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1 NAME | |
2 MACCSKeysFingerprints.pl - Generate MACCS key fingerprints for SD files | |
3 | |
4 SYNOPSIS | |
5 MACCSKeysFingerprints.pl SDFile(s)... | |
6 | |
7 MACCSKeysFingerprints.pl [--AromaticityModel *AromaticityModelType*] | |
8 [--BitsOrder *Ascending | Descending*] [-b, --BitStringFormat | |
9 *BinaryString | HexadecimalString*] [--CompoundID *DataFieldName or | |
10 LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode | |
11 *DataField | MolName | LabelPrefix | MolNameOrLabelPrefix*] | |
12 [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode | |
13 *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*] | |
14 [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent | |
15 *Yes | No*] [-m, --mode *MACCSKeyBits | MACCSKeyCount*] [--OutDelim | |
16 *comma | tab | semicolon*] [--output *SD | FP | text | all*] [-o, | |
17 --overwrite] [-q, --quote *Yes | No*] [-r, --root *RootName*] [-s, | |
18 --size *number*] [-v, --VectorStringFormat *IDsAndValuesString | | |
19 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*] | |
20 [-w, --WorkingDir *DirName*] | |
21 | |
22 DESCRIPTION | |
23 Generate MACCS (Molecular ACCess System) keys fingerprints [ Ref 45-47 ] | |
24 for *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s) | |
25 containing fingerprints bit-vector or vector strings corresponding to | |
26 molecular fingerprints. | |
27 | |
28 Multiple SDFile names are separated by spaces. The valid file extensions | |
29 are *.sdf* and *.sd*. All other file names are ignored. All the SD files | |
30 in a current directory can be specified either by **.sdf* or the current | |
31 directory name. | |
32 | |
33 For each MACCS keys definition, atoms are processed to determine their | |
34 membership to the key and the appropriate molecular fingerprints strings | |
35 are generated. An atom can belong to multiple MACCS keys. | |
36 | |
37 For *MACCSKeyBits* value of -m, --mode option, a fingerprint bit-vector | |
38 string containing zeros and ones is generated and for *MACCSKeyCount* | |
39 value, a fingerprint vector string corresponding to number of MACCS keys | |
40 [ Ref 45-47 ] is generated. | |
41 | |
42 *MACCSKeyBits | MACCSKeyCount* values for -m, --mode option along with | |
43 two possible *166 | 322* values of -s, --size supports generation of | |
44 four different types of MACCS keys fingerprint: *MACCS166KeyBits, | |
45 MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount*. | |
46 | |
47 Example of *SD* file containing MAACS keys fingerprints string data: | |
48 | |
49 ... ... | |
50 ... ... | |
51 $$$$ | |
52 ... ... | |
53 ... ... | |
54 ... ... | |
55 41 44 0 0 0 0 0 0 0 0999 V2000 | |
56 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
57 ... ... | |
58 2 3 1 0 0 0 0 | |
59 ... ... | |
60 M END | |
61 > <CmpdID> | |
62 Cmpd1 | |
63 | |
64 > <MACCSKeysFingerprints> | |
65 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;000000000 | |
66 00000000000000000000000000000000100100001001000000001001000000001110001 | |
67 00101010111100011011000100110110000011011110100110111111111111011111111 | |
68 11111111110111000 | |
69 | |
70 $$$$ | |
71 ... ... | |
72 ... ... | |
73 | |
74 Example of *FP* file containing MAACS keys fingerprints string data: | |
75 | |
76 # | |
77 # Package = MayaChemTools 7.4 | |
78 # Release Date = Oct 21, 2010 | |
79 # | |
80 # TimeStamp = Fri Mar 11 14:57:24 2011 | |
81 # | |
82 # FingerprintsStringType = FingerprintsBitVector | |
83 # | |
84 # Description = MACCSKeyBits | |
85 # Size = 166 | |
86 # BitStringFormat = BinaryString | |
87 # BitsOrder = Ascending | |
88 # | |
89 Cmpd1 00000000000000000000000000000000000000000100100001001000000001... | |
90 Cmpd2 00000000000000000000000010000000001000000010000000001000000000... | |
91 ... ... | |
92 ... .. | |
93 | |
94 Example of CSV *Text* file containing MAACS keys fingerprints string | |
95 data: | |
96 | |
97 "CompoundID","MACCSKeysFingerprints" | |
98 "Cmpd1","FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending; | |
99 00000000000000000000000000000000000000000100100001001000000001001000000 | |
100 00111000100101010111100011011000100110110000011011110100110111111111111 | |
101 01111111111111111110111000" | |
102 ... ... | |
103 ... ... | |
104 | |
105 The current release of MayaChemTools generates the following types of | |
106 MACCS keys fingerprints bit-vector and vector strings: | |
107 | |
108 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 | |
109 0000000000000000000000000000000001001000010010000000010010000000011100 | |
