rdworks 0.25.7__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (69) hide show
  1. rdworks/__init__.py +35 -0
  2. rdworks/autograph/__init__.py +4 -0
  3. rdworks/autograph/autograph.py +184 -0
  4. rdworks/autograph/centroid.py +90 -0
  5. rdworks/autograph/dynamictreecut.py +135 -0
  6. rdworks/autograph/nmrclust.py +123 -0
  7. rdworks/autograph/rckmeans.py +74 -0
  8. rdworks/bitqt/__init__.py +1 -0
  9. rdworks/bitqt/bitqt.py +355 -0
  10. rdworks/conf.py +374 -0
  11. rdworks/descriptor.py +36 -0
  12. rdworks/display.py +206 -0
  13. rdworks/ionized.py +170 -0
  14. rdworks/matchedseries.py +260 -0
  15. rdworks/mol.py +1522 -0
  16. rdworks/mollibr.py +887 -0
  17. rdworks/pka.py +38 -0
  18. rdworks/predefined/Asinex_fragment.xml +20 -0
  19. rdworks/predefined/Astex_RO3.xml +16 -0
  20. rdworks/predefined/Baell2010_PAINS/Baell2010A.xml +52 -0
  21. rdworks/predefined/Baell2010_PAINS/Baell2010B.xml +169 -0
  22. rdworks/predefined/Baell2010_PAINS/Baell2010C.xml +1231 -0
  23. rdworks/predefined/Baell2010_PAINS/PAINS-less-than-015-hits.xml +2048 -0
  24. rdworks/predefined/Baell2010_PAINS/PAINS-less-than-150-hits.xml +278 -0
  25. rdworks/predefined/Baell2010_PAINS/PAINS-more-than-150-hits.xml +83 -0
  26. rdworks/predefined/Baell2010_PAINS/makexml.py +70 -0
  27. rdworks/predefined/Brenk2008_Dundee/makexml.py +21 -0
  28. rdworks/predefined/CNS.xml +18 -0
  29. rdworks/predefined/ChEMBL_Walters/BMS.xml +543 -0
  30. rdworks/predefined/ChEMBL_Walters/Dundee.xml +318 -0
  31. rdworks/predefined/ChEMBL_Walters/Glaxo.xml +168 -0
  32. rdworks/predefined/ChEMBL_Walters/Inpharmatica.xml +276 -0
  33. rdworks/predefined/ChEMBL_Walters/LINT.xml +174 -0
  34. rdworks/predefined/ChEMBL_Walters/MLSMR.xml +351 -0
  35. rdworks/predefined/ChEMBL_Walters/PAINS.xml +1446 -0
  36. rdworks/predefined/ChEMBL_Walters/SureChEMBL.xml +501 -0
  37. rdworks/predefined/ChEMBL_Walters/makexml.py +40 -0
  38. rdworks/predefined/Hann1999_Glaxo/Hann1999.xml +168 -0
  39. rdworks/predefined/Hann1999_Glaxo/Hann1999Acid.xml +102 -0
  40. rdworks/predefined/Hann1999_Glaxo/Hann1999Base.xml +6 -0
  41. rdworks/predefined/Hann1999_Glaxo/Hann1999ElPh.xml +6 -0
  42. rdworks/predefined/Hann1999_Glaxo/Hann1999NuPh.xml +6 -0
  43. rdworks/predefined/Hann1999_Glaxo/makexml.py +83 -0
  44. rdworks/predefined/Kazius2005/Kazius2005.xml +114 -0
  45. rdworks/predefined/Kazius2005/makexml.py +66 -0
  46. rdworks/predefined/ZINC_druglike.xml +24 -0
  47. rdworks/predefined/ZINC_fragment.xml +14 -0
  48. rdworks/predefined/ZINC_leadlike.xml +15 -0
  49. rdworks/predefined/fragment.xml +7 -0
  50. rdworks/predefined/ionized/simple_smarts_pattern.csv +57 -0
  51. rdworks/predefined/ionized/smarts_pattern.csv +107 -0
  52. rdworks/predefined/misc/makexml.py +119 -0
  53. rdworks/predefined/misc/reactive-part-2.xml +104 -0
  54. rdworks/predefined/misc/reactive-part-3.xml +74 -0
  55. rdworks/predefined/misc/reactive.xml +321 -0
  56. rdworks/readin.py +312 -0
  57. rdworks/rgroup.py +2173 -0
