-
Notifications
You must be signed in to change notification settings - Fork 0
/
manuscript.bib
560 lines (508 loc) · 17.5 KB
/
manuscript.bib
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
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
@report{anderson:1987,
title = {{{SMILES}}: {{A Line Notation}} and {{Computerized Interpreter}} for {{Chemical Structures}}},
author = {Anderson, Eric and Veith, Gilman D. and Weininger, David},
date = {1987-08},
number = {EPA/600/M-87/021},
institution = {{US Environmental Protection Agency}},
url = {https://nepis.epa.gov/Exe/ZyPURL.cgi?Dockey=2000CAUR.TXT}
}
@article{balaban:1985,
title = {Applications of Graph Theory in Chemistry},
author = {Balaban, Alexandru T.},
date = {1985-08-01},
journaltitle = {J. Chem. Inf. Comput. Sci.},
volume = {25},
number = {3},
pages = {334--343},
issn = {0095-2338},
doi = {10.1021/ci00047a033},
langid = {english}
}
@online{bison,
title = {Bison, {{The YACC-compatible Parser Generator}}},
url = {http://dinosaur.compilertools.net/bison/index.html},
urldate = {2022-08-21}
}
@online{cdxml,
title = {{{CDX Format Specification}}: {{The CDXML}} Text-Based File Format},
url = {https://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/IntroCDXML.htm},
urldate = {2022-03-17}
}
@article{clark:2011,
title = {Accurate {{Specification}} of {{Molecular Structures}}: {{The Case}} for {{Zero-Order Bonds}} and {{Explicit Hydrogen Counting}}},
shorttitle = {Accurate {{Specification}} of {{Molecular Structures}}},
author = {Clark, Alex M.},
date = {2011-12-27},
journaltitle = {J. Chem. Inf. Model.},
volume = {51},
number = {12},
pages = {3149--3157},
issn = {1549-9596, 1549-960X},
doi = {10.1021/ci200488k},
langid = {english}
}
@book{crockford:2008,
title = {{{JavaScript}}: The Good Parts ; [Unearthing the Excellence in {{JavaScript}}]},
shorttitle = {{{JavaScript}}},
author = {Crockford, Douglas},
date = {2008},
series = {Unearthing the Excellence in {{JavaScript}}},
edition = {1. ed},
publisher = {{O'Reilly}},
location = {{Beijing Köln}},
isbn = {978-0-596-51774-8},
langid = {english},
pagetotal = {153}
}
@online{ctfileFormats,
title = {{{CTfile Formats}} - {{Dassault Systèmes}}},
url = {https://discover.3ds.com/ctfile-documentation-request-form},
urldate = {2022-03-17}
}
@online{cxsmiles,
title = {Chemaxon {{Extended SMILES}} and {{SMARTS}} - {{CXSMILES}} and {{CXSMARTS}} | {{Chemaxon Docs}}},
url = {https://docs.chemaxon.com/display/docs/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md},
urldate = {2022-03-17}
}
@online{daylightTheory,
title = {Daylight {{Theory Manual}}},
url = {https://www.daylight.com/dayhtml/doc/theory/},
urldate = {2022-03-17}
}
@online{daylightToolkit,
title = {Daylight {{Toolkit}}},
url = {https://www.daylight.com/products/toolkit.html},
urldate = {2022-03-17}
}
@article{degtyarenko:2007,
title = {{{ChEBI}}: A Database and Ontology for Chemical Entities of Biological Interest},
shorttitle = {{{ChEBI}}},
author = {Degtyarenko, K. and de Matos, P. and Ennis, M. and Hastings, J. and Zbinden, M. and McNaught, A. and Alcantara, R. and Darsow, M. and Guedj, M. and Ashburner, M.},
options = {useprefix=true},
date = {2007-12-23},
journaltitle = {Nucleic Acids Research},
volume = {36},
pages = {D344-D350},
issn = {0305-1048, 1362-4962},
