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/Inpharmatica.xml ADDED
@@ -0,0 +1,276 @@
1
+ <?xml version="1.0" ?>
2
+ <Inpharmatica>
3
+ <substructure name="(1) Filter1_2_halo_ether">
4
+ <SMARTS>[Cl,Br,I][CX4][CX4][$([O,S,N]*),Cl,Br,I]</SMARTS>
5
+ </substructure>
6
+ <substructure name="(2) Filter2_acyl_phosphyl_sulfonyl_halide">
7
+ <SMARTS>[C,S,P](=O)[F,Cl,Br,I]</SMARTS>
8
+ </substructure>
9
+ <substructure name="(3) Filter3_allyl_halide">
10
+ <SMARTS>[F,Cl,Br,I][CX4]C=C</SMARTS>
11
+ </substructure>
12
+ <substructure name="(4) Filter4_alpha_halo_carbonyl">
13
+ <SMARTS>[Br,Cl,I][C!H0]C=[O,S]</SMARTS>
14
+ </substructure>
15
+ <substructure name="(5) Filter5_azo">
16
+ <SMARTS>[!#7,#1]~[NX2R0]=[NX2R0]~[!#7,#1]</SMARTS>
17
+ </substructure>
18
+ <substructure name="(6) Filter6_benzyl_halide">
19
+ <SMARTS>[Br,Cl,I][CX4]c</SMARTS>
20
+ </substructure>
21
+ <substructure name="(7) Filter7_diazo">
22
+ <SMARTS>[!#7]~[NX2]~[NX1]</SMARTS>
23
+ </substructure>
24
+ <substructure name="(8) Filter8_thio_isocyanat_diimin">
25
+ <SMARTS>N=C=[N,O,P,S]</SMARTS>
26
+ </substructure>
27
+ <substructure name="(9) Filter9_metal">
28
+ <SMARTS>[!#1!#6!#7!#8!#9!#15!#16!#17]~[*,#1]</SMARTS>
29
+ </substructure>
30
+ <substructure name="(10) Filter10_Terminal_vinyl">
31
+ <SMARTS>[CH2]=[CH][N,O,P,S;R0]</SMARTS>
32
+ </substructure>
33
+ <substructure name="(11) Filter11_nitrosamin">
34
+ <SMARTS>[NR0]~[NX2]~[OX1]</SMARTS>
35
+ </substructure>
36
+ <substructure name="(12) Filter12_nitroso">
37
+ <SMARTS>[*,#1]~[NX2]~[OX1]</SMARTS>
38
+ </substructure>
39
+ <substructure name="(13) Filter13_PS_double_bond">
40
+ <SMARTS>S=P~[*,#1]</SMARTS>
41
+ </substructure>
42
+ <substructure name="(14) Filter14_thio_oxopyrylium_salt">
43
+ <SMARTS>c1ccc[s,o;X2]c1</SMARTS>
44
+ </substructure>
45
+ <substructure name="(15) Filter15_thiosulfate">
46
+ <SMARTS>[SX4](~S)(~O)(~O)~*</SMARTS>
47
+ </substructure>
48
+ <substructure name="(16) Filter16_trialkyl_phosphin">
49
+ <SMARTS>[PX3]([#6])([#6])[#6]</SMARTS>
50
+ </substructure>
51
+ <substructure name="(17) Filter17_trialkyl_phosphin2">
52
+ <SMARTS>[PX4](~[!O!S])([#6])([#6])[#6]</SMARTS>
53
+ </substructure>
54
+ <substructure name="(18) Filter18_oxime_ester">
55
+ <SMARTS>[!#7,#1]C=NO[C,S,P](=O)*</SMARTS>
56
+ </substructure>
57
+ <substructure name="(19) Filter19_hydroxyimide_ester">
58
+ <SMARTS>O=C[NX3](C=O)OC(=O)*</SMARTS>
59
+ </substructure>
60
+ <substructure name="(20) Filter20_hydrazine">
61
+ <SMARTS>[Nv3X3][Nv3X3!H0]</SMARTS>
62
+ </substructure>
63