110 0100101010111100011011000100110110000011011110100110111111111111011111 | |
111 11111111111110111000 | |
112 | |
113 FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 | |
114 000000021210210e845f8d8c60b79dffbffffd1 | |
115 | |
116 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 | |
117 1110011111100101111111000111101100110000000000000011100010000000000000 | |
118 0000000000000000000000000000000000000000000000101000000000000000000000 | |
119 0000000000000000000000000000000000000000000000000000000000000000000000 | |
120 0000000000000000000000000000000000000011000000000000000000000000000000 | |
121 0000000000000000000000000000000000000000 | |
122 | |
123 FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 | |
124 e7af3edc000c1100000000000000500000000000000000000000000000000300000000 | |
125 000000000 | |
126 | |
127 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri | |
128 ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
129 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 | |
130 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0 | |
131 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1 | |
132 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1 | |
133 | |
134 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri | |
135 ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0 | |
136 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0 | |
137 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
138 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0 | |
139 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... | |
140 | |
141 OPTIONS | |
142 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel | | |
143 MMFFAromaticityModel | ChemAxonBasicAromaticityModel | | |
144 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | | |
145 MayaChemToolsAromaticityModel* | |
146 Specify aromaticity model to use during detection of aromaticity. | |
147 Possible values in the current release are: *MDLAromaticityModel, | |
148 TriposAromaticityModel, MMFFAromaticityModel, | |
149 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, | |
150 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default | |
151 value: *MayaChemToolsAromaticityModel*. | |
152 | |
153 The supported aromaticity model names along with model specific | |
154 control parameters are defined in AromaticityModelsData.csv, which | |
155 is distributed with the current release and is available under | |
156 lib/data directory. Molecule.pm module retrieves data from this file | |
157 during class instantiation and makes it available to method | |
158 DetectAromaticity for detecting aromaticity corresponding to a | |
159 specific model. | |
160 | |
161 --BitsOrder *Ascending | Descending* | |
162 Bits order to use during generation of fingerprints bit-vector | |
163 string for *MACCSKeyBits* value of -m, --mode option. Possible | |
164 values: *Ascending, Descending*. Default: *Ascending*. | |
165 | |
166 *Ascending* bit order which corresponds to first bit in each byte as | |
167 the lowest bit as opposed to the highest bit. | |
168 | |
169 Internally, bits are stored in *Ascending* order using Perl vec | |
170 function. Regardless of machine order, big-endian or little-endian, | |
171 vec function always considers first string byte as the lowest byte | |
172 and first bit within each byte as the lowest bit. | |
173 | |
174 -b, --BitStringFormat *BinaryString | HexadecimalString* | |
175 Format of fingerprints bit-vector string data in output SD, FP or | |
176 CSV/TSV text file(s) specified by --output used during | |
177 *MACCSKeyBits* value of -m, --mode option. Possible values: | |
178 *BinaryString, HexadecimalString*. Default value: *BinaryString*. | |
179 | |
180 *BinaryString* corresponds to an ASCII string containing 1s and 0s. | |
181 *HexadecimalString* contains bit values in ASCII hexadecimal format. | |
182 | |
183 Examples: | |
184 | |
185 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 | |
186 0000000000000000000000000000000001001000010010000000010010000000011100 | |
187 0100101010111100011011000100110110000011011110100110111111111111011111 | |
188 11111111111110111000 | |
189 | |
190 FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 | |
191 000000021210210e845f8d8c60b79dffbffffd1 | |
192 | |
193 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 | |
194 1110011111100101111111000111101100110000000000000011100010000000000000 | |
195 0000000000000000000000000000000000000000000000101000000000000000000000 | |
196 0000000000000000000000000000000000000000000000000000000000000000000000 | |
