lazar 0.0.1

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Files changed (98) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +10 -0
  3. data/.yardopts +4 -0
  4. data/Gemfile +2 -0
  5. data/LICENSE +674 -0
  6. data/README.md +44 -0
  7. data/Rakefile +1 -0
  8. data/VERSION +1 -0
  9. data/ext/lazar/extconf.rb +87 -0
  10. data/java/CdkDescriptorInfo.class +0 -0
  11. data/java/CdkDescriptorInfo.java +22 -0
  12. data/java/CdkDescriptors.class +0 -0
  13. data/java/CdkDescriptors.java +141 -0
  14. data/java/Jmol.jar +0 -0
  15. data/java/JoelibDescriptorInfo.class +0 -0
  16. data/java/JoelibDescriptorInfo.java +15 -0
  17. data/java/JoelibDescriptors.class +0 -0
  18. data/java/JoelibDescriptors.java +60 -0
  19. data/java/Rakefile +15 -0
  20. data/java/cdk-1.4.19.jar +0 -0
  21. data/java/joelib2.jar +0 -0
  22. data/java/log4j.jar +0 -0
  23. data/lazar.gemspec +29 -0
  24. data/lib/SMARTS_InteLigand.txt +983 -0
  25. data/lib/algorithm.rb +21 -0
  26. data/lib/bbrc.rb +165 -0
  27. data/lib/classification.rb +107 -0
  28. data/lib/compound.rb +254 -0
  29. data/lib/crossvalidation.rb +187 -0
  30. data/lib/dataset.rb +334 -0
  31. data/lib/descriptor.rb +247 -0
  32. data/lib/error.rb +66 -0
  33. data/lib/feature.rb +97 -0
  34. data/lib/lazar-model.rb +170 -0
  35. data/lib/lazar.rb +69 -0
  36. data/lib/neighbor.rb +25 -0
  37. data/lib/opentox.rb +22 -0
  38. data/lib/overwrite.rb +119 -0
  39. data/lib/regression.rb +199 -0
  40. data/lib/rest-client-wrapper.rb +98 -0
  41. data/lib/similarity.rb +58 -0
  42. data/lib/unique_descriptors.rb +120 -0
  43. data/lib/validation.rb +114 -0
  44. data/mongoid.yml +8 -0
  45. data/test/all.rb +5 -0
  46. data/test/compound.rb +100 -0
  47. data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +13553 -0
  48. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv +436 -0
  49. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv +568 -0
  50. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv +87 -0
  51. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv +978 -0
  52. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv +1120 -0
  53. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv +1113 -0
  54. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv +850 -0
  55. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv +829 -0
  56. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Rat.csv +1198 -0
  57. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv +1505 -0
  58. data/test/data/EPAFHM.csv +618 -0
  59. data/test/data/EPAFHM.medi.csv +100 -0
  60. data/test/data/EPAFHM.mini.csv +22 -0
  61. data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv +581 -0
  62. data/test/data/FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv +1217 -0
  63. data/test/data/ISSCAN-multi.csv +59 -0
  64. data/test/data/LOAEL_log_mg_corrected_smiles.csv +568 -0
  65. data/test/data/LOAEL_log_mmol_corrected_smiles.csv +568 -0
  66. data/test/data/acetaldehyde.sdf +14 -0
  67. data/test/data/boiling_points.ext.sdf +11460 -0
  68. data/test/data/cpdb_100.csv +101 -0
  69. data/test/data/hamster_carcinogenicity.csv +86 -0
  70. data/test/data/hamster_carcinogenicity.mini.bool_float.csv +11 -0
  71. data/test/data/hamster_carcinogenicity.mini.bool_int.csv +11 -0