doi = {10.1093/nar/gkm791},
issue = {Database},
langid = {english}
}
@thesis{denjoed:2010,
title = {Parsing and {{Conversion}} of {{SMILES-strings}} to {{Molecular Graphs}}},
author = {den Joed, Anton},
options = {useprefix=true},
date = {2010},
institution = {{Leiden University}},
location = {{Universiteit Leiden}},
url = {https://theses.liacs.nl/203},
langid = {english}
}
@online{depictArchive,
title = {Depict {{Archive Page}}},
url = {https://web.archive.org/web/20070113052758/https://www.daylight.com/daycgi/depict},
urldate = {2022-03-17}
}
@article{dietz:1995,
title = {Yet {{Another Representation}} of {{Molecular Structure}}},
author = {Dietz, Andreas},
date = {1995-09-01},
journaltitle = {J. Chem. Inf. Model.},
volume = {35},
number = {5},
pages = {787--802},
issn = {1549-9596},
doi = {10.1021/ci00027a001},
langid = {english},
keywords = {dietz}
}
@article{drefahl:2011,
title = {{{CurlySMILES}}: A Chemical Language to Customize and Annotate Encodings of Molecular and Nanodevice Structures},
shorttitle = {{{CurlySMILES}}},
author = {Drefahl, Axel},
date = {2011-12},
journaltitle = {J Cheminform},
volume = {3},
number = {1},
pages = {1},
issn = {1758-2946},
doi = {10.1186/1758-2946-3-1},
langid = {english}
}
@article{edmonds:1965,
title = {Paths, {{Trees}}, and {{Flowers}}},
author = {Edmonds, Jack},
date = {1965},
journaltitle = {Can. J. Math.},
volume = {17},
pages = {449--467},
doi = {10.4153/CJM-1965-045-4},
langid = {english}
}
@online{extendingVersioningLanguages,
title = {[{{Editorial Draft}}] {{Extending}} and {{Versioning Languages}}: {{Terminology}}},
url = {https://www.w3.org/2001/tag/doc/versioning},
urldate = {2022-10-02}
}
@article{gasteiger:2018,
title = {Leaving Us with Fond Memories, Smiles, {{SMILES}} and, Alas, Tears: A Tribute to {{David Weininger}}, 1952–2016},
shorttitle = {Leaving Us with Fond Memories, Smiles, {{SMILES}} and, Alas, Tears},
author = {Gasteiger, Johann and Martin, Yvonne and Nicholls, Anthony and Oprea, Tudor I. and Stouch, Terry},
date = {2018-02},
journaltitle = {J Comput Aided Mol Des},
volume = {32},
number = {2},
pages = {313--319},
issn = {0920-654X, 1573-4951},
doi = {10.1007/s10822-018-0104-3},
langid = {english}
}
@article{gaulton:2012,
title = {{{ChEMBL}}: A Large-Scale Bioactivity Database for Drug Discovery},
shorttitle = {{{ChEMBL}}},
author = {Gaulton, A. and Bellis, L. J. and Bento, A. P. and Chambers, J. and Davies, M. and Hersey, A. and Light, Y. and McGlinchey, S. and Michalovich, D. and Al-Lazikani, B. and Overington, J. P.},
date = {2012-01-01},
journaltitle = {Nucleic Acids Research},
volume = {40},
number = {D1},
pages = {D1100-D1107},
issn = {0305-1048, 1362-4962},
doi = {10.1093/nar/gkr777},
langid = {english}
}
@article{hanson:2016,
title = {Jmol {{SMILES}} and {{Jmol SMARTS}}: Specifications and Applications},
shorttitle = {Jmol {{SMILES}} and {{Jmol SMARTS}}},
author = {Hanson, Robert M.},
date = {2016-12},
journaltitle = {J Cheminform},
volume = {8},
number = {1},
pages = {50},
issn = {1758-2946},
doi = {10.1186/s13321-016-0160-4},
langid = {english}
}
@article{hatton:2007,
title = {Language Subsetting in an Industrial Context: {{A}} Comparison of {{MISRA C}} 1998 and {{MISRA C}} 2004},
shorttitle = {Language Subsetting in an Industrial Context},
author = {Hatton, Les},