+ <substructure name="(21) Filter21_cyanhydrin">
64
+ <SMARTS>[NX1]#C[CX4][OH]</SMARTS>
65
+ </substructure>
66
+ <substructure name="(22) Filter22_sulfonium_salt">
67
+ <SMARTS>*[SX3](*)*</SMARTS>
68
+ </substructure>
69
+ <substructure name="(23) Filter23_ortho_quinone">
70
+ <SMARTS>C1(C=CC=CC1=O)=O</SMARTS>
71
+ </substructure>
72
+ <substructure name="(24) Filter24_react_imide">
73
+ <SMARTS>*C([F,Cl,Br,I,$(OS(=O)(=O)*)])=[NX2]*</SMARTS>
74
+ </substructure>
75
+ <substructure name="(25) Filter25_sulfonyl_halide">
76
+ <SMARTS>*S(=O)(=O)[F,Cl,Br,I]</SMARTS>
77
+ </substructure>
78
+ <substructure name="(26) Filter26_alkyl_halide">
79
+ <SMARTS>AA[CH2][F,Cl,Br,I,$(OS(=O)(=O)*)]</SMARTS>
80
+ </substructure>
81
+ <substructure name="(27) Filter27_anhydride">
82
+ <SMARTS>*[C,S](=O)O[C,S](=O)*</SMARTS>
83
+ </substructure>
84
+ <substructure name="(28) Filter28_halo_pyrimidine">
85
+ <SMARTS>c1nc(ncc1)[Br,I]</SMARTS>
86
+ </substructure>
87
+ <substructure name="(29) Filter29_thioester">
88
+ <SMARTS>CC(=[OX1,SX1,NH])[SX2][*,#1]</SMARTS>
89
+ </substructure>
90
+ <substructure name="(30) Filter30_beta_halo_carbonyl">
91
+ <SMARTS>[#6,#1]C(=O)CC[Br,I]</SMARTS>
92
+ </substructure>
93
+ <substructure name="(31) Filter31_so_bond">
94
+ <SMARTS>[*,#1][SX2R0]O[*,#1]</SMARTS>
95
+ </substructure>
96
+ <substructure name="(32) Filter32_oo_bond">
97
+ <SMARTS>[*,#1][OR0]O[*,#1]</SMARTS>
98
+ </substructure>
99
+ <substructure name="(33) Filter33_c10_alkyl">
100
+ <SMARTS>[CH3][CH2][CH2][CH2][CH2][CH2][CH2][CH2][CH2][CH2]</SMARTS>
101
+ </substructure>
102
+ <substructure name="(34) Filter34_isotope">
103
+ <SMARTS>[2#1,3#1,13C,14C,15N,125I,23F,22Na,32P,33P,35S,45Ca,57Co,103Ru,141Ce]</SMARTS>
104
+ </substructure>
105
+ <substructure name="(35) Filter35_pp_bond">
106
+ <SMARTS>P-P</SMARTS>
107
+ </substructure>
108
+ <substructure name="(36) Filter36_ss_double_bond">
109
+ <SMARTS>S=S</SMARTS>
110
+ </substructure>
111
+ <substructure name="(37) Filter37_silicate">
112
+ <SMARTS>[Si]~O</SMARTS>
113
+ </substructure>
114
+ <substructure name="(38) Filter38_aldehyde">
115
+ <SMARTS>O=[CH]*</SMARTS>
116
+ </substructure>
117
+ <substructure name="(39) Filter39_imine">
118
+ <SMARTS>C[CR0]=[NR0][*!O]</SMARTS>
119
+ </substructure>
120
+ <substructure name="(40) Filter40_epoxide_aziridine">
121
+ <SMARTS>C1C[N,S,O]1</SMARTS>
122
+ </substructure>
123
+ <substructure name="(41) Filter41_12_dicarbonyl">
124
+ <SMARTS>*C(=O)C(=O)*</SMARTS>
125
+ </substructure>
126
+ <substructure name="(42) Filter42_12_dicarbonyl_tautomer">
127