  72. data/test/data/hamster_carcinogenicity.mini.bool_string.csv +11 -0
  73. data/test/data/hamster_carcinogenicity.mini.csv +11 -0
  74. data/test/data/hamster_carcinogenicity.ntriples +618 -0
  75. data/test/data/hamster_carcinogenicity.sdf +2805 -0
  76. data/test/data/hamster_carcinogenicity.xls +0 -0
  77. data/test/data/hamster_carcinogenicity.yaml +352 -0
  78. data/test/data/hamster_carcinogenicity_with_errors.csv +88 -0
  79. data/test/data/kazius.csv +4070 -0
  80. data/test/data/multi_cell_call.csv +1067 -0
  81. data/test/data/multi_cell_call_no_dup.csv +1057 -0
  82. data/test/data/multicolumn.csv +8 -0
  83. data/test/data/rat_feature_dataset.csv +1179 -0
  84. data/test/data/wrong_dataset.csv +8 -0
  85. data/test/dataset-long.rb +117 -0
  86. data/test/dataset.rb +199 -0
  87. data/test/descriptor-long.rb +26 -0
  88. data/test/descriptor.rb +83 -0
  89. data/test/error.rb +24 -0
  90. data/test/feature.rb +65 -0
  91. data/test/fminer-long.rb +38 -0
  92. data/test/fminer.rb +52 -0
  93. data/test/lazar-fminer.rb +50 -0
  94. data/test/lazar-long.rb +72 -0
  95. data/test/lazar-physchem-short.rb +27 -0
  96. data/test/setup.rb +6 -0
  97. data/test/validation.rb +41 -0
  98. metadata +212 -0
data/test/data/LOAEL_log_mmol_corrected_smiles.csv ADDED
@@ -0,0 +1,568 @@
1
+ SMILES,LOAEL_log_mmol_kg_bw_day
2
+ 'C1=C(C(=CC(=C1NN=C3C2=C(C=C([S]([O-])(=O)=O)C=C2)C=CC3=O)OC)[S]([O-])(=O)=O)C.[Na+].[Na+]',2.12309380508316
3
+ 'O1C(=O)C(O)=C(O)C1C(O)CO',1.76137662853832
4
+ 'C1(C)=C(C=CC(C)=CC=CC(C)=CC=CC=C(C)C=CC=C(C)C(=O)OC)C(C)(C)CCC1',2.95101092705237
5
+ 'c(cccc1)(c1)C(C)C',2.41523206875268
6
+ 'O=C(OCCCC)c(c(ccc1)C(=O)OCCCC)c1',2.66642980233607
7
+ 'O=C(OCC)c(c(ccc1)C(=O)OCC)c1',1.69992305435084
8
+ 'O=C(OC(OC(OC1C)C)C1)C',3.14412407646651
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+ 'Oc(c(ccc1)C)c1C',4.30879341594785
10
+ 'Oc(ccc(c1C)C)c1',3.94081663065326
11
+ 'O=C(OCC)C=C',2.60605102798022
12
+ 'c(cccc1)(c1)CC',2.41532120099855
13
+ 'OCCO',2.39492662325430
14
+ 'c(ccc1C(=O)OCC(=O)OCC)cc1C(=O)OCC',2.04964162538818
15
+ 'O=C',2.56368333860036
16
+ 'O=C(O)C=CC(=O)O',2.03090237239810
17
+ 'OCC(O)CO',1.12645271808123
18
+ 'O=C(OC)c(ccc(O)c1)c1',2.00617304782278
19
+ 'O=C(OCCC)c(ccc(O)c1)c1',2.07966468441907
20
+ 'CC(CCC(=O)(O))C3CCC4C2CCC1CC(O)CCC1(C)C2CCC34C',2.87687871256153
21
+ 'OC(C(CCC1C)C(C)C)C1',2.42080757876423
22
+ 'O=C(O)C(=C)C',2.54049719303574
23
+ 'O=C(OC)c(c(O)ccc1)c1',2.62596180611118
24
+ 'Oc(cccc1)c1',2.43708305310291
25
+ 'O=C(OCCC)c(cc(O)c(O)c1O)c1',2.3902301635117
26
+ 'OCC(O)C1C(O)=C(O)C(=O)O1',2.05436782171583
27
+ 'c(cccc1)(c1)C=C',3.69543631002744
28
+ 'O=Cc(occ1)c1',3.20450009536782
29
+ 'NCCNc1cccc2ccccc12',3.37247609215110
30
+ 'CN(C)(C)CCCl',2.64921593816204
31
+ 'O=C(Nc(ccc(c1)C(=O)CCl)c1)C',2.12695072080225
32
+ 'c(ccc(c1)Cl)(c1)C(c(ccc(c2)Cl)c2)C(Cl)(Cl)Cl',4.04444942813338
33
+ 'CC(Oc1cc(Cl)c(Cl)cc1Cl)C(=O)(O)',4.491054148917
34
+ 'O=N(=O)C(=CC=C1OC)C=C1N=NC(C(O)=C2C(=O)NC(=CC=C4)C=C4N(=O)=O)=C(C=C3)C(=C2)C=C3',2.36568501290040
35
+ 'O=N(=O)C(C=C1)=CC(OCCO)=C1NCCO',3.02438986505162
36
+ 'Cc1cccc(CC)c1N(C(=O)CCl)COCC',3.73201897895503
37
+ 'C1=C(C(=CC=C1OC2=CC=C(C=C2Cl)C(F)(F)F)[N+](=O)[O-])C(=O)[O-].[Na+]',3.32865137721601
38
+ 'CCc1cccc(CC)c1N(COC)C(=O)CCl',4.25489772423536
39
+ 'O=C(Nc(ccc(OCC)c1N)c1)C',2.21459876477238
40
+ 'Oc(ccc(N)c1)c1',2.20160364320713