197 0000000000000000000000000000000000000011000000000000000000000000000000 | |
198 0000000000000000000000000000000000000000 | |
199 | |
200 FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 | |
201 e7af3edc000c1100000000000000500000000000000000000000000000000300000000 | |
202 000000000 | |
203 | |
204 --CompoundID *DataFieldName or LabelPrefixString* | |
205 This value is --CompoundIDMode specific and indicates how compound | |
206 ID is generated. | |
207 | |
208 For *DataField* value of --CompoundIDMode option, it corresponds to | |
209 datafield label name whose value is used as compound ID; otherwise, | |
210 it's a prefix string used for generating compound IDs like | |
211 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound | |
212 IDs which look like Cmpd<Number>. | |
213 | |
214 Examples for *DataField* value of --CompoundIDMode: | |
215 | |
216 MolID | |
217 ExtReg | |
218 | |
219 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of | |
220 --CompoundIDMode: | |
221 | |
222 Compound | |
223 | |
224 The value specified above generates compound IDs which correspond to | |
225 Compound<Number> instead of default value of Cmpd<Number>. | |
226 | |
227 --CompoundIDLabel *text* | |
228 Specify compound ID column label for FP or CSV/TSV text file(s) used | |
229 during *CompoundID* value of --DataFieldsMode option. Default: | |
230 *CompoundID*. | |
231 | |
232 --CompoundIDMode *DataField | MolName | LabelPrefix | | |
233 MolNameOrLabelPrefix* | |
234 Specify how to generate compound IDs and write to FP or CSV/TSV text | |
235 file(s) along with generated fingerprints for *FP | text | all* | |
236 values of --output option: use a *SDFile(s)* datafield value; use | |
237 molname line from *SDFile(s)*; generate a sequential ID with | |
238 specific prefix; use combination of both MolName and LabelPrefix | |
239 with usage of LabelPrefix values for empty molname lines. | |
240 | |
241 Possible values: *DataField | MolName | LabelPrefix | | |
242 MolNameOrLabelPrefix*. Default: *LabelPrefix*. | |
243 | |
244 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line | |
245 in *SDFile(s)* takes precedence over sequential compound IDs | |
246 generated using *LabelPrefix* and only empty molname values are | |
247 replaced with sequential compound IDs. | |
248 | |
249 This is only used for *CompoundID* value of --DataFieldsMode option. | |
250 | |
251 --DataFields *"FieldLabel1,FieldLabel2,..."* | |
252 Comma delimited list of *SDFiles(s)* data fields to extract and | |
253 write to CSV/TSV text file(s) along with generated fingerprints for | |
254 *text | all* values of --output option. | |
255 | |
256 This is only used for *Specify* value of --DataFieldsMode option. | |
257 | |
258 Examples: | |
259 | |
260 Extreg | |
261 MolID,CompoundName | |
262 | |
263 -d, --DataFieldsMode *All | Common | Specify | CompoundID* | |
264 Specify how data fields in *SDFile(s)* are transferred to output | |
265 CSV/TSV text file(s) along with generated fingerprints for *text | | |
266 all* values of --output option: transfer all SD data field; transfer | |
267 SD data files common to all compounds; extract specified data | |
268 fields; generate a compound ID using molname line, a compound | |
269 prefix, or a combination of both. Possible values: *All | Common | | |
270 specify | CompoundID*. Default value: *CompoundID*. | |
271 | |
272 -f, --Filter *Yes | No* | |
273 Specify whether to check and filter compound data in SDFile(s). | |
274 Possible values: *Yes or No*. Default value: *Yes*. | |
275 | |
276 By default, compound data is checked before calculating fingerprints | |
277 and compounds containing atom data corresponding to non-element | |
278 symbols or no atom data are ignored. | |
279 | |
280 --FingerprintsLabel *text* | |
281 SD data label or text file column label to use for fingerprints | |
282 string in output SD or CSV/TSV text file(s) specified by --output. | |
283 Default value: *MACCSKeyFingerprints*. | |
284 | |
285 -h, --help | |
286 Print this help message. | |
287 | |
288 -k, --KeepLargestComponent *Yes | No* | |
289 Generate fingerprints for only the largest component in molecule. | |
290 Possible values: *Yes or No*. Default value: *Yes*. | |
291 | |
292 For molecules containing multiple connected components, fingerprints | |
293 can be generated in two different ways: use all connected components | |
294 or just the largest connected component. By default, all atoms | |
295 except for the largest connected component are deleted before | |
296 generation of fingerprints. | |
297 | |
298 -m, --mode *MACCSKeyBits | MACCSKeyCount* | |