  58. rdworks/scaffold.py +520 -0
  59. rdworks/std.py +143 -0
  60. rdworks/stereoisomers.py +127 -0
  61. rdworks/tautomers.py +20 -0
  62. rdworks/units.py +63 -0
  63. rdworks/utils.py +495 -0
  64. rdworks/xml.py +260 -0
  65. rdworks-0.25.7.dist-info/METADATA +37 -0
  66. rdworks-0.25.7.dist-info/RECORD +69 -0
  67. rdworks-0.25.7.dist-info/WHEEL +5 -0
  68. rdworks-0.25.7.dist-info/licenses/LICENSE +21 -0
  69. rdworks-0.25.7.dist-info/top_level.txt +1 -0
rdworks/predefined/ChEMBL_Walters/SureChEMBL.xml ADDED
@@ -0,0 +1,501 @@
1
+ <?xml version="1.0" ?>
2
+ <SureChEMBL>
3
+ <substructure name="(1) 2,2-dimethyl-4,5-dicarboxy-dithiole">
4
+ <SMARTS>C1(C)(C)SC(C(=O)O)=C(C(=O)O)S1</SMARTS>
5
+ </substructure>
6
+ <substructure name="(2) 2,3,4_trihydroxyphenyl">
7
+ <SMARTS>c([OH])c([OH])c([OH])</SMARTS>
8
+ </substructure>
9
+ <substructure name="(3) 2,3,5_trihydroxyphenyl">
10
+ <SMARTS>c([OH])c([OH])cc([OH])</SMARTS>
11
+ </substructure>
12
+ <substructure name="(4) acid_anhydrides">
13
+ <SMARTS>C(=O)OC(=O)</SMARTS>
14
+ </substructure>
15
+ <substructure name="(5) acid_halides">
16
+ <SMARTS>[S,C](=[O,S])[F,Br,Cl,I]</SMARTS>
17
+ </substructure>
18
+ <substructure name="(6) Acridine">
19
+ <SMARTS>c1c2cc4ccccc4nc2ccc1</SMARTS>
20
+ </substructure>
21
+ <substructure name="(7) Active_Phosphate">
22
+ <SMARTS>P(=S)([OH1,O$(O[#6])])([OH1,O$(O[#6])])[S,O]</SMARTS>
23
+ </substructure>
24
+ <substructure name="(8) acyl_cyanide">
25
+ <SMARTS>C(=O)-C#N</SMARTS>
26
+ </substructure>
27
+ <substructure name="(9) Adjacent_Ring_Double_Bonds">
28
+ <SMARTS>[*;R]=[*;R]=[*;R]</SMARTS>
29
+ </substructure>
30
+ <substructure name="(10) Aldehyde">
31
+ <SMARTS>[#6][C!H0]=O</SMARTS>
32
+ </substructure>
33
+ <substructure name="(11) Aliphatic_Triflate">
34
+ <SMARTS>COS(=O)(=O)C(F)(F)F</SMARTS>
35
+ </substructure>
36
+ <substructure name="(12) alkyl_halides">
37
+ <SMARTS>[Br,Cl,I][CX4;CH,CH2]</SMARTS>
38
+ </substructure>
39
+ <substructure name="(13) AlkylEnamine">
40
+ <SMARTS>[C;H1$(C([#6;!$(C=O)])),H0$(C([#6;!$(C=O)])[#6;!$(C=O)])]=[CH1]!@N([#6;!$(C(=O))])[#6;!$(C(=O))]</SMARTS>
41
+ </substructure>
42
+ <substructure name="(14) Allene">
43
+ <SMARTS>*=C=*</SMARTS>
44
+ </substructure>
45
+ <substructure name="(15) Alpha_Halo_Carbonyl">
46
+ <SMARTS>[C;!$(C[N])](=O)!@[C;h1,h2;H1,H2][F,Cl,Br,I]</SMARTS>
47
+ </substructure>
48
+ <substructure name="(16) amidotetrazole">
49
+ <SMARTS>c1nnnn1C=O</SMARTS>
50
+ </substructure>
51
+ <substructure name="(17) Amino_Naphtalimide">
52
+ <SMARTS>c1(N)ccc(C(=O)NC3(=O))c(c3ccc2)c21</SMARTS>
53
+ </substructure>
54
+ <substructure name="(18) Aminonitrile">
55
+ <SMARTS>NC#N</SMARTS>
56
+ </substructure>
57
+ <substructure name="(19) Anhydride">
58
+ <SMARTS>[#6]C(=O)OC(=O)[#6]</SMARTS>
59
+ </substructure>
60
+ <substructure name="(20) Any_Carbazide">
61
+ <SMARTS>O=*N=[N+]=[N-]</SMARTS>
62
+ </substructure>
63
+ <substructure name="(21) aromatic_azides">
64
+ <SMARTS>cN=N=N</SMARTS>
65
+ </substructure>
66