date = {2007-05},
journaltitle = {Information and Software Technology},
volume = {49},
number = {5},
pages = {475--482},
issn = {09505849},
doi = {10.1016/j.infsof.2006.07.004},
langid = {english}
}
@article{heller:2015,
title = {{{InChI}}, the {{IUPAC International Chemical Identifier}}},
author = {Heller, Stephen R and McNaught, Alan and Pletnev, Igor and Stein, Stephen and Tchekhovskoi, Dmitrii},
date = {2015-12},
journaltitle = {J Cheminform},
volume = {7},
number = {1},
pages = {23},
issn = {1758-2946},
doi = {10.1186/s13321-015-0068-4},
langid = {english}
}
@article{irwin:2005,
title = {{{ZINC}} − {{A Free Database}} of {{Commercially Available Compounds}} for {{Virtual Screening}}},
author = {Irwin, John J. and Shoichet, Brian K.},
date = {2005-01-01},
journaltitle = {J. Chem. Inf. Model.},
volume = {45},
number = {1},
pages = {177--182},
issn = {1549-9596, 1549-960X},
doi = {10.1021/ci049714+},
langid = {english}
}
@online{jchembase,
title = {{{JChem Base}} | {{Chemaxon Docs}}},
url = {https://docs.chemaxon.com/display/docs/jchem-base.md},
urldate = {2022-03-17}
}
@article{kerber:2006,
title = {If {{It}}'s {{Resonance}}, {{What Is Resonating}}?},
author = {Kerber, Robert C.},
date = {2006-02},
journaltitle = {J. Chem. Educ.},
volume = {83},
number = {2},
pages = {223},
issn = {0021-9584, 1938-1328},
doi = {10.1021/ed083p223},
langid = {english}
}
@article{kim:2016,
title = {{{PubChem Substance}} and {{Compound}} Databases},
author = {Kim, Sunghwan and Thiessen, Paul A. and Bolton, Evan E. and Chen, Jie and Fu, Gang and Gindulyte, Asta and Han, Lianyi and He, Jane and He, Siqian and Shoemaker, Benjamin A. and Wang, Jiyao and Yu, Bo and Zhang, Jian and Bryant, Stephen H.},
date = {2016-01-04},
journaltitle = {Nucleic Acids Res},
volume = {44},
number = {D1},
pages = {D1202-D1213},
issn = {0305-1048, 1362-4962},
doi = {10.1093/nar/gkv951},
langid = {english}
}
@article{lewis:1916,
title = {The {{Atom}} and the {{Molecule}}},
author = {Lewis, Gilbert},
date = {1916},
journaltitle = {J. Am. Chem. Soc.},
number = {38},
pages = {672},
doi = {10.1021/ja02261a002}
}
@article{lin:2019,
title = {{{BigSMILES}}: {{A Structurally-Based Line Notation}} for {{Describing Macromolecules}}},
shorttitle = {{{BigSMILES}}},
author = {Lin, Tzyy-Shyang and Coley, Connor W. and Mochigase, Hidenobu and Beech, Haley K. and Wang, Wencong and Wang, Zi and Woods, Eliot and Craig, Stephen L. and Johnson, Jeremiah A. and Kalow, Julia A. and Jensen, Klavs F. and Olsen, Bradley D.},
date = {2019-09-25},
journaltitle = {ACS Cent. Sci.},
volume = {5},
number = {9},
pages = {1523--1531},
issn = {2374-7943, 2374-7951},
doi = {10.1021/acscentsci.9b00476},
langid = {english}
}
@online{mayfield:2022,
title = {{{CXSMILES Gotchas}} – {{Part}} 1: {{Bond Indexes}} – {{NextMove Software}}},
author = {Mayfield, John},
url = {https://nextmovesoftware.com/blog/2022/04/08/cxsmiles-gotchas-part-1-bond-indexes/},
urldate = {2022-09-11},
organization = {{NextMove Software Blog}}
}
@article{mislow:1984,
title = {Stereoisomerism and Local Chirality},
author = {Mislow, Kurt and Siegel, Jay},
date = {1984-05},
journaltitle = {J. Am. Chem. Soc.},
volume = {106},
number = {11},
pages = {3319--3328},
issn = {0002-7863, 1520-5126},
doi = {10.1021/ja00323a043},
langid = {english}
