}
}
}
|