+ <substructure name="(22) Azanitrone">
67
+ <SMARTS>N=[N+]([O-])C</SMARTS>
68
+ </substructure>
69
+ <substructure name="(23) azoalkanals">
70
+ <SMARTS>[N;R0]=[N;R0]CC=O</SMARTS>
71
+ </substructure>
72
+ <substructure name="(24) Azobenzene">
73
+ <SMARTS>c1ccccc1[N!r]=[N!r]c2ccccc2</SMARTS>
74
+ </substructure>
75
+ <substructure name="(25) Azocyanamide">
76
+ <SMARTS>[N;R0]=[N;R0]C#N</SMARTS>
77
+ </substructure>
78
+ <substructure name="(26) b-Carbonyl_Quaternary_Nitrogen">
79
+ <SMARTS>C(=O)CC[N+,n+]</SMARTS>
80
+ </substructure>
81
+ <substructure name="(27) benzylic_quaternary_nitrogen">
82
+ <SMARTS>cC[N+,NX4]</SMARTS>
83
+ </substructure>
84
+ <substructure name="(28) beta-carbonyl_quaternary_nitrogen">
85
+ <SMARTS>C(=O)C[N+,n+,NX4,nX4]</SMARTS>
86
+ </substructure>
87
+ <substructure name="(29) Beta-Fluoro-ethyl-ON">
88
+ <SMARTS>[C;H2$(CF),H1$(C(F)F)]!@[CH2][N,O]</SMARTS>
89
+ </substructure>
90
+ <substructure name="(30) biotin_analogue">
91
+ <SMARTS>C12C(NC(N1)=O)CSC2</SMARTS>
92
+ </substructure>
93
+ <substructure name="(31) carbazides">
94
+ <SMARTS>C(=O)N=N=N</SMARTS>
95
+ </substructure>
96
+ <substructure name="(32) carbodiimides">
97
+ <SMARTS>N=C=N</SMARTS>
98
+ </substructure>
99
+ <substructure name="(33) CCl3-CHO_releasing">
100
+ <SMARTS>C(Cl)(Cl)(Cl)C([O,S])[NX3]</SMARTS>
101
+ </substructure>
102
+ <substructure name="(34) Chloramidine">
103
+ <SMARTS>[Cl]C([C&amp;R0])=N</SMARTS>
104
+ </substructure>
105
+ <substructure name="(35) Conjugated_Dithioether">
106
+ <SMARTS>SC(=[!r])S</SMARTS>
107
+ </substructure>
108
+ <substructure name="(36) Crown_Ether_12CRO4">
109
+ <SMARTS>O1CCOCCOCCOCC1</SMARTS>
110
+ </substructure>
111
+ <substructure name="(37) Crown_Ether_15CRO5">
112
+ <SMARTS>O1CCOCCOCCOCCOCC1</SMARTS>
113
+ </substructure>
114
+ <substructure name="(38) Crown_Ether_16CRO6">
115
+ <SMARTS>O1CCOCCOCCOCCOCCOCC1</SMARTS>
116
+ </substructure>
117
+ <substructure name="(39) crown_ethers">
118
+ <SMARTS>[O;R1][C;R1][C;R1][O;R1][C;R1][C;R1][O;R1]</SMARTS>
119
+ </substructure>
120
+ <substructure name="(40) cyanamide">
121
+ <SMARTS>N[CH2]C#N</SMARTS>
122
+ </substructure>
123
+ <substructure name="(41) Cyanophosphonate">
124
+ <SMARTS>P(OCC)(OCC)(=O)C#N</SMARTS>
125
+ </substructure>
126
+ <substructure name="(42) Cyanohydrin">
127
+ <SMARTS>N#CC[OH1]</SMARTS>
128
+ </substructure>
129
+ <substructure name="(43) di_and_triphosphates">
130
+ <SMARTS>P(=O)([OH])OP(=O)[OH]</SMARTS>
131
+ </substructure>
132
+ <substructure name="(44) Diacetylene">
133
+ <SMARTS>C#CC#C</SMARTS>
134
+ </substructure>
135
+ <substructure name="(45) Diazoalkane">
136
+ <SMARTS>C=[N+]=[N-]</SMARTS>
137
+ </substructure>
138
+ <substructure name="(46) Diazonium_Salt">
139
+ <SMARTS>[N+]#N</SMARTS>
140
+ </substructure>
141
+ <substructure name="(47) Diene">
142
+ <SMARTS>C!@=[CH1]-C!@=[CH1]-[CX3](=O)</SMARTS>
143
+ </substructure>
144
+ <substructure name="(48) Dinitrobenzene_1">
145
+ <SMARTS>c1c([N+](=O)[O-])c([N+](=O)[O-])ccc1</SMARTS>
146
+ </substructure>