+ <SMARTS>[*!$(C[OH])]=C([OH])C(=O)*</SMARTS>
128
+ </substructure>
129
+ <substructure name="(43) Filter43_michael_acceptor_sp1">
130
+ <SMARTS>C#CC=O</SMARTS>
131
+ </substructure>
132
+ <substructure name="(44) Filter44_michael_acceptor2">
133
+ <SMARTS>[#6,#1,OH0][C!$(C1(=O)C=CC(=O)C=C1)](=O)C=[C!$(C[Nv3X3,OH])]</SMARTS>
134
+ </substructure>
135
+ <substructure name="(45) Filter45_allyl_halide2">
136
+ <SMARTS>[Br,Cl,I][CX4]C=[C,N,P]</SMARTS>
137
+ </substructure>
138
+ <substructure name="(46) Filter46_nhalide">
139
+ <SMARTS>N[F,Cl,Br,I]</SMARTS>
140
+ </substructure>
141
+ <substructure name="(47) Filter47_so2f">
142
+ <SMARTS>O=S(=O)(*)F</SMARTS>
143
+ </substructure>
144
+ <substructure name="(48) Filter48_foso">
145
+ <SMARTS>O=S(*)OF</SMARTS>
146
+ </substructure>
147
+ <substructure name="(49) Filter49_halogen">
148
+ <SMARTS>[*,#1]~[F,Cl,Br,I]~[*,#1]</SMARTS>
149
+ </substructure>
150
+ <substructure name="(50) Filter50_grignard">
151
+ <SMARTS>C[Mg][F,Cl,Br,I]</SMARTS>
152
+ </substructure>
153
+ <substructure name="(51) Filter51_pn3">
154
+ <SMARTS>N[PX3](N)N</SMARTS>
155
+ </substructure>
156
+ <substructure name="(52) Filter52_NC_haloamine">
157
+ <SMARTS>NC[F,Cl,Br,I]</SMARTS>
158
+ </substructure>
159
+ <substructure name="(53) Filter53_para_quinones">
160
+ <SMARTS>O=C1C=CC(=O)C=C1</SMARTS>
161
+ </substructure>
162
+ <substructure name="(54) Filter56_SS_bond">
163
+ <SMARTS>S-S</SMARTS>
164
+ </substructure>
165
+ <substructure name="(55) Filter57_polyphenol1">
166
+ <SMARTS>Oc1cc(O)cc(O)c1</SMARTS>
167
+ </substructure>
168
+ <substructure name="(56) Filter58_polyphenol2">
169
+ <SMARTS>Oc1c(O)cc(O)cc1</SMARTS>
170
+ </substructure>
171
+ <substructure name="(57) Filter59_phoshorous_ylide">
172
+ <SMARTS>C=P</SMARTS>
173
+ </substructure>
174
+ <substructure name="(58) Filter60_Acyclic_N-S">
175
+ <SMARTS>N!@[SX2]</SMARTS>
176
+ </substructure>
177
+ <substructure name="(59) Filter61_phosphor_halide_and_P_S_bond">
178
+ <SMARTS>[#15]~[F,Cl,Br,I,#16]</SMARTS>
179
+ </substructure>
180
+ <substructure name="(60) Filter62_oxo_thio_halide">
181
+ <SMARTS>[O,S]~[Cl,Br,I]</SMARTS>
182
+ </substructure>
183
+ <substructure name="(61) Filter63_polyaromatic">
184
+ <SMARTS>a1aaaa2ccc3ccccc3c12</SMARTS>
185
+ </substructure>
186
+ <substructure name="(62) Filter64_halo_ketone_sulfone">
187
+ <SMARTS>[#6][C,S](=[O,S])C[F,Cl,Br,I]</SMARTS>
188
+ </substructure>
189
+ <substructure name="(63) Filter65_alkyl_sulfonate">
190
+ <SMARTS>[#6][P,S](~[OX1])(~[OX1])O[C!H0]</SMARTS>
191
+ </substructure>