41
+ 'CC(N)CC(=CC=C1)C=C1',4.43202666692597
42
+ 'O(c(ccc(c1)C=CC)c1)C',2.63429468422019
43
+ 'COc1ccc(N)cc1',2.41466474972438
44
+ 'O=C(O)c(c(N)ccc1)c1',1.69766082403086
45
+ 'Clc2cccc(c2)c1ccccc1',4.67360340221543
46
+ 'O=C(NC(C(=O)OC)Cc(cccc1)c1)C(N)CC(=O)O',3.30147753146833
47
+ 'n1c2ccc(Cl)cc2ncc1Oc3ccc(OC(C)C(=O)OCC)cc3',5.00327683569969
48
+ 'COC(=O)NS(=O)(=O)c1ccc(N)cc1',3.10691015775373
49
+ 'S=P(OC)(OC)SCN1N=Nc2ccccc2C1(=O)',5.94520088604013
50
+ 'CNC(=O)Oc1ccccc1OC(C)C',3.62167823549204
51
+ 'CC(C)(C)C(=O)C(Oc1ccc(Cl)cc1)n2cncn2',4.07003600375764
52
+ 'O=S(O)(=O)C(=CC=C1)C=C1CN(CC)=C(C=C2)C=CC2=C(C(C=C3)=CC=C3N(C)C)C(C=C4)=CC=C4N(CC)CC(C=C5)=CC(=C5)S(=O)(=O)O',2.99569446127058
53
+ 'c(c(cccc1)c1)(cccc2)c2',2.79016633269067
54
+ 'BrC(Cl)Cl',3.10044647372987
55
+ 'ClC(Cl)C(Cl)(Cl)SN2C(=O)C1CC=CCC1C2(=O)',4.46372003271591
56
+ 'O=C(Oc(c(c(ccc1)cc2)c1)c2)NC',4.11054922260167
57
+ 'CC1=C(SCCO1)C(=O)Nc2ccccc2',3.89450458533419
58
+ 'ClC1CC2C(C1Cl)C3(Cl)C(=C(Cl)C2(Cl)C3(Cl)Cl)Cl',6.18118555259066
59
+ 'O=C(O)CCl',3.49829685836143
60
+ 'ClC(=CC=C1N)C=C1',4.32760254782945
61
+ 'CC(C)OC(=O)C(O)(c1ccc(Cl)cc1)c2ccc(Cl)cc2',4.57623015760927
62
+ 'n1c(OC)nc(C)nc1NC(=O)NS(=O)(=O)c2ccccc2Cl',4.15566728690676
63
+ 'OS(=O)(=O)C(C(=CC=C2)C1=C2)=CC=C1N=NC(C(O)=C3N=NC(C(C=C5)=C4C=C5)=CC=C4S(O)(=O)=O)=CC(=C3O)CO',2.91745349144784
64
+ 'S=P(OCC)(OCC)Oc1ccc2C(C)=C(Cl)C(=O)Oc2c1',5.65653611167129
65
+ 'CNP(=O)(OC)Oc1ccc(cc1Cl)C(C)(C)C',4.86289269710557
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+ 'C(C1C2C(C(O)C(O1)OC8C(OC(OC7C(OC(OC6C(OC(OC5C(C(C(OC4C(C(C(OC3C(C(C(O2)OC3CO)O)O)OC4CO)O)O)OC5CO)O)O)C(C6O)O)CO)C(C7O)O)CO)C(C8O)O)CO)O)O',2.85087205247326
67
+ 'n1c(N)nc(N)nc1NC2CC2',4.04449742637606
68
+ 'COC(=O)c1c(Cl)c(Cl)c(C(=O)OC)c(Cl)c1Cl',2.82212129862366
69
+ 'O=C(O)C(Cl)(Cl)C',3.70545399970477
70
+ 'Nc1cc(N)c(O)cc1',3.69597355155454
71
+ 'FC(F)(Cl)Cl',2.90638355650622
72
+ 'ClCCl',3.23010431252803
73
+ 'O=P(OC)(OC)OC=C(Cl)Cl',4.98261676287965
74
+ 'OC(c1ccc(Cl)cc1)(c2ccc(Cl)cc2)C(Cl)(Cl)Cl',4.26774140719551
75
+ 'ClC4=C(Cl)C5(Cl)C3C1CC(C2OC12)C3C4(Cl)C5(Cl)Cl',6.88185159467056
76
+ 'CN(=C1C(C=C2)=CC=C2)N(C)C(=C1)C(C=C3)=CC=C3',3.2998650117386
77
+ 'O=C(NC(=O)c(c(F)ccc1)c1F)Nc(ccc(c2)Cl)c2',4.58922787551359
78
+ 'CC1=C(C)S(=O)(=O)CCS1(=O)=O',4.32277979319225
79
+ 'O=C(NC)CSP(OC)(OC)=S',5.96238343177818
80
+ 'COc1ccc(N)c(OC)c1',2.74428856020296
81
+ 'COP(=O)OC',3.04158586769746
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+ 'CC(=C(N(=O)=O)C=C1N(=O)=O)C=C1',3.72891101170516
83
+ 'CN(C)C(=O)C(c1ccccc1)c2ccccc2',3.90184372972497
84
+ 'N(c(cccc1)c1)c(cccc2)c2',3.73709625897028
85
+ 'C(C=C1)(=N(C=C1)CC2)C(N2=C3)=CC=C3',5.50194904825203
86
+ 'CCOP(=S)(OCC)SCCSCC',6.43839047104826
87
+ 'NC(=S)NNC(N)=S',2.20039466208170
88
+ 'O=C(N(C)C)Nc(ccc(c1Cl)Cl)c1',4.58938077582749
89
+ 'O=P(O)(O)CCCl',2.98375855767924
90
+ 'O=C(OCC)C(O1)C1(c(cccc2)c2)C',3.07133013436744
91
+ 'COC(=O)NC(=NC1=C2)NC1=CC(=C2)SC(C=C3)=CC=C3',4.30008455052816
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+ 'CN1C=C(c2ccccc2)C(=O)C(c3cc(C(F)(F)F)ccc3)=C1',4.11967251914367
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+ 'c1cc(C(F)(F)F)cc(Cl)c1NC(C(C)C)C(=O)OC(C(#N))c2cccc(Oc3ccccc3)c2',5.30355258529792
94
+ 'S=P(OCC)(Sc1ccccc1)CC',5.192858916992
95