147
+ <substructure name="(49) Dinitrobenzene_2">
148
+ <SMARTS>c1c([N+](=O)[O-])ccc([N+](=O)[O-])c1</SMARTS>
149
+ </substructure>
150
+ <substructure name="(50) Dinitrobenzene_3">
151
+ <SMARTS>c1c([N+](=O)[O-])cc([N+](=O)[O-])cc1</SMARTS>
152
+ </substructure>
153
+ <substructure name="(51) disulfides">
154
+ <SMARTS>[SX2][SX2]</SMARTS>
155
+ </substructure>
156
+ <substructure name="(52) Dithiocarbamate">
157
+ <SMARTS>NC(=S)S</SMARTS>
158
+ </substructure>
159
+ <substructure name="(53) Dithiole-2-thione">
160
+ <SMARTS>S1SC=CC1=S</SMARTS>
161
+ </substructure>
162
+ <substructure name="(54) Dithiole-3-thione">
163
+ <SMARTS>S1C=CSC1=C</SMARTS>
164
+ </substructure>
165
+ <substructure name="(55) Dithiomethylene_acetal">
166
+ <SMARTS>S[C;!$(C=*)]S</SMARTS>
167
+ </substructure>
168
+ <substructure name="(56) Enyne">
169
+ <SMARTS>C=!@CC#C</SMARTS>
170
+ </substructure>
171
+ <substructure name="(57) epoxides,_thioepoxides,_aziridines">
172
+ <SMARTS>C1[O,S,N]C1</SMARTS>
173
+ </substructure>
174
+ <substructure name="(58) ester_of_HOBT">
175
+ <SMARTS>C(=O)Onnn</SMARTS>
176
+ </substructure>
177
+ <substructure name="(59) Flavin">
178
+ <SMARTS>c1cccc(NC(=NC(=[N,S,O])NC(=O)3)C3=N2)c12</SMARTS>
179
+ </substructure>
180
+ <substructure name="(60) Fluorescein">
181
+ <SMARTS>c1cc(O)cc(OC(=CC(=O)C=C3)C3=C2)c12</SMARTS>
182
+ </substructure>
183
+ <substructure name="(61) Fluorinated_Carbon_1">
184
+ <SMARTS>C(C(CF)F)F</SMARTS>
185
+ </substructure>
186
+ <substructure name="(62) Fluorinated_Carbon_2">
187
+ <SMARTS>C(C(F)F)(F)F</SMARTS>
188
+ </substructure>
189
+ <substructure name="(63) four_member_lactones">
190
+ <SMARTS>C1(=O)OCC1</SMARTS>
191
+ </substructure>
192
+ <substructure name="(64) geminal_amines">
193
+ <SMARTS>[NH1;!r][CX4][NH1;!r]</SMARTS>
194
+ </substructure>
195
+ <substructure name="(65) geminal_dinitriles">
196
+ <SMARTS>N#CCC#N</SMARTS>
197
+ </substructure>
198
+ <substructure name="(66) halo-pyridine,_-diazoles_and_-triazoles">
199
+ <SMARTS>[Cl,Br,I]c1[c,n][c,n][c,n][c,n]n1</SMARTS>
200
+ </substructure>
201
+ <substructure name="(67) hydrazothiourea">
202
+ <SMARTS>N=NC(S)N</SMARTS>
203
+ </substructure>
204
+ <substructure name="(68) Imidazolium">
205
+ <SMARTS>c1[n+]([#6])ccn1([#6])</SMARTS>
206
+ </substructure>
207
+ <substructure name="(69) Imine2">
208
+ <SMARTS>[#6,#8,#16]-[CH1]=[NH1]</SMARTS>
209
+ </substructure>
210
+ <substructure name="(70) imines_(not_ring)">
211
+ <SMARTS>[#6][C;R0](=[N;R0,O0])[#6]</SMARTS>
212
+ </substructure>
213
+ <substructure name="(71) isocyanates_and_isothiocyanates">
214
+ <SMARTS>N=C=[S,O]</SMARTS>
215
+ </substructure>
216
+ <substructure name="(72) isonitrile">
217
+ <SMARTS>[N+]#[C-]</SMARTS>
218
+ </substructure>
219
+ <substructure name="(73) ketene">
220
+ <SMARTS>C=C=O</SMARTS>
221
+ </substructure>
222
+ <substructure name="(74) Lawesson_Reagent_Derivatives">
223
+ <SMARTS>P(=S)(S)S</SMARTS>
224
+ </substructure>
225
+ <substructure name="(75) methylidene-1,3-dithiole">