299 Specify type of MACCS keys [ Ref 45-47 ] fingerprints to generate | |
300 for molecules in *SDFile(s)*. Possible values: *MACCSKeyBits, | |
301 MACCSKeyCount*. Default value: *MACCSKeyBits*. | |
302 | |
303 For *MACCSKeyBits* value of -m, --mode option, a fingerprint | |
304 bit-vector string containing zeros and ones is generated and for | |
305 *MACCSKeyCount* value, a fingerprint vector string corresponding to | |
306 number of MACCS keys is generated. | |
307 | |
308 *MACCSKeyBits | MACCSKeyCount* values for -m, --mode option along | |
309 with two possible *166 | 322* values of -s, --size supports | |
310 generation of four different types of MACCS keys fingerprint: | |
311 *MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, | |
312 MACCS322KeyCount*. | |
313 | |
314 Definition of MACCS keys uses the following atom and bond symbols to | |
315 define atom and bond environments: | |
316 | |
317 Atom symbols for 166 keys [ Ref 47 ]: | |
318 | |
319 A : Any valid periodic table element symbol | |
320 Q : Hetro atoms; any non-C or non-H atom | |
321 X : Halogens; F, Cl, Br, I | |
322 Z : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I | |
323 | |
324 Atom symbols for 322 keys [ Ref 46 ]: | |
325 | |
326 A : Any valid periodic table element symbol | |
327 Q : Hetro atoms; any non-C or non-H atom | |
328 X : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I | |
329 Z is neither defined nor used | |
330 | |
331 Bond types: | |
332 | |
333 - : Single | |
334 = : Double | |
335 T : Triple | |
336 # : Triple | |
337 ~ : Single or double query bond | |
338 % : An aromatic query bond | |
339 | |
340 None : Any bond type; no explicit bond specified | |
341 | |
342 $ : Ring bond; $ before a bond type specifies ring bond | |
343 ! : Chain or non-ring bond; ! before a bond type specifies chain bond | |
344 | |
345 @ : A ring linkage and the number following it specifies the | |
346 atoms position in the line, thus @1 means linked back to the first | |
347 atom in the list. | |
348 | |
349 Aromatic: Kekule or Arom5 | |
350 | |
351 Kekule: Bonds in 6-membered rings with alternate single/double bonds | |
352 or perimeter bonds | |
353 Arom5: Bonds in 5-membered rings with two double bonds and a hetro | |
354 atom at the apex of the ring. | |
355 | |
356 MACCS 166 keys [ Ref 45-47 ] are defined as follows: | |
357 | |
358 Key Description | |
359 | |
360 1 ISOTOPE | |
361 2 103 < ATOMIC NO. < 256 | |
362 3 GROUP IVA,VA,VIA PERIODS 4-6 (Ge...) | |
363 4 ACTINIDE | |
364 5 GROUP IIIB,IVB (Sc...) | |
365 6 LANTHANIDE | |
366 7 GROUP VB,VIB,VIIB (V...) | |
367 8 QAAA@1 | |
368 9 GROUP VIII (Fe...) | |
369 10 GROUP IIA (ALKALINE EARTH) | |
370 11 4M RING | |
371 12 GROUP IB,IIB (Cu...) | |
372 13 ON(C)C | |
373 14 S-S | |
374 15 OC(O)O | |
375 16 QAA@1 | |
376 17 CTC | |
377 18 GROUP IIIA (B...) | |
378 19 7M RING | |
379 20 SI | |
380 21 C=C(Q)Q | |
381 22 3M RING | |
382 23 NC(O)O | |
383 24 N-O | |
384 25 NC(N)N | |
385 26 C$=C($A)$A | |
386 27 I | |
387 28 QCH2Q | |
388 29 P | |
389 30 CQ(C)(C)A | |
390 31 QX | |
391 32 CSN | |
392 33 NS | |
393 34 CH2=A | |
394 35 GROUP IA (ALKALI METAL) | |
395 36 S HETEROCYCLE | |
396 37 NC(O)N | |
397 38 NC(C)N | |
398 39 OS(O)O | |
399 40 S-O | |
400 41 CTN | |
401 42 F | |
402 43 QHAQH | |
403 44 OTHER | |
404 45 C=CN | |
405 46 BR | |
406 47 SAN | |
407 48 OQ(O)O | |
408 49 CHARGE | |
409 50 C=C(C)C | |
410 51 CSO | |
411 52 NN | |
412 53 QHAAAQH | |
413 54 QHAAQH | |
414 55 OSO | |
415 56 ON(O)C | |
416 57 O HETEROCYCLE | |
417 58 QSQ | |
418 59 Snot%A%A | |
419 60 S=O | |
420 61 AS(A)A | |
421 62 A$A!A$A | |
422 63 N=O | |
423 64 A$A!S | |
424 65 C%N | |
425 66 CC(C)(C)A | |
426 67 QS | |
427 68 QHQH (&...) | |
428 69 QQH | |
429 70 QNQ | |
430 71 NO | |
431 72 OAAO | |
432 73 S=A | |
433 74 CH3ACH3 | |
434 75 A!N$A | |
435 76 C=C(A)A | |
436 77 NAN | |
437 78 C=N | |
438 79 NAAN | |
439 80 NAAAN | |
440 81 SA(A)A | |
441 82 ACH2QH | |
442 83 QAAAA@1 | |
443 84 NH2 | |
444 85 CN(C)C | |
445 86 CH2QCH2 | |
446 87 X!A$A | |
447 88 S | |
448 89 OAAAO | |
449 90 QHAACH2A | |
450 91 QHAAACH2A | |
451 92 OC(N)C | |
452 93 QCH3 | |
453 94 QN | |
454 95 NAAO | |
455 96 5M RING | |
456 97 NAAAO | |
457 98 QAAAAA@1 | |
458 99 C=C | |
459 100 ACH2N | |
460 101 8M RING | |
461 102 QO | |
462 103 CL | |
463 104 QHACH2A | |
464 105 A$A($A)$A | |
465 106 QA(Q)Q | |
466 107 XA(A)A | |
467 108 CH3AAACH2A | |
468 109 ACH2O | |
469 110 NCO | |
470 111 NACH2A | |
471 112 AA(A)(A)A | |
472 113 Onot%A%A | |
473 114 CH3CH2A | |
474 115 CH3ACH2A | |
475 116 CH3AACH2A | |
476 117 NAO | |
477 118 ACH2CH2A > 1 | |