+ 'n1c(C)nc(OC)nc1NC(=O)NS(=O)(=O)c2ccsc2C(=O)OC',4.19021010110931
96
+ 'C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl',4.76466896003284
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+ 'O=N(=O)N(CN1N(=O)=O)CN(C1)N(=O)=O',5.17048924956396
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+ 'O=C(N=C(N(C1(=O))C)N(C)C)N1C(CCCC2)C2',3.70296927879496
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+ 'n(c(c(ccc1)cc2)c1O)c2',3.00650487851870
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+ 'c1cc(Cl)cc(Cl)c1C(OCC=C)Cn2cncc2',3.87095923630552
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+ 'COc1cccc(OC)c1C(=O)Nc2onc(C(C)(CC)CC)c2',3.81664542550781
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+ 'n1c(OC)cc(OC)nc1NC(=O)NS(=O)(=O)Cc2ccccc2C(=O)OC',3.12325069281768
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+ 'CCOC(=O)CC(SP(=S)(OC)OC)C(=O)OCC',3.82001485148442
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+ 'CN(C)(CCC1)CC1',2.88160770091708
105
+ 'O=P(SCCCC)(SCCCC)SCCCC',5.40072574498715
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+ 'COCC(=O)N(C(C)C(=O)OC)c1c(C)cccc1C',3.65023995836629
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+ 'S=P(OC)(OC)SCN1C(=O)SC(OC)=N1',5.17945311726922
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+ 'CNC(=O)ON=C(C)SC',4.21007789203115
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+ 'COP(=S)(OC)Oc1ccc(cc1)N(=O)(=O)',6.02235818715591
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+ 'O=C1N(N)C(SC)=NN=C1C(C)(C)C',4.15490651136806
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+ 'COP(=O)(OC)OC(Br)C(Cl)(Cl)Br',5.27964840060116
112
+ 'OC(C(N)C1O)C(C)OC1(C)OC(CC(C)(C(C2O)C(O)=O)OC(O)(C2)CC(O)CC(C)(O3)C3C=C4)C=CC=CC=CC=CCC(C)OC4=O',3.99258108069112
113
+ 'O=N(=O)c(ccc(c1N)C)c1',4.27918373941654
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+ 'O=N(=O)c(c(N)ccc1N)c1',3.24556564669417
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+ 'O=C(O)C(=C(N)C=C1N(=O)=O)C=C1',2.18667157840130
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+ 'O=N(=O)c(c(c(ccc1)cc2)c1)c2',3.0209838975238
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+ 'c12c(N=Nc3ccccc3)c(O)ccc1cc(S(=O)(=O)O)cc2',3.26105456902449
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+ 'CC(C)Oc1cc(c(Cl)cc1Cl)N2N=C(OC2(=O))C(C)(C)C',4.83912722706429
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+ 'CNC(=O)ON=C(SC)C(=O)N(C)C',4.64199221806157
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+ 'CCOP(=S)(OCC)Oc1ccc(cc1)N(=O)=O',4.92021372679140
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+ 'Oc(c(c(c(c1Cl)Cl)Cl)Cl)c1Cl',4.42543075349016
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+ 'NC(=N)NC(=N)NCCc1ccccc1',3.44898061811695
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+ 'COP(=S)(OC)SCN2C(=O)c1ccccc1C2(=O)',4.20046887469431
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+ 'CCN(CC)C(=O)C(Cl)=C(C)OP(=O)(OC)OC',4.38676470716829
125
+ 'ClC3C6(Cl)C4C2C1OC1C5C2C3(Cl)C(Cl)(C45)C6(Cl)Cl',5.73572355899233
126
+ 'O=C(OC(=O)c1cccc2)c12',2.09688233455707
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+ 'Nc1c(Cl)c(Cl)nc(C(=O)(O))c1Cl',3.60469254298773
128
+ 'CCN(CC)c1nc(C)cc(OP(=S)(OC)OC)n1',5.08683453410041
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+ 'Nc3ccc2cc1ccc(N)cc1nc2c3',3.64856042750458