226
+ <SMARTS>S1C=CSC1=S</SMARTS>
227
+ </substructure>
228
+ <substructure name="(76) Michael_Phenyl_Ketone">
229
+ <SMARTS>c1ccccc1C(=O)C=!@CC(=O)!@*</SMARTS>
230
+ </substructure>
231
+ <substructure name="(77) N-halo">
232
+ <SMARTS>[NX3,NX4][F,Cl,Br,I]</SMARTS>
233
+ </substructure>
234
+ <substructure name="(78) Nitrobenz-azadiazole_1">
235
+ <SMARTS>c1ccc(n[o,s]n2)c2c1[N+](=O)[O-]</SMARTS>
236
+ </substructure>
237
+ <substructure name="(79) Nitrobenz-azadiazole_2">
238
+ <SMARTS>c1c([N+](=O)[O-])cc(n[o,s]n2)c2c1</SMARTS>
239
+ </substructure>
240
+ <substructure name="(80) nitrosamine">
241
+ <SMARTS>N-[N;X2](=O)</SMARTS>
242
+ </substructure>
243
+ <substructure name="(81) nitroso">
244
+ <SMARTS>[N&amp;D2](=O)</SMARTS>
245
+ </substructure>
246
+ <substructure name="(82) noname">
247
+ <SMARTS>N1=C[S,NH1]C(=[C,N,P][C,N,O,P])C1(=O)</SMARTS>
248
+ </substructure>
249
+ <substructure name="(83) N-Oxide_aliphatic">
250
+ <SMARTS>[N+!$(N=O)][O-X1]</SMARTS>
251
+ </substructure>
252
+ <substructure name="(84) N-S_(not_sulfonamides)">
253
+ <SMARTS>[#6][S!$(S(~[OD1])~[OD1])][N;H0]</SMARTS>
254
+ </substructure>
255
+ <substructure name="(85) Orthoester">
256
+ <SMARTS>C(O)(O)[OH]</SMARTS>
257
+ </substructure>
258
+ <substructure name="(86) o-tertbutylphenol">
259
+ <SMARTS>c1c([OH1])c(C(C)(C)C)ccc1</SMARTS>
260
+ </substructure>
261
+ <substructure name="(87) Oxobenzothiepine">
262
+ <SMARTS>C1(=O)C=CCSC=C1</SMARTS>
263
+ </substructure>
264
+ <substructure name="(88) P_or_S_Halides">
265
+ <SMARTS>[P,S][Cl,Br,F,I]</SMARTS>
266
+ </substructure>
267
+ <substructure name="(89) p-Aminoaryl_diazo">
268
+ <SMARTS>Nc1aaa(N!@=N)aa1</SMARTS>
269
+ </substructure>
270
+ <substructure name="(90) PCP">
271
+ <SMARTS>PCP</SMARTS>
272
+ </substructure>
273
+ <substructure name="(91) paranitrophenyl_esters">
274
+ <SMARTS>C(=O)Oc1ccc([N+](=O)[O-])cc1</SMARTS>
275
+ </substructure>
276
+ <substructure name="(92) pentahalophenyl">
277
+ <SMARTS>c1c([F,Cl])c([F,Cl])c([F,Cl])c([F,Cl])c1([F,Cl])</SMARTS>
278
+ </substructure>
279
+ <substructure name="(93) pentafluorophenyl_esters">
280
+ <SMARTS>C(=O)Oc1c(F)c(F)c(F)c(F)c1(F)</SMARTS>
281
+ </substructure>
282
+ <substructure name="(94) peroxide">
283
+ <SMARTS>[#8]~[#8]</SMARTS>
284
+ </substructure>
285
+ <substructure name="(95) Phenanthrene">
286
+ <SMARTS>c12cccc3c1c4c(cc3)cccc4cc2</SMARTS>
287
+ </substructure>
288
+ <substructure name="(96) Phenylester">
289
+ <SMARTS>C(=O)!@Oc1ccccc1</SMARTS>
290
+ </substructure>
291
+ <substructure name="(97) phosphonate_esters">
292
+ <SMARTS>[#6]P(=O)(~O)O[#6]</SMARTS>
293
+ </substructure>
294
+ <substructure name="(98) phosphoramides">
295
+ <SMARTS>NP(=O)(N)N</SMARTS>
296
+ </substructure>
297
+ <substructure name="(99) phosphorane">
298
+ <SMARTS>C=P</SMARTS>
299
+ </substructure>
300
+ <substructure name="(100) Phosphorus_Halide">
301
+ <SMARTS>[S,P][F,Cl,Br,I]</SMARTS>
302
+ </substructure>
303
+ <substructure name="(101) Polyene">
304
+ <SMARTS>C=!@CC=!@C</SMARTS>
305