478 119 N=A | |
479 120 HETEROCYCLIC ATOM > 1 (&...) | |
480 121 N HETEROCYCLE | |
481 122 AN(A)A | |
482 123 OCO | |
483 124 QQ | |
484 125 AROMATIC RING > 1 | |
485 126 A!O!A | |
486 127 A$A!O > 1 (&...) | |
487 128 ACH2AAACH2A | |
488 129 ACH2AACH2A | |
489 130 QQ > 1 (&...) | |
490 131 QH > 1 | |
491 132 OACH2A | |
492 133 A$A!N | |
493 134 X (HALOGEN) | |
494 135 Nnot%A%A | |
495 136 O=A > 1 | |
496 137 HETEROCYCLE | |
497 138 QCH2A > 1 (&...) | |
498 139 OH | |
499 140 O > 3 (&...) | |
500 141 CH3 > 2 (&...) | |
501 142 N > 1 | |
502 143 A$A!O | |
503 144 Anot%A%Anot%A | |
504 145 6M RING > 1 | |
505 146 O > 2 | |
506 147 ACH2CH2A | |
507 148 AQ(A)A | |
508 149 CH3 > 1 | |
509 150 A!A$A!A | |
510 151 NH | |
511 152 OC(C)C | |
512 153 QCH2A | |
513 154 C=O | |
514 155 A!CH2!A | |
515 156 NA(A)A | |
516 157 C-O | |
517 158 C-N | |
518 159 O > 1 | |
519 160 CH3 | |
520 161 N | |
521 162 AROMATIC | |
522 163 6M RING | |
523 164 O | |
524 165 RING | |
525 166 FRAGMENTS | |
526 | |
527 MACCS 322 keys set as defined in tables 1, 2 and 3 [ Ref 46 ] | |
528 include: | |
529 | |
530 . 26 atom properties of type P, as listed in Table 1 | |
531 . 32 one-atom environments, as listed in Table 3 | |
532 . 264 atom-bond-atom combinations listed in Table 4 | |
533 | |
534 Total number of keys in three tables is : 322 | |
535 | |
536 Atom symbol, X, used for 322 keys [ Ref 46 ] doesn't refer to | |
537 Halogens as it does for 166 keys. In order to keep the definition of | |
538 322 keys consistent with the published definitions, the symbol X is | |
539 used to imply "others" atoms, but it's internally mapped to symbol X | |
540 as defined for 166 keys during the generation of key values. | |
541 | |
542 Atom properties-based keys (26): | |
543 | |
544 Key Description | |
545 1 A(AAA) or AA(A)A - atom with at least three neighbors | |
546 2 Q - heteroatom | |
547 3 Anot%not-A - atom involved in one or more multiple bonds, not aromatic | |
548 4 A(AAAA) or AA(A)(A)A - atom with at least four neighbors | |
549 5 A(QQ) or QA(Q) - atom with at least two heteroatom neighbors | |
550 6 A(QQQ) or QA(Q)Q - atom with at least three heteroatom neighbors | |
551 7 QH - heteroatom with at least one hydrogen attached | |
552 8 CH2(AA) or ACH2A - carbon with at least two single bonds and at least | |
553 two hydrogens attached | |
554 9 CH3(A) or ACH3 - carbon with at least one single bond and at least three | |
555 hydrogens attached | |
556 10 Halogen | |
557 11 A(-A-A-A) or A-A(-A)-A - atom has at least three single bonds | |
558 12 AAAAAA@1 > 2 - atom is in at least two different six-membered rings | |
559 13 A($A$A$A) or A$A($A)$A - atom has more than two ring bonds | |
560 14 A$A!A$A - atom is at a ring/chain boundary. When a comparison is done | |
561 with another atom the path passes through the chain bond. | |
562 15 Anot%A%Anot%A - atom is at an aromatic/nonaromatic boundary. When a | |
563 comparison is done with another atom the path | |
564 passes through the aromatic bond. | |
565 16 A!A!A - atom with more than one chain bond | |
566 17 A!A$A!A - atom is at a ring/chain boundary. When a comparison is done | |
567 with another atom the path passes through the ring bond. | |
568 18 A%Anot%A%A - atom is at an aromatic/nonaromatic boundary. When a | |
569 comparison is done with another atom the | |
570 path passes through the nonaromatic bond. | |
571 19 HETEROCYCLE - atom is a heteroatom in a ring. | |
572 20 rare properties: atom with five or more neighbors, atom in | |
573 four or more rings, or atom types other than | |
574 H, C, N, O, S, F, Cl, Br, or I | |
575 21 rare properties: atom has a charge, is an isotope, has two or | |
576 more multiple bonds, or has a triple bond. | |
577 22 N - nitrogen | |
578 23 S - sulfur | |
579 24 O - oxygen | |
580 25 A(AA)A(A)A(AA) - atom has two neighbors, each with three or | |
581 more neighbors (including the central atom). | |
582 26 CHACH2 - atom has two hydrocarbon (CH2) neighbors | |
583 | |
584 Atomic environments properties-based keys (32): | |
585 | |
586 Key Description | |
587 27 C(CC) | |
588 28 C(CCC) | |
589 29 C(CN) | |
590 30 C(CCN) | |
591 31 C(NN) | |
592 32 C(NNC) | |
593 33 C(NNN) | |
594 34 C(CO) | |
595 35 C(CCO) | |
596 36 C(NO) | |
597 37 C(NCO) | |
598 38 C(NNO) | |
599 39 C(OO) | |
600 40 C(COO) | |
601 41 C(NOO) | |
602 42 C(OOO) | |
603 43 Q(CC) | |
604 44 Q(CCC) | |
605 45 Q(CN) | |
606 46 Q(CCN) | |
607 47 Q(NN) | |
608 48 Q(CNN) | |
609 49 Q(NNN) | |
610 50 Q(CO) | |
611 51 Q(CCO) | |
612 52 Q(NO) | |
613 53 Q(CNO) | |
614 54 Q(NNO) | |
615 55 Q(OO) | |
616 56 Q(COO) | |
617 57 Q(NOO) | |