192
+ <substructure name="(64) Filter66_c4_perfluoralkyl">
193
+ <SMARTS>C(F)(F)C(F)(F)C(F)(F)C(F)(F)</SMARTS>
194
+ </substructure>
195
+ <substructure name="(65) Filter67_S_or_O_C_triplebond_N">
196
+ <SMARTS>[O,S]C#N</SMARTS>
197
+ </substructure>
198
+ <substructure name="(66) Filter68_anthracene_acridine">
199
+ <SMARTS>a1aaac2cc3ccccc3cc12</SMARTS>
200
+ </substructure>
201
+ <substructure name="(67) Filter69_thio_carbonate">
202
+ <SMARTS>[O,S]C(=[O,S])[O,S]</SMARTS>
203
+ </substructure>
204
+ <substructure name="(68) Filter70_AlkylCN2">
205
+ <SMARTS>*(C#N)C#N</SMARTS>
206
+ </substructure>
207
+ <substructure name="(69) Filter71_thio_anhydride">
208
+ <SMARTS>*C(=[O,S])[O,S]C(=[O,S])*</SMARTS>
209
+ </substructure>
210
+ <substructure name="(70) Filter72_hydrated_di_ketone">
211
+ <SMARTS>C(=O)C([OH])[OH]</SMARTS>
212
+ </substructure>
213
+ <substructure name="(71) Filter73_thio_ketone">
214
+ <SMARTS>CC(=S)C</SMARTS>
215
+ </substructure>
216
+ <substructure name="(72) Filter74_thiol">
217
+ <SMARTS>*[SX2H]</SMARTS>
218
+ </substructure>
219
+ <substructure name="(73) Filter75_alkyl_Br_I">
220
+ <SMARTS>[C!H0][Br,I]</SMARTS>
221
+ </substructure>
222
+ <substructure name="(74) Filter76_S_ester">
223
+ <SMARTS>CC(=S)O</SMARTS>
224
+ </substructure>
225
+ <substructure name="(75) Filter77_alkyl_NO2">
226
+ <SMARTS>[*!#7]~[#6]-,=CN(~O)(~O)</SMARTS>
227
+ </substructure>
228
+ <substructure name="(76) Filter78_bicyclic_Imide">
229
+ <SMARTS>*~@C1C(=O)NC(=O)C(~@*)1</SMARTS>
230
+ </substructure>
231
+ <substructure name="(77) Filter79_maleimide">
232
+ <SMARTS>[CH]1C(=O)NC(=O)[CH]=1</SMARTS>
233
+ </substructure>
234
+ <substructure name="(78) Filter80_Thioepoxide_aziridone">
235
+ <SMARTS>[N,S]1[C,N,S][C,N,S]1</SMARTS>
236
+ </substructure>
237
+ <substructure name="(79) Filter81_Thiocarbamate">
238
+ <SMARTS>S!@C(=!@[O,S])!@[#7]</SMARTS>
239
+ </substructure>
240
+ <substructure name="(80) Filter82_pyridinium">
241
+ <SMARTS>[c,n]1[c,n][c,n][c,n][c,n]n(C)1</SMARTS>
242
+ </substructure>
243
+ <substructure name="(81) Filter83_per_halo_chain">
244
+ <SMARTS>[F,Cl,Br,I]C-,=;!@C([F,Cl,Br,I])-,=;!@C([F,Cl,Br,I])</SMARTS>
245
+ </substructure>
246
+ <substructure name="(82) Filter84_nitrogen_mustard">
247
+ <SMARTS>[N,P,Se,S][C!H0]C[Br,Cl,I]</SMARTS>
248
+ </substructure>
249
+ <substructure name="(83) Filter85_keto_acrylonitrile">
250
+ <SMARTS>*C(=O)C(=!@[C!H0])C#N</SMARTS>
251
+ </substructure>
252
+ <substructure name="(84) Filter86_cyanamide">
253
+ <SMARTS>N#C[#7!$(N(C#N)=C(N)NC)]</SMARTS>
254