+ </substructure>
306
+ <substructure name="(102) polyenes">
307
+ <SMARTS>C=CC=CC=CC=C</SMARTS>
308
+ </substructure>
309
+ <substructure name="(103) polyene_chain_between_aromatics">
310
+ <SMARTS>cC=CC=CC=Cc</SMARTS>
311
+ </substructure>
312
+ <substructure name="(104) polyines">
313
+ <SMARTS>CC#CC#CC</SMARTS>
314
+ </substructure>
315
+ <substructure name="(105) Polynuclear_Aromatic_1">
316
+ <SMARTS>c1cccc(cc(cccc2)c2c3)c13</SMARTS>
317
+ </substructure>
318
+ <substructure name="(106) Polynuclear_Aromatic_2">
319
+ <SMARTS>c1cccc(c(cccc2)c2cc3)c13</SMARTS>
320
+ </substructure>
321
+ <substructure name="(107) Polysulfide">
322
+ <SMARTS>*[SX2][SX2][SX2]*</SMARTS>
323
+ </substructure>
324
+ <substructure name="(108) Sulphur_Halide">
325
+ <SMARTS>[#16][F,Cl,Br,I]</SMARTS>
326
+ </substructure>
327
+ <substructure name="(109) pyrene_fragments">
328
+ <SMARTS>c1c2cccc3c2c4c(cc3)cccc4c1</SMARTS>
329
+ </substructure>
330
+ <substructure name="(110) Pyrylium">
331
+ <SMARTS>c1ccc[o+]c1</SMARTS>
332
+ </substructure>
333
+ <substructure name="(111) reactive_carbonyls">
334
+ <SMARTS>[C;!r](=[O,S])[S;!r]</SMARTS>
335
+ </substructure>
336
+ <substructure name="(112) reactive_carbonyls">
337
+ <SMARTS>[C;!r](=[O,S])[CD2;!r][F,Br,Cl]</SMARTS>
338
+ </substructure>
339
+ <substructure name="(113) Ring_Triple_Bond">
340
+ <SMARTS>[C,c;R]#[C,c;R]</SMARTS>
341
+ </substructure>
342
+ <substructure name="(114) S=N_(not_ring)">
343
+ <SMARTS>[S;R0]=[N;R0]</SMARTS>
344
+ </substructure>
345
+ <substructure name="(115) Sulfonate_Ester">
346
+ <SMARTS>O=[SX4](=O)OC</SMARTS>
347
+ </substructure>
348
+ <substructure name="(116) sulfonyl_cyanide">
349
+ <SMARTS>S(=O)(=O)C#N</SMARTS>
350
+ </substructure>
351
+ <substructure name="(117) Sulphate_Ester">
352
+ <SMARTS>COS(=O)O[C,c]</SMARTS>
353
+ </substructure>
354
+ <substructure name="(118) sulphonates">
355
+ <SMARTS>COS(=O)(=O)[C,c]</SMARTS>
356
+ </substructure>
357
+ <substructure name="(119) Sulphur_Nitrogen_single_bond">
358
+ <SMARTS>[SX2H0]!@[N]</SMARTS>
359
+ </substructure>
360
+ <substructure name="(120) Tetraazinane">
361
+ <SMARTS>C1NNC=NN1</SMARTS>
362
+ </substructure>
363
+ <substructure name="(121) Thiocyanate">
364
+ <SMARTS>SC#N</SMARTS>
365
+ </substructure>
366
+ <substructure name="(122) thioesters">
367
+ <SMARTS>C[O,S;R0][C;R0](=S)</SMARTS>
368
+ </substructure>
369
+ <substructure name="(123) thioles_(not_aromatic)">
370
+ <SMARTS>[!a][SX2;H1]</SMARTS>
371
+ </substructure>
372
+ <substructure name="(124) Thiophosphothionate">
373
+ <SMARTS>P(=S)(-[S;H1,H0$(S(P)C)])(-[O;H1,H0$(O(P)C)])(-N(C)C)</SMARTS>
374
+ </substructure>
375
+ <substructure name="(125) thiourea">
376
+ <SMARTS>[N;!r][C;!r](=S)[N;!r]</SMARTS>
377
+ </substructure>
378
+ <substructure name="(126) Three_Membered_Heterocycle">
379
+ <SMARTS>*1[O,S]*1</SMARTS>
380
+ </substructure>
381
+ <substructure name="(127) Tri_Pentavalent_S">
382
+ <SMARTS>[#16v3,#16v5]</SMARTS>
383
+ </substructure>
384
+ <substructure name="(128) Triacyloxime">