130
+ 'CCC(=O)Nc1ccc(Cl)c(Cl)c1',4.03758556402413
131
+ 'Clc1cc(Cl)ccc1C2(Cn3ncnc3)OC(CCC)CO2',4.13636586052483
132
+ 'O=C(N)c(nccn1)c1',2.19322585277166
133
+ 'Oc1cc(O)c2C(=O)C(O)=C(c3cc(O)c(O)cc3)Oc2c1',2.17199481319419
134
+ 'CCC(O)(C)C#C',3.32910149752408
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+ 'CC(C(NCC)=C1)=CC(C1=O2)=C(C(C2=C3)=CC(C)=C3NCC)C(=CC=C4)C(=C4)C(=O)OCC',4.56776852431159
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+ 'O=C(NS(=O)(=O)c1cccc2)c12',1.70634501494627
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+ 'c1cc(Cl)ccc1C2SC(=O)N(C(=O)NC3CCCCC3)C2C',3.34350563448343
138
+ 'n(c(nc(n1)NCC)NCC)c1Cl',4.60564260851438
139
+ 'O=[S](NC1CCCCC1)(=O)[O-].[Na+]',1.74712743618051
140
+ 'O=C(OCC(C1OCC(C1O)O)O)CCCCCCCCCCC',1.70187402783236
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+ 'O(CC1O)C(C1O)C(O)COC(=O)CCCCCCCCCCCCCCCCC',1.77657920852493
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+ 'O=S(=O)(Nc(nc(cc1C)C)n1)c(ccc(N)c2)c2',3.92604632938062
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+ 'CCNc1nc(NC(C)(C)C)nc(SC)n1',4.2065674883771
144
+ 'Oc(c(cc(c1)C(C)(C)C)Cl)c1',2.93192524190336
145
+ 'C(C(Cl)Cl)(Cl)Cl',3.19149572716769
146
+ 'COP(=O)(OC)OC(=CCl)c1cc(Cl)c(Cl)cc1Cl',3.5634357799466
147
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327
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328
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329
+ 'C1=CC=C(C(=C1)C(C2=CC=C(C=C2)F)(C3=CN=CN=C3)O)Cl',5.10001384041789
330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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340
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341
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342
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343
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344
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
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359
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360
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361
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362
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363
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364
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365
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366
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367
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368
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369
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370
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371
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372
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373
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374
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375
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376
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377
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378
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379
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380
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381
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382
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383