}
@online{misraC,
title = {{{MISRA Website}}},
url = {https://www.misra.org.uk/},
urldate = {2022-03-18}
}
@article{murray-rust:2011,
title = {{{CML}}: {{Evolution}} and Design},
shorttitle = {{{CML}}},
author = {Murray-Rust, Peter and Rzepa, Henry S},
date = {2011-12},
journaltitle = {J Cheminform},
volume = {3},
number = {1},
pages = {44},
issn = {1758-2946},
doi = {10.1186/1758-2946-3-44},
langid = {english}
}
@article{oboyle:2011,
title = {Open {{Babel}}: {{An}} Open Chemical Toolbox},
shorttitle = {Open {{Babel}}},
author = {O'Boyle, Noel M and Banck, Michael and James, Craig A and Morley, Chris and Vandermeersch, Tim and Hutchison, Geoffrey R},
date = {2011-12},
journaltitle = {J. Cheminform.},
volume = {3},
number = {1},
pages = {33},
issn = {1758-2946},
doi = {10.1186/1758-2946-3-33},
langid = {english}
}
@article{oboyle:2012,
title = {Towards a {{Universal SMILES}} Representation - {{A}} Standard Method to Generate Canonical {{SMILES}} Based on the {{InChI}}},
author = {O’Boyle, Noel M},
date = {2012},
journaltitle = {J. Cheminform.},
volume = {4},
number = {1},
pages = {22},
issn = {1758-2946},
doi = {10.1186/1758-2946-4-22},
langid = {english}
}
@online{oetk,
title = {{{OEChem TK}} | {{OEChem Toolkit}} | {{Cheminformatics}}},
url = {https://www.eyesopen.com/oechem-tk},
urldate = {2022-03-17}
}
@online{opensmiles,
title = {{{OpenSMILES Home Page}}},
url = {http://opensmiles.org/},
urldate = {2022-03-17}
}
@article{parr:2014,
title = {Adaptive {{LL}}(*) {{Parsing}}: {{The Power}} of {{Dynamic Analysis}}},
author = {Parr, Terence and Harwell, Sam and Fisher, Kathleen},
date = {2014-10-15},
journaltitle = {ACM SIGPLAN Not.},
volume = {49},
number = {10},
pages = {579--598},
doi = {10.1145/2714064.2660202},
langid = {english}
}
@online{periodicTable,
title = {Periodic {{Table}} of {{Elements}} - {{IUPAC}} | {{International Union}} of {{Pure}} and {{Applied Chemistry}}},
url = {https://iupac.org/what-we-do/periodic-table-of-elements/},
urldate = {2022-03-18}
}
@incollection{randic:2018,
title = {Aromaticity {{Revisited}}},
booktitle = {Advances in {{Quantum Chemistry}}},
author = {Randić, Milan},
date = {2018},
volume = {77},
pages = {167--199},
publisher = {{Elsevier}},
doi = {10.1016/bs.aiq.2017.09.001},
isbn = {978-0-12-813710-9},
langid = {english}
}
@online{rdkit,
title = {{{RDKit}}},
url = {https://www.rdkit.org/},
urldate = {2022-03-17}
}
@article{sageson:1997,
title = {Names and Symbols of Transfermium Elements ({{IUPAC Recommendations}} 1997)},
author = {Sageson, A. M.},
date = {1997-01-01},
journaltitle = {Pure Appl. Chem.},
volume = {69},
number = {12},
pages = {2471--2474},
issn = {1365-3075, 0033-4545},
doi = {10.1351/pac199769122471},
langid = {english}
}
@online{smilesPlusGitHub,
title = {{{IUPAC SMILES}}+},
url = {https://github.com/IUPAC/IUPAC_SMILES_plus},
urldate = {2022-03-17}
}
@online{smilesPlusSpecification,
title = {{{IUPAC SMILES}}+ {{Specification}}},
url = {https://iupac.org/projects/project-details/?project_nr=2019-002-2-024},
urldate = {2022-03-17}
}
@article{sousa:2021,
title = {Generative {{Deep Learning}} for {{Targeted Compound Design}}},
author = {Sousa, Tiago and Correia, João and Pereira, Vítor and Rocha, Miguel},
date = {2021-11-22},
journaltitle = {J. Chem. Inf. Model.},
volume = {61},