385
+ <SMARTS>C(=O)N(C(=O))OC(=O)</SMARTS>
386
+ </substructure>
387
+ <substructure name="(129) Triazole">
388
+ <SMARTS>c1cnnn1!@C!@[NH1][#6]</SMARTS>
389
+ </substructure>
390
+ <substructure name="(130) triflate">
391
+ <SMARTS>OS(=O)(=O)(C(F)(F)(F))</SMARTS>
392
+ </substructure>
393
+ <substructure name="(131) Triphenyl_Boranyl">
394
+ <SMARTS>B(c1ccccc1)(c2ccccc2)c3ccccc3</SMARTS>
395
+ </substructure>
396
+ <substructure name="(132) triphenylphosphines">
397
+ <SMARTS>P(c1aaaaa1)(c1aaaaa1)(c1aaaaa1)</SMARTS>
398
+ </substructure>
399
+ <substructure name="(133) Triphenyl_Silyl">
400
+ <SMARTS>[Si](c1ccccc1)(c2ccccc2)(c3ccccc3)</SMARTS>
401
+ </substructure>
402
+ <substructure name="(134) Vinyl_Halide">
403
+ <SMARTS>[Cl,Br,I]C=[!O!R]</SMARTS>
404
+ </substructure>
405
+ <substructure name="(135) Vinyl_Sulphone">
406
+ <SMARTS>[#6][CH1]!@=[CH1][S;H1,H0$(S(C)C)](=O)(=O)</SMARTS>
407
+ </substructure>
408
+ <substructure name="(136) sulphates">
409
+ <SMARTS>[#6]S(=O)(=O)O</SMARTS>
410
+ </substructure>
411
+ <substructure name="(137) tropone">
412
+ <SMARTS>C1C(=O)C=CC=CC=1</SMARTS>
413
+ </substructure>
414
+ <substructure name="(138) Oxime">
415
+ <SMARTS>[#6]C(=!@N[$(OC),$([OH])])[#6]</SMARTS>
416
+ </substructure>
417
+ <substructure name="(139) hydrazone">
418
+ <SMARTS>[#6]C(=!@NNa)[#6]</SMARTS>
419
+ </substructure>
420
+ <substructure name="(140) Nitrosone_not_nitro">
421
+ <SMARTS>[$(N(~!@[#6])!@O);!$([N+]([O-])=O)]</SMARTS>
422
+ </substructure>
423
+ <substructure name="(141) Thiocarbonyl_substructure">
424
+ <SMARTS>C=S</SMARTS>
425
+ </substructure>
426
+ <substructure name="(142) enamine_like">
427
+ <SMARTS>C=[NH]</SMARTS>
428
+ </substructure>
429
+ <substructure name="(143) analine">
430
+ <SMARTS>c1ccccc1[NH2,NH3+]</SMARTS>
431
+ </substructure>
432
+ <substructure name="(144) acid_anhydrides_2">
433
+ <SMARTS>[#6]C(=O)!@OC(=!@[N,O])[#6]</SMARTS>
434
+ </substructure>
435
+ <substructure name="(145) trifluroacetate_amide">
436
+ <SMARTS>FC(F)(F)C(=O)N</SMARTS>
437
+ </substructure>
438
+ <substructure name="(146) triple_bond">
439
+ <SMARTS>[#6]C#[CH]</SMARTS>
440
+ </substructure>
441
+ <substructure name="(147) Allene">
442
+ <SMARTS>C=C=C</SMARTS>
443
+ </substructure>
444
+ <substructure name="(148) thiatetrazolidine">
445
+ <SMARTS>[$(Sc1nnn[nH,n-]1),$(Sc1nn[nH,n-]n1)]</SMARTS>
446
+ </substructure>
447
+ <substructure name="(149) glycol">
448
+ <SMARTS>[#6][O;R0][$(C([#6])[#6]),$([CH][#6]),$([CH2])][O;R0][#6]</SMARTS>
449
+ </substructure>
450
+ <substructure name="(150) oxy-amide">
451
+ <SMARTS>[#6]C(=O)!@C!@C(=O)N</SMARTS>
452
+ </substructure>
453
+ <substructure name="(151) formate_formide">
454
+ <SMARTS>O=[CH][O,N][#6]</SMARTS>
455
+ </substructure>
456
+ <substructure name="(152) pyranone">
457
+ <SMARTS>O=C1C=COC=C1</SMARTS>
458
+ </substructure>
459
+ <substructure name="(153) Coumarin">
460
+ <SMARTS>c1cc2C=CC(=O)Oc2cc1</SMARTS>
461
+ </substructure>
462
+ <substructure name="(154) aminothiazole">
463