+ 'CCSC(=O)N1CCCCCC1',4.10198823735002
384
+ 'CCC1=CC=C(C=C1)C(=O)NN(C(=O)C2=CC(=CC(=C2)C)C)C(C)(C)C',3.86588082257473
385
+ 'ClC(Cl)C(Cl)(Cl)SN2C(=O)C1CC=CCC1C2(=O)',4.36681001970786
386
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387
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388
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389
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390
+ 'C1=CC=C(C(=C1)C(C2=CC=C(C=C2)Cl)(C3=CN=CN=C3)O)Cl',5.15835722073531
391
+ '[O-]Br(=O)=O',4.3215481796762
392
+ 'OP(=O)OCC',2.4395258763695
393
+ 'COP(N)(=O)SC',6.14961682124539
394
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395
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396
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397
+ 'O=C(OCC(CCCC)CC)CCCCC(=O)OCC(CCCC)CC',2.39277487311710
398
+ 'CN(C=Nc1ccc(C)cc1C)C=Nc2ccc(C)cc2C',4.46746902029786
399
+ [C@@]14([C@@H]5OCC1=CC=C[C@@H]([C@H](O[C@H]2C[C@@H]([C@H]([C@@H](O2)C)O[C@H]3C[C@@H]([C@H]([C@@H](O3)C)O)OC)OC)C(=CC[C@@H]6C[C@H](OC([C@@H]4C=C([C@H]5O)C)=O)C[C@]7(O6)O[C@@H]([C@H](C=C7)C)[C@H](CC)C)C)C)O,5.64002822248439
400
+ 'O=C(N(S(=O)(=O)Nc1cccc2)C(C)C)c12',3.83664755457448
401
+ 'S=P(OC)(OC)SCN1C(=O)SC(OC)=N1',5.38357309992515
402
+ 'C(#N)Cl',2.94356799915553
403
+ 'C(#N)Br',2.93862388168010
404
+ 'C1=CC(=CC=C1C(C2=CC=C(C=C2)Cl)C(Cl)(Cl)Cl)Cl',6.15165939778125
405
+ 'c(cccc1)(c1)C(C)C',2.56004605053309
406
+ 'CCCN(CCC)C(=O)SCC',3.87925249559703
407
+ 'NC(CCCC1)C1',3.21824710516194
408
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409
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410
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411
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412
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413
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414
+ 'c(cccc1)(c1)C=C',2.56281074475285
415
+ 'COC(=O)c1ccccc1S(=O)(=O)NC(=O)Nc2nc(OC)nc(C)n2',3.18339945768247
416
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417
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418
+ 'C(Cl)(Br)Br',3.86380195834146
419
+ 'C=C(Cl)Cl',3.84038967397096
420
+ 'C(C=CCl)Cl',4.33763486202989
421
+ 'COP(=O)(OC)OC(=CCl)c1cc(Cl)c(Cl)cc1Cl',3.86446577561058
422
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423
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424
+ 'O=C(NCCCC1)C1',2.95677386828604
425
+ 'c(cccc1)(c1)Cl',2.97219087736775
426
+ 'C(Cl)(Cl)Cl',3.29877173860401
427
+ 'ClCCl',3.20825373509371
428
+ 'C1C2C3C(C1C4C2O4)C5(C(=C(C3(C5(Cl)Cl)Cl)Cl)Cl)Cl',6.48391158599853
429
+ 'OCCO',1.79286663192634
430
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431
+ 'C(F)(Cl)(Cl)Cl',2.59506047452425
432
+ 'CCc1cccc(CC)c1N(COC)C(=O)CCl',4.28486094761281
433
+ 'c1ccccc1c2c(C)c(COC(=O)C3C(C)(C)C3C=C(Cl)C(F)(F)F)ccc2',4.92723460128442
434
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435
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436
+ 'c(cccc1)(c1)CC',2.56208837510252
437
+ 'O=C(N(SC(Cl)(Cl)Cl)C(=O)c1cccc2)c12',3.87004900844397
438
+ 'Clc1cc(C(F)(F)F)cnc1Oc2ccc(OC(C)C(=O)OC)cc2',5.57487232351041
439
+ 'C#N',2.94040947259108
440
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441
+ 'c1c(C(F)(F)F)cccc1N2C(=O)C(Cl)=C(NC)C=N2',3.77270454387038
442
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443