618 58 Q(OOO) | |
619 | |
620 Note: The first symbol is the central atom, with atoms bonded to the | |
621 central atom listed in parentheses. Q is any non-C, non-H atom. If | |
622 only two atoms are in parentheses, there is no implication | |
623 concerning the other atoms bonded to the central atom. | |
624 | |
625 Atom-Bond-Atom properties-based keys: (264) | |
626 | |
627 Key Description | |
628 59 C-C | |
629 60 C-N | |
630 61 C-O | |
631 62 C-S | |
632 63 C-Cl | |
633 64 C-P | |
634 65 C-F | |
635 66 C-Br | |
636 67 C-Si | |
637 68 C-I | |
638 69 C-X | |
639 70 N-N | |
640 71 N-O | |
641 72 N-S | |
642 73 N-Cl | |
643 74 N-P | |
644 75 N-F | |
645 76 N-Br | |
646 77 N-Si | |
647 78 N-I | |
648 79 N-X | |
649 80 O-O | |
650 81 O-S | |
651 82 O-Cl | |
652 83 O-P | |
653 84 O-F | |
654 85 O-Br | |
655 86 O-Si | |
656 87 O-I | |
657 88 O-X | |
658 89 S-S | |
659 90 S-Cl | |
660 91 S-P | |
661 92 S-F | |
662 93 S-Br | |
663 94 S-Si | |
664 95 S-I | |
665 96 S-X | |
666 97 Cl-Cl | |
667 98 Cl-P | |
668 99 Cl-F | |
669 100 Cl-Br | |
670 101 Cl-Si | |
671 102 Cl-I | |
672 103 Cl-X | |
673 104 P-P | |
674 105 P-F | |
675 106 P-Br | |
676 107 P-Si | |
677 108 P-I | |
678 109 P-X | |
679 110 F-F | |
680 111 F-Br | |
681 112 F-Si | |
682 113 F-I | |
683 114 F-X | |
684 115 Br-Br | |
685 116 Br-Si | |
686 117 Br-I | |
687 118 Br-X | |
688 119 Si-Si | |
689 120 Si-I | |
690 121 Si-X | |
691 122 I-I | |
692 123 I-X | |
693 124 X-X | |
694 125 C=C | |
695 126 C=N | |
696 127 C=O | |
697 128 C=S | |
698 129 C=Cl | |
699 130 C=P | |
700 131 C=F | |
701 132 C=Br | |
702 133 C=Si | |
703 134 C=I | |
704 135 C=X | |
705 136 N=N | |
706 137 N=O | |
707 138 N=S | |
708 139 N=Cl | |
709 140 N=P | |
710 141 N=F | |
711 142 N=Br | |
712 143 N=Si | |
713 144 N=I | |
714 145 N=X | |
715 146 O=O | |
716 147 O=S | |
717 148 O=Cl | |
718 149 O=P | |
719 150 O=F | |
720 151 O=Br | |
721 152 O=Si | |
722 153 O=I | |
723 154 O=X | |
724 155 S=S | |
725 156 S=Cl | |
726 157 S=P | |
727 158 S=F | |
728 159 S=Br | |
729 160 S=Si | |
730 161 S=I | |
731 162 S=X | |
732 163 Cl=Cl | |
733 164 Cl=P | |
734 165 Cl=F | |
735 166 Cl=Br | |
736 167 Cl=Si | |
737 168 Cl=I | |
738 169 Cl=X | |
739 170 P=P | |
740 171 P=F | |
741 172 P=Br | |
742 173 P=Si | |
743 174 P=I | |
744 175 P=X | |
745 176 F=F | |
746 177 F=Br | |
747 178 F=Si | |
748 179 F=I | |
749 180 F=X | |
750 181 Br=Br | |
751 182 Br=Si | |
752 183 Br=I | |
753 184 Br=X | |
754 185 Si=Si | |
755 186 Si=I | |
756 187 Si=X | |
757 188 I=I | |
758 189 I=X | |
759 190 X=X | |
760 191 C#C | |
761 192 C#N | |
762 193 C#O | |
763 194 C#S | |
764 195 C#Cl | |
765 196 C#P | |
766 197 C#F | |
767 198 C#Br | |
768 199 C#Si | |
769 200 C#I | |
770 201 C#X | |
771 202 N#N | |
772 203 N#O | |
773 204 N#S | |
774 205 N#Cl | |
775 206 N#P | |
776 207 N#F | |
777 208 N#Br | |
778 209 N#Si | |
779 210 N#I | |
780 211 N#X | |
781 212 O#O | |
782 213 O#S | |
783 214 O#Cl | |
784 215 O#P | |
785 216 O#F | |
786 217 O#Br | |
787 218 O#Si | |
788 219 O#I | |
789 220 O#X | |
790 221 S#S | |
791 222 S#Cl | |
792 223 S#P | |
793 224 S#F | |
794 225 S#Br | |
795 226 S#Si | |
796 227 S#I | |
797 228 S#X | |
798 229 Cl#Cl | |
799 230 Cl#P | |
800 231 Cl#F | |
801 232 Cl#Br | |
802 233 Cl#Si | |
803 234 Cl#I | |
804 235 Cl#X | |
805 236 P#P | |
806 237 P#F | |
807 238 P#Br | |
808 239 P#Si | |
809 240 P#I | |
810 241 P#X | |
811 242 F#F | |
812 243 F#Br | |
813 244 F#Si | |
814 245 F#I | |
815 246 F#X | |
816 247 Br#Br | |
817 248 Br#Si | |
818 249 Br#I | |
819 250 Br#X | |
820 251 Si#Si | |
821 252 Si#I | |
822 253 Si#X | |
823 254 I#I | |
824 255 I#X | |
825 256 X#X | |
826 257 C$C | |
827 258 C$N | |
828 259 C$O | |
829 260 C$S | |
830 261 C$Cl | |
831 262 C$P | |
832 263 C$F | |
833 264 C$Br | |
834 265 C$Si | |
835 266 C$I | |
836 267 C$X | |
837 268 N$N | |
838 269 N$O | |
839 270 N$S | |
840 271 N$Cl | |
841 272 N$P | |
842 273 N$F | |
843 274 N$Br | |
844 275 N$Si | |
845 276 N$I | |
846 277 N$X | |
847 278 O$O | |
848 279 O$S | |
849 280 O$Cl | |
850 281 O$P | |
851 282 O$F | |
852 283 O$Br | |
853 284 O$Si | |
854 285 O$I | |
855 286 O$X | |
856 287 S$S | |
857 288 S$Cl | |
858 289 S$P | |
859 290 S$F | |
860 291 S$Br | |
861 292 S$Si | |
862 293 S$I | |
863 294 S$X | |
864 295 Cl$Cl | |
865 296 Cl$P | |
866 297 Cl$F | |
867 298 Cl$Br | |
868 299 Cl$Si | |
869 300 Cl$I | |
870 301 Cl$X | |
871 302 P$P | |
872 303 P$F | |
873 304 P$Br | |
874 305 P$Si | |
875 306 P$I | |
876 307 P$X | |
877 308 F$F | |
878 309 F$Br | |
879 310 F$Si | |
880 311 F$I | |
881 312 F$X | |
882 313 Br$Br | |
883 314 Br$Si | |
884 315 Br$I | |