+ <SMARTS>s1ccnc1[N!H0]</SMARTS>
464
+ </substructure>
465
+ <substructure name="(155) Thiazolidinone">
466
+ <SMARTS>O=C1CSCN1</SMARTS>
467
+ </substructure>
468
+ <substructure name="(156) Thiomorpholinedione">
469
+ <SMARTS>N1C(=O)CSCC1=O</SMARTS>
470
+ </substructure>
471
+ <substructure name="(157) oxepine">
472
+ <SMARTS>O1C=CC=CC=C1</SMARTS>
473
+ </substructure>
474
+ <substructure name="(158) phenylethene">
475
+ <SMARTS>c1ccccc1!@[CH]=!@[C!H0]</SMARTS>
476
+ </substructure>
477
+ <substructure name="(159) Ethene">
478
+ <SMARTS>C=[CH2]</SMARTS>
479
+ </substructure>
480
+ <substructure name="(160) cyclobutene">
481
+ <SMARTS>C1CC=C1</SMARTS>
482
+ </substructure>
483
+ <substructure name="(161) poly_sub_atomatic">
484
+ <SMARTS>*!@c1c(!@*)c(!@*)c(!@*)c(!@*)c1</SMARTS>
485
+ </substructure>
486
+ <substructure name="(162) Isotopes">
487
+ <SMARTS>[2#1,3#1,11C,11c,14C,14c,125I,32P,33P,35S]</SMARTS>
488
+ </substructure>
489
+ <substructure name="(163) Undesirable_Elements_Salts">
490
+ <SMARTS>[Ac,Ag,Am,Ar,As,At,Au,Ba,Be,Bi,Bk,Cd,Ce,Cf,Cm,Cr,Cs,Dy,Er,Eu,Fr,Ga,Gd,Ge,He,Hf,Ho,In,Ir,Kr,La,Lu,Mo,Nb,Nd,Ne,Ni,Np,Os,Pa,Pb,Pd,Pm,Po,Pr,Pt,Pu,Ra,Rb,Re,Rh,Rn,Ru,Sb,Sc,Se,Sm,Sr,Ta,Tb,Tc,Te,Th,Ti,Tl,Tm,U,V,W,Xe,Y,Yb,Zr]</SMARTS>
491
+ </substructure>
492
+ <substructure name="(164) Metal_Carbon_bond">
493
+ <SMARTS>[#6;$([#6]~[#3,#11,#12,#13,#19,#20,#26,#27,#28,#29,#30])]</SMARTS>
494
+ </substructure>
495
+ <substructure name="(165) Aromatic_N-Oxide_more_than_one">
496
+ <SMARTS>[n+][O-X1].[n+][O-X1]</SMARTS>
497
+ </substructure>
498
+ <substructure name="(166) Nitro_more_than_one">
499
+ <SMARTS>[N+](=O)[O-].[N+](=O)[O-]</SMARTS>
500
+ </substructure>
501
+ </SureChEMBL>
rdworks/predefined/ChEMBL_Walters/makexml.py ADDED
@@ -0,0 +1,40 @@
1
+ from __future__ import print_function
2
+ from xml.etree.ElementTree import Element, SubElement, tostring
3
+ from xml.dom import minidom
4
+ from rdkit import Chem
5
+ import csv
6
+
7
+ sources= []
8
+
9
+ root= None
10
+ count= 0
11
+
12
+ with open("alert_collection.csv","r") as csvfile:
13
+ rows = csv.reader(csvfile, delimiter=",",quotechar='"')
14
+ next(rows) # skip header
15
+ for row in rows:
16
+ name, smarts, source= row[2],row[3],row[4]
17
+ try:
18
+ m= Chem.MolFromSmarts(smarts)
19
+ except:
20
+ print("INVALID SMARTS @", name, smarts, source)
21
+ continue
22
+ if not (source in sources):
23
+ if len(sources) > 0:
24
+ last_source = sources[-1]
25
+ with open(last_source+".xml","w") as g:
26
+ coarse= tostring(root,'utf-8')
27
+ g.write( minidom.parseString( coarse ).toprettyxml(indent=" ") )
28
+ sources.append(source)
29
+ root = Element(source)
30
+ count = 0
31
+ count += 1
32
+ entry= SubElement (root, 'group')
33
+ entry.set('name','('+str(count)+') '+name)
34
+ sub= SubElement(entry,'SMARTS')
35
+ sub.text = smarts
36
+
37
+ last_source = sources[-1]
38
+ with open(last_source+".xml","w") as g:
39
+ coarse= tostring(root,'utf-8')
40
+ g.write( minidom.parseString( coarse ).toprettyxml(indent=" ") )