+ </substructure>
255
+ <substructure name="(85) Filter87_crowns">
256
+ <SMARTS>[N,O,S]-@[#6!$(*(~@*)(~@*)~@*)]@[#6!$(*(~@*)(~@*)~@*)]-@[N,O,S]-@[#6!$(*(~@*)(~@*)~@*)]@[#6!$(*(~@*)(~@*)~@*)]-@[O,N]-@[#6!$(*(~@*)(~@*)~@*)]@[#6!$(*(~@*)(~@*)~@*)]-@[N,O,S]-@C</SMARTS>
257
+ </substructure>
258
+ <substructure name="(86) Filter88_ene_sulfone">
259
+ <SMARTS>[C!H0]=CS(=O)(=O)*</SMARTS>
260
+ </substructure>
261
+ <substructure name="(87) Filter89_hydroxylamine">
262
+ <SMARTS>[*!$(C=O)]!@N!@O[*,#1]</SMARTS>
263
+ </substructure>
264
+ <substructure name="(88) Filter90_N_double_bond_S">
265
+ <SMARTS>N=!@S</SMARTS>
266
+ </substructure>
267
+ <substructure name="(89) Filter92_trityl">
268
+ <SMARTS>*(c1ccccc1)(c1ccccc1)(c1ccccc1)</SMARTS>
269
+ </substructure>
270
+ <substructure name="(90) Filter93_acetyl_urea">
271
+ <SMARTS>C(=O)!@N!@C(=O)[#7]</SMARTS>
272
+ </substructure>
273
+ <substructure name="(91) Filter94_2_halo_pyridine">
274
+ <SMARTS>c1nc(ccc1)[Br,I,Cl,F]</SMARTS>
275
+ </substructure>
276
+ </Inpharmatica>
rdworks/predefined/ChEMBL_Walters/LINT.xml ADDED
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1
+ <?xml version="1.0" ?>
2
+ <LINT>
3
+ <substructure name="(1) aromatic NO2">
4
+ <SMARTS>O~N(=O)-c(:*):*</SMARTS>
5
+ </substructure>
6
+ <substructure name="(2) deuterium">
7
+ <SMARTS>[2H]</SMARTS>
8
+ </substructure>
9
+ <substructure name="(3) C13">
10
+ <SMARTS>[13#6]</SMARTS>
11
+ </substructure>
12
+ <substructure name="(4) 2-chloropyridine">
13
+ <SMARTS>n1c(cccc1)Cl</SMARTS>
14
+ </substructure>
15
+ <substructure name="(5) aniline">
16
+ <SMARTS>[NH2D1]-c(:*):*</SMARTS>
17
+ </substructure>
18
+ <substructure name="(6) Si,B,Se atoms">
19
+ <SMARTS>[Si,B,Se]</SMARTS>
20
+ </substructure>
21
+ <substructure name="(7) hetero imides">
22
+ <SMARTS>[!#6]-[CH2]-N1C(=O)CCC(=O)1</SMARTS>
23
+ </substructure>
24
+ <substructure name="(8) poly ethers">
25
+ <SMARTS>O[CH2][CH2]O-!@[CH2][CH2]O</SMARTS>
26
+ </substructure>
27
+ <substructure name="(9) acyclic imines">
28
+ <SMARTS>C-!@[NX2]=[C!R,#1]-C</SMARTS>
29
+ </substructure>
30
+ <substructure name="(10) alkyl esters of S or P">
31
+ <SMARTS>[S,P](=O)OC</SMARTS>
32
+ </substructure>
33
+ <substructure name="(11) ugly P compounds">
34
+ <SMARTS>P(=[O,S])[C,N]([C,N])[C,N]</SMARTS>
35
+ </substructure>
36
+ <substructure name="(12) acyclic N-,=N and not N bound to carbonyl or sulfone">
37
+ <SMARTS>[N;!$(N-[C,S]=*)]-,=;!@[N;!$(N-[C,S]=*)]</SMARTS>
38
+ </substructure>
39
+ <substructure name="(13) acyclic N-C-N">
40
+ <SMARTS>N-!@[CX4]-!@N</SMARTS>