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444
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445
+ 'C(=C)Cl',4.68192429615426
446
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447
+ 'CC1(C(C1(C)C)C(=O)OC(C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C',4.14541137996302
448
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449
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450
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451
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452
+ 'Clc1cc(C(F)(F)F)ccc1Oc2cc(OCC)c(N(=O)(=O))cc2',4.55834892852739
453
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454
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455
+ 'CC(C)OC(=O)C(C1=CC=C(C=C1)Br)(C2=CC=C(C=C2)Br)O',4.21658723866328
456
+ 'C[N+](C)(C)CCCl',2.97460527968547
457
+ 'CCC(=C1C(=O)CC(CC1=O)CC(C)SCC)NOCC=CCl',3.62169695860399
458
+ 'CC1=NC(=NC(=C1)C2CC2)NC3=CC=CC=C3',3.80128998933051
459
+ 'N(c(cccc1)c1)c(cccc2)c2',3.83051794413252
460
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461
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462
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463
+ 'C(F)(F)(F)c1ccccc1C(=O)Nc2cccc(OC(C)C)c2',3.57009941427408
464
+ 'C(CCCCN=C(N)N)CCCNCCCCCCCCN=C(N)N',4.27216545257855
465
+ 'C1CN(C(=N1)N[N+](=O)[O-])CC2=CN=C(C=C2)Cl',4.17721556192143
466
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467
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468
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469
+ 'C1=CC(=C(C(=C1)F)C(=O)NC(=O)NC2=CC(=C(C=C2)OC(C(OC(F)(F)F)F)(F)F)Cl)F',4.13628410350378
470
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471
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472
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473
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475
+ 'C1=CC=C(C(=C1)C2=NN=C(N=N2)C3=CC=CC=C3Cl)Cl',4.24360591089568
476
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477
+ 'C1CC1NC2=NC(=C(C(=N2)N)C#N)N',3.93679970507275
478
+ 'C(C=C1)(=N(C=C1)CC2)C(N2=C3)=CC=C3',5.50950218614247
479
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480
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481
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482
+ 'CC1CN(CC(O1)C)CC(C)CC2=CC=C(C=C2)C(C)(C)C',5.25168418782516
483
+ 'C[Si](CN1C=NC=N1)(C2=CC=C(C=C2)F)C3=CC=C(C=C3)F',5.19782165018731
484
+ 'c1cc(Cl)cc(Cl)c1C(OCC=C)Cn2cncc2',4.29692796857781
485
+ 'CN(=CC=C1C(C=C2)=CC=N2C)C=C1',4.86356300300759
486
+ 'CCCCOCCOCCOCC1=CC2=C(C=C1CCC)OCO2',3.52947976153744
487
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488
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490
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491
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492
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493
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494
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496
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497
+ 'ClC(Cl)=CC1C(C)(C)C1C(=O)OC(C(#N))c2cccc(Oc3ccccc3)c2',3.92043344378224
498
+ 'ClC1CC2C(C1Cl)C3(Cl)C(=C(Cl)C2(Cl)C3(Cl)Cl)Cl',6.21460930807761
499
+ 'ClC4=C(Cl)C5(Cl)C3C1CC(C2OC12)C3C4(Cl)C5(Cl)Cl',6.58082159900658
500
+ 'C1C2C3C(C1C4C2O4)C5(C(=C(C3(C5(Cl)Cl)Cl)Cl)Cl)Cl',6.18288159033454