885 316 Br$X | |
886 317 Si$Si | |
887 318 Si$I | |
888 319 Si$X | |
889 320 I$I | |
890 321 I$X | |
891 322 X$X | |
892 | |
893 --OutDelim *comma | tab | semicolon* | |
894 Delimiter for output CSV/TSV text file(s). Possible values: *comma, | |
895 tab, or semicolon* Default value: *comma*. | |
896 | |
897 --output *SD | FP | text | all* | |
898 Type of output files to generate. Possible values: *SD, FP, text, or | |
899 all*. Default value: *text*. | |
900 | |
901 -o, --overwrite | |
902 Overwrite existing files. | |
903 | |
904 -q, --quote *Yes | No* | |
905 Put quote around column values in output CSV/TSV text file(s). | |
906 Possible values: *Yes or No*. Default value: *Yes*. | |
907 | |
908 -r, --root *RootName* | |
909 New file name is generated using the root: <Root>.<Ext>. Default for | |
910 new file names: <SDFileName><MACCSKeysFP>.<Ext>. The file type | |
911 determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values are | |
912 used for SD, FP, comma/semicolon, and tab delimited text files, | |
913 respectively.This option is ignored for multiple input files. | |
914 | |
915 -s, --size *number* | |
916 Size of MACCS keys [ Ref 45-47 ] set to use during fingerprints | |
917 generation. Possible values: *166 or 322*. Default value: *166*. | |
918 | |
919 -v, --VectorStringFormat *ValuesString | IDsAndValuesString | | |
920 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString* | |
921 Format of fingerprints vector string data in output SD, FP or | |
922 CSV/TSV text file(s) specified by --output used during | |
923 *MACCSKeyCount* value of -m, --mode option. Possible values: | |
924 *ValuesString, IDsAndValuesString | IDsAndValuesPairsString | | |
925 ValuesAndIDsString | ValuesAndIDsPairsString*. Defaultvalue: | |
926 *ValuesString*. | |
927 | |
928 Examples: | |
929 | |
930 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri | |
931 ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
932 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 | |
933 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0 | |
934 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1 | |
935 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1 | |
936 | |
937 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri | |
938 ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0 | |
939 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0 | |
940 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |
941 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0 | |
942 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... | |
943 | |
944 -w, --WorkingDir *DirName* | |
945 Location of working directory. Default: current directory. | |
946 | |
947 EXAMPLES | |
948 To generate MACCS keys fingerprints of size 166 in binary bit-vector | |
949 string format and create a SampleMACCS166FPBin.csv file containing | |
950 sequential compound IDs along with fingerprints bit-vector strings data, | |
951 type: | |
952 | |
953 % MACCSKeysFingerprints.pl -r SampleMACCS166FPBin -o Sample.sdf | |
954 | |
955 To generate MACCS keys fingerprints of size 166 in binary bit-vector | |
956 string format and create SampleMACCS166FPBin.sdf, | |
957 SampleMACCS166FPBin.csv and SampleMACCS166FPBin.csv files containing | |
958 sequential compound IDs in CSV file along with fingerprints bit-vector | |
959 strings data, type: | |
960 | |
961 % MACCSKeysFingerprints.pl --output all -r SampleMACCS166FPBin | |
962 -o Sample.sdf | |
963 | |
964 To generate MACCS keys fingerprints of size 322 in binary bit-vector | |
965 string format and create a SampleMACCS322FPBin.csv file containing | |
966 sequential compound IDs along with fingerprints bit-vector strings data, | |
967 type: | |
968 | |
969 % MACCSKeysFingerprints.pl -size 322 -r SampleMACCS322FPBin -o Sample.sdf | |
970 | |
971 To generate MACCS keys fingerprints of size 166 corresponding to count | |
972 of keys in ValuesString format and create a SampleMACCS166FPCount.csv | |
973 file containing sequential compound IDs along with fingerprints vector | |
974 strings data, type: | |
975 | |
976 % MACCSKeysFingerprints.pl -m MACCSKeyCount -r SampleMACCS166FPCount | |
977 -o Sample.sdf | |
978 | |
979 To generate MACCS keys fingerprints of size 322 corresponding to count | |
980 of keys in ValuesString format and create a SampleMACCS322FPCount.csv | |
981 file containing sequential compound IDs along with fingerprints vector | |
982 strings data, type: | |
983 | |
984 % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 | |
985 -r SampleMACCS322FPCount -o Sample.sdf | |
986 | |