number = {11},
pages = {5343--5361},
issn = {1549-9596, 1549-960X},
doi = {10.1021/acs.jcim.0c01496},
langid = {english}
}
@article{steinbeck:2003,
title = {The {{Chemistry Development Kit}} ({{CDK}}): {{An Open-Source Java Library}} for {{Chemo-}} and {{Bioinformatics}}},
shorttitle = {The {{Chemistry Development Kit}} ({{CDK}})},
author = {Steinbeck, Christoph and Han, Yongquan and Kuhn, Stefan and Horlacher, Oliver and Luttmann, Edgar and Willighagen, Egon},
date = {2003-03-01},
journaltitle = {J. Chem. Inf. Comput. Sci.},
volume = {43},
number = {2},
pages = {493--500},
issn = {0095-2338},
doi = {10.1021/ci025584y},
langid = {english}
}
@book{thain:2020,
title = {Introduction to Compilers and Language Design},
author = {Thain, Douglas},
date = {2020},
edition = {Second Edition},
publisher = {{University of Notre Dame}},
url = {https://www3.nd.edu/~dthain/compilerbook/},
isbn = {9798655180260},
langid = {english},
annotation = {OCLC: 1236392116}
}
@article{weininger:1988,
title = {{{SMILES}}, a Chemical Language and Information System. 1. {{Introduction}} to Methodology and Encoding Rules},
author = {Weininger, David},
date = {1988-02-01},
journaltitle = {J. Chem. Inf. Model.},
volume = {28},
number = {1},
pages = {31--36},
issn = {1549-9596},
doi = {10.1021/ci00057a005},
langid = {english}
}
@article{weininger:1989,
title = {{{SMILES}}. 2. {{Algorithm}} for Generation of Unique {{SMILES}} Notation},
author = {Weininger, David and Weininger, Arthur and Weininger, Joseph L.},
date = {1989-05-01},
journaltitle = {J. Chem. Inf. Model.},
volume = {29},
number = {2},
pages = {97--101},
issn = {1549-9596},
doi = {10.1021/ci00062a008},
langid = {english}
}
@incollection{weininger:2003,
title = {{{SMILES-A Language}} for {{Molecules}} and {{Reactions}}},
booktitle = {Handbook of {{Chemoinformatics}}},
author = {Weininger, David},
editor = {Gasteiger, Johann},
date = {2003},
pages = {80--102},
publisher = {{Wiley-VCH Verlag GmbH}},
location = {{Weinheim, Germany}},
doi = {10.1002/9783527618279.ch5},
isbn = {978-3-527-61827-9 978-3-527-30680-0},
langid = {english}
}
@online{wikipediaCAS,
title = {Talk:{{CAS Registry Number}} - {{Wikipedia}}},
url = {https://en.wikipedia.org/wiki/Talk:CAS_Registry_Number},
urldate = {2022-03-17}
}
@article{wilkinson:2016,
title = {The {{FAIR Guiding Principles}} for Scientific Data Management and Stewardship},
author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Mercè and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J.G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and ’t Hoen, Peter A.C and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
options = {useprefix=true},
date = {2016-12},
journaltitle = {Sci Data},
volume = {3},
number = {1},
pages = {160018},
issn = {2052-4463},
doi = {10.1038/sdata.2016.18},
langid = {english}
}
@article{wiswesser:1968,
title = {107 {{Years}} of {{Line-Formula Notations}} (1861-1968)},
author = {Wiswesser, William J.},
date = {1968-08},
journaltitle = {J. Chem. Doc.},
volume = {8},
number = {3},
pages = {146--150},
issn = {0021-9576, 1541-5732},
doi = {10.1021/c160030a007},
langid = {english}
}
@online{xmlspec,
title = {Extensible {{Markup Language}} ({{XML}}) 1.0 ({{Fifth Edition}})},
url = {https://www.w3.org/TR/REC-xml/},
urldate = {2023-01-20}
}