501
+ 'C1(C(C(C(C(C1Cl)Cl)Cl)Cl)Cl)Cl',4.79154110643314
502
+ 'CCC(=O)Nc1ccc(Cl)c(Cl)c1',3.45780196740732
503
+ 'C1(=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl)[N+](=O)[O-]',3.32418644119937
504
+ 'C1C2C(COS(=O)O1)C3(C(=C(C2(C3(Cl)Cl)Cl)Cl)Cl)Cl',5.14711652367221
505
+ 'O=C(N(SC(Cl)(Cl)Cl)C(=O)c1cccc2)c12',3.77313899543591
506
+ 'CC(C(=O)O)OC1=CC=C(C=C1)OC2=C(C=C(C=N2)C(F)(F)F)Cl',6.55834892852739
507
+ 'CCCCC(CN1C=NC=N1)(C#N)C2=CC=C(C=C2)Cl',4.46933393793126
508
+ 'Clc1cc(Cl)cc(Cl)c1OCCN(CCC)C(=O)n2cncc2',4.86838559832397
509
+ 'COP(=O)(NC(=O)(C))SC',4.86490452310016
510
+ 'CCOP(=O)(OCC)OC(=CCl)C1=C(C=C(C=C1)Cl)Cl',5.3796920956126
511
+ 'CCOP(=S)(OCC)SCCSCC',6.09596779022605
512
+ 'O=P(O)(O)CCCl',4.0806685706873
513
+ 'CCCSP(=O)(OCC)SCCC',4.95305958493745
514
+ 'CCOP(=O)(NC(C)C)Oc1ccc(SC)c(C)c1',5.25150573076352
515
+ 'COP(=S)(OC)Oc1ccc(SC)c(C)c1',5.58722449762503
516
+ 'OC(=O)C(N)CCP(C)(=O)O',4.71391476838473
517
+ 'OC(=O)CNCP(O)(O)=O',2.75095321211059
518
+ 'CCOC(=O)CC(SP(=S)(OC)OC)C(=O)OCC',2.96268235505315
519
+ 'COP(N)(=O)SC',5.68721882334643
520
+ 'CC(=CC(=O)OC)OP(=O)(OC)OC',5.80646736824669
521
+ 'CCOP(=S)(OCC)SCSCC',6.2114833717655
522
+ 'CCOP(=S)(OCC)SCSC(C)(C)C',6.68189008451404
523
+ 'S=P(OC)(OC)SCN1N=Nc2ccccc2C1(=O)',5.08988368084419
524
+ 'CCOP(=S)(OCC)OC1=NC(=C(C=C1Cl)Cl)Cl',5.54479494223028
525
+ 'CCOP(=S)(OCC)OC1=NC(=NC(=C1)C)C(C)C',4.71993889259734
526
+ 'CCC1=NC(=CC(=N1)OP(=S)(OC)OC)OCC',5.8126040303238
527
+ 'S=P(OC)(OC)SCN1C(=O)SC(OC)=N1',5.27636313027728
528
+ 'CCOP(=S)(OCC)SCN1C2=C(C=C(C=C2)Cl)OC1=O',5.26459183786176
529
+ 'COP(=S)(OC)SCN2C(=O)c1ccccc1C2(=O)',4.54725636091897
530
+ 'CCOC(=O)C1=CN2C(=CC(=N2)OP(=S)(OCC)OCC)N=C1C',4.97007298557879
531
+ 'CCOP(=S)(OCC)OC1=NN(C=N1)C2=CC=CC=C2',5.38203437103643
532
+ 'O=C(Oc(c(c(ccc1)cc2)c1)c2)NC',3.52552257057249
533
+ 'CC1=CC(=CC(=C1SC)C)OC(=O)NC',4.38429231462288
534
+ 'CNC(=O)ON=C(C)SC',3.90904789636717
535
+ 'CCCOC(=O)NCCCN(C)C',2.44226598159187
536
+ 'COC(=O)NC1=NC2=CC=CC=C2N1',3.40639632281981
537
+ 'CC1=C(N=C(N=C1OC(=O)N(C)C)N(C)C)C',4.2871938165512
538
+ 'CNC(=O)CCSCCSP(=O)(OC)OC',5.72599715999116
539
+ 'N(C(=S)SSC(N(C)C)=S)(C)C',4.30181261256647
540
+ 'C1=NNC(=N1)N',4.22572249207399
541
+ 'CCCCCCCCc1cc(N(=O)(=O))c(OC(=O)C=CC)c(c1)N(=O)(=O)',3.75539000391453
542
+ 'C1=CC=C(C=C1)[Sn](C2=CC=CC=C2)C3=CC=CC=C3',6.0669625480302
543
+ 'O=C(NC(=O)c(c(F)ccc1)c1F)Nc(ccc(c2)Cl)c2',4.64721982249128
544
+ 'N(C(=S)NC1)C1',4.91236296409098
545
+ 'C1=CC(=C(C(=C1)F)C(=O)NC(=O)NC2=CC(=C(C(=C2F)Cl)F)Cl)F',4.18310948429116
546
+ 'CCCSC1=CC2=C(C=C1)N=C(N2)NC(=O)OC',4.12275865288522
547
+ 'C1CN(CCN1CCCC(=O)C2=CC=C(C=C2)F)C3=CC=CC=N3',3.45437537377312
548
+ 'CC1(C2C(C3C(C(=O)C(=C(N)O)C(=O)C3(C(=O)C2=C(C4=C(C=CC(=C41)Cl)O)O)O)N(C)C)O)O',1.97849569899962
549
+ 'CC1=CC(=C(C=C1NC(=O)C2=CC(=CC(=C2O)I)I)Cl)C(C#N)C3=CC=C(C=C3)Cl',4.82156180249896
550
+ 'CN1CC2CC1CN2C3=C(C=C4C(=C3)N(C=C(C4=O)C(=O)O)C5CC5)F',3.85415878578584
551
+ 'C1=CC(=CC=C1C(C#N)C2=C(C=CC(=C2Cl)N3C(=O)NC(=O)C=N3)Cl)Cl',4.43418336046643
552
+ 'CC1=NC=C(N1C)[N+](=O)[O-]',3.97352186635665
553
+ 'CCN1CCN(CC1)C2=C(C=C3C(=C2)N(C=C(C3=O)C(=O)O)C4CC4)F',4.14059829999974
554
+ 'CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)NC(=O)C)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O',5.95429183284051
555
+ 'COCC(=O)NC1=C