987 To generate MACCS keys fingerprints of size 166 in hexadecimal | |
988 bit-vector string format with ascending bits order and create a | |
989 SampleMACCS166FPHex.csv file containing compound IDs from MolName along | |
990 with fingerprints bit-vector strings data, type: | |
991 | |
992 % MACCSKeysFingerprints.pl -m MACCSKeyBits --size 166 --BitStringFormat | |
993 HexadecimalString --BitsOrder Ascending --DataFieldsMode CompoundID | |
994 --CompoundIDMode MolName -r SampleMACCS166FPBin -o Sample.sdf | |
995 | |
996 To generate MACCS keys fingerprints of size 166 corresponding to count | |
997 of keys in IDsAndValuesString format and create a | |
998 SampleMACCS166FPCount.csv file containing compound IDs from MolName line | |
999 along with fingerprints vector strings data, type: | |
1000 | |
1001 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 | |
1002 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID | |
1003 --CompoundIDMode MolName -r SampleMACCS166FPCount -o Sample.sdf | |
1004 | |
1005 To generate MACCS keys fingerprints of size 166 corresponding to count | |
1006 of keys in IDsAndValuesString format and create a | |
1007 SampleMACCS166FPCount.csv file containing compound IDs using specified | |
1008 data field along with fingerprints vector strings data, type: | |
1009 | |
1010 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 | |
1011 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID | |
1012 --CompoundIDMode DataField --CompoundID Mol_ID -r | |
1013 SampleMACCS166FPCount -o Sample.sdf | |
1014 | |
1015 To generate MACCS keys fingerprints of size 322 corresponding to count | |
1016 of keys in ValuesString format and create a SampleMACCS322FPCount.tsv | |
1017 file containing compound IDs derived from combination of molecule name | |
1018 line and an explicit compound prefix along with fingerprints vector | |
1019 strings data in a column labels MACCSKeyCountFP, type: | |
1020 | |
1021 % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 --DataFieldsMode | |
1022 CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd | |
1023 --CompoundIDLabel MolID --FingerprintsLabel MACCSKeyCountFP --OutDelim | |
1024 Tab -r SampleMACCS322FPCount -o Sample.sdf | |
1025 | |
1026 To generate MACCS keys fingerprints of size 166 corresponding to count | |
1027 of keys in ValuesString format and create a SampleMACCS166FPCount.csv | |
1028 file containing specific data fields columns along with fingerprints | |
1029 vector strings data, type: | |
1030 | |
1031 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 | |
1032 --VectorStringFormat ValuesString --DataFieldsMode Specify --DataFields | |
1033 Mol_ID -r SampleMACCS166FPCount -o Sample.sdf | |
1034 | |
1035 To generate MACCS keys fingerprints of size 322 corresponding to count | |
1036 of keys in ValuesString format and create a SampleMACCS322FPCount.csv | |
1037 file containing common data fields columns along with fingerprints | |
1038 vector strings data, type: | |
1039 | |
1040 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 322 | |
1041 --VectorStringFormat ValuesString --DataFieldsMode Common -r | |
1042 SampleMACCS322FPCount -o Sample.sdf | |
1043 | |
1044 To generate MACCS keys fingerprints of size 166 corresponding to count | |
1045 of keys in ValuesString format and create SampleMACCS166FPCount.sdf, | |
1046 SampleMACCS166FPCount.fpf and SampleMACCS166FPCount.csv files containing | |
1047 all data fields columns in CSV file along with fingerprints vector | |
1048 strings data, type: | |
1049 | |
1050 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --output all | |
1051 --VectorStringFormat ValuesString --DataFieldsMode All -r | |
1052 SampleMACCS166FPCount -o Sample.sdf | |
1053 | |
1054 AUTHOR | |
1055 Manish Sud <msud@san.rr.com> | |
1056 | |
1057 SEE ALSO | |
1058 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, | |
1059 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, | |
1060 PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl, | |
1061 TopologicalAtomTorsionsFingerprints.pl, | |
1062 TopologicalPharmacophoreAtomPairsFingerprints.pl, | |
1063 TopologicalPharmacophoreAtomTripletsFingerprints.pl | |
1064 | |
1065 COPYRIGHT | |
1066 Copyright (C) 2015 Manish Sud. All rights reserved. | |
1067 | |
1068 This file is part of MayaChemTools. | |
1069 | |
1070 MayaChemTools is free software; you can redistribute it and/or modify it | |
1071 under the terms of the GNU Lesser General Public License as published by | |
1072 the Free Software Foundation; either version 3 of the License, or (at | |
1073 your option) any later version. | |
1074 |