41
+ </substructure>
42
+ <substructure name="(14) acyclic N-S">
43
+ <SMARTS>N-!@[SX2]-*</SMARTS>
44
+ </substructure>
45
+ <substructure name="(15) mustards">
46
+ <SMARTS>[N,S,O][CH2][CH2]-[F,Cl,Br,I]</SMARTS>
47
+ </substructure>
48
+ <substructure name="(16) aldehyde">
49
+ <SMARTS>O=[C!H0]</SMARTS>
50
+ </substructure>
51
+ <substructure name="(17) 1,2-dicarbonyl not in ring">
52
+ <SMARTS>O=[CX3]-!@[CX3]=O</SMARTS>
53
+ </substructure>
54
+ <substructure name="(18) carbamate, T-boc Protected">
55
+ <SMARTS>NC(OC([CH3])([CH3])[CH3])=O</SMARTS>
56
+ </substructure>
57
+ <substructure name="(19) carbamate, CBZ Protected">
58
+ <SMARTS>NC(O[CH2]c1ccccc1)=O</SMARTS>
59
+ </substructure>
60
+ <substructure name="(20) carbamate include di-substitued N">
61
+ <SMARTS>OC(=O)-!@[NX3]</SMARTS>
62
+ </substructure>
63
+ <substructure name="(21) acyl halide">
64
+ <SMARTS>O=C-[F,Cl,Br,I]</SMARTS>
65
+ </substructure>
66
+ <substructure name="(22) alkyl halide">
67
+ <SMARTS>[CH2]-[Cl,Br,I]</SMARTS>
68
+ </substructure>
69
+ <substructure name="(23) alpha halo carbonyl">
70
+ <SMARTS>O=C-C-[F,Cl,Br,I]</SMARTS>
71
+ </substructure>
72
+ <substructure name="(24) sufonyl halide">
73
+ <SMARTS>S(=O)(=O)-[F,Cl,Br,I]</SMARTS>
74
+ </substructure>
75
+ <substructure name="(25) N:C-SCH2 substructures">
76
+ <SMARTS>[ND1]=C-!@[SX2]-[CH2D2]</SMARTS>
77
+ </substructure>
78
+ <substructure name="(26) 26">
79
+ <SMARTS>N-C(=S)-N</SMARTS>
80
+ </substructure>
81
+ <substructure name="(27) terminal vinyl">
82
+ <SMARTS>[CH2D1]=[CD2]-!@*</SMARTS>
83
+ </substructure>
84
+ <substructure name="(28) 28">
85
+ <SMARTS>S=P~*</SMARTS>
86
+ </substructure>
87
+ <substructure name="(29) thio cyanates">
88
+ <SMARTS>S-C#N</SMARTS>
89
+ </substructure>
90
+ <substructure name="(30) thiols">
91
+ <SMARTS>*-[S!H0]</SMARTS>
92
+ </substructure>
93
+ <substructure name="(31) thionyl">
94
+ <SMARTS>[Sv4](=O)(-!@[!#1])-!@[!#1]</SMARTS>
95
+ </substructure>
96
+ <substructure name="(32) n-haloamines">
97
+ <SMARTS>N-[F,Cl,Br,I]</SMARTS>
98
+ </substructure>
99
+ <substructure name="(33) N-C-Hal or cyano methyl">
100
+ <SMARTS>N-C-[F,Cl,Br,I,$(C#N)]</SMARTS>
101
+ </substructure>
102
+ <substructure name="(34) alpha beta-unsaturated ketones; center of Michael reactivity">
103
+ <SMARTS>[$(C#N),$(N(~O)~O),$(C=O),$(S(=O)=O),$(C(F)(F)F),Cl][C!H0]=[C!H0]</SMARTS>
104
+ </substructure>
105
+ <substructure name="(35) aliphatic ketone not ring and not di-carbonyl">
106
+ <SMARTS>[C;!$(C=*)][C!R](=O)[CH2D2]</SMARTS>
107
+ </substructure>
108
+ <substructure name="(36) aliphatic ester, not lactones">
109
+ <SMARTS>C[C!R](=O)[O!R][CH2D2]</SMARTS>
110
+ </substructure>
111
+ <substructure name="(37) long aliphatic chain, 6+">
112
+ <SMARTS>[CH2][CH2][CH2]-!@[CH2][CH2][CH2]</SMARTS>
113
+ </substructure>
114
+ <substructure name="(38) quinones">
115
+ <SMARTS>O=[#6]1[#6]:,=[#6][#6](=O)[#6]:,=[#6]1</SMARTS>
116
+ </substructure>
117
+ <substructure name="(39) acyclic C=C-O">
118
+ <SMARTS>C=C-!@O-*</SMARTS>
119
+ </substructure>
120
+ <substructure name="(40) acyclic C=N-H">
121
+ <SMARTS>[NH1X2]=[C!R;!$(C(-N)(=[NH1])-N)]</SMARTS>
122
+ </substructure>
123
+ <substructure name="(41) acyclic NO not nitro">
124
+ <SMARTS>O-!@[N;!$(N(=O)=O);!$([N+](=O)[O-])]</SMARTS>
125
+ </substructure>
126
+ <substructure name="(42) 42">
127
+ <SMARTS>S-S</SMARTS>
128
+ </substructure>
129
+ <substructure name="(43) 43">
130
+ <SMARTS>O~O</SMARTS>
131
+ </substructure>
132
+ <substructure name="(44) thioester">
133
+ <SMARTS>C-C(=O)[SD2]</SMARTS>
134
+ </substructure>
135
+ <substructure name="(45) aziridine-like N in 3-membered ring">
136
+ <SMARTS>N~1~*~*1</SMARTS>
137
+ </substructure>
138
+ <substructure name="(46) epoxides">
139
+ <SMARTS>O~1C~*1</SMARTS>
140
+ </substructure>
141
+ <substructure name="(47) aryl iodide">
142
+ <SMARTS>I-c:*</SMARTS>
143
+ </substructure>
144
+ <substructure name="(48) aryl bromide">
145
+ <SMARTS>Br-c:*</SMARTS>
146
+ </substructure>
147
+ <substructure name="(49) multiple aromatic rings">
148
+ <SMARTS>a1aaa2a(a1)aaa(a2):a</SMARTS>
149
+ </substructure>
150
+ <substructure name="(50) multiple aromatic rings">
151
+ <SMARTS>[!#1]-,:1-:a2a(-:[!#1]:3:a1aaaa3)aaaa2</SMARTS>
152
+ </substructure>
153
+ <substructure name="(51) S/PO3 substructures">
154
+ <SMARTS>[P,S](~O)(~O)~O</SMARTS>
155
+ </substructure>
156
+ <substructure name="(52) adamantyl">
157
+ <SMARTS>C12CC3CC(C1)CC(C2)C3</SMARTS>
158
+ </substructure>
159
+ <substructure name="(53) too many cyano Groups (&gt;1)">
160
+ <SMARTS>C#N.C#N</SMARTS>
161
+ </substructure>
162
+ <substructure name="(54) too many COOH substructures (&gt;1)">
163
+ <SMARTS>[CX3](=O)[OH1].[CX3](=O)[OH1]</SMARTS>
164
+ </substructure>
165
+ <substructure name="(55) amino acid">
166
+ <SMARTS>[NH2][CX4]C(=O)O</SMARTS>
167
+ </substructure>
168
+ <substructure name="(56) chlorates">
169
+ <SMARTS>Cl~O</SMARTS>
170
+ </substructure>
171
+ <substructure name="(57) high halogen content (&gt;3)">
172
+ <SMARTS>[F,Cl,Br,I].[F,Cl,Br,I].[F,Cl,Br,I].[F,Cl,Br,I]</SMARTS>
173
+ </substructure>
174
+ </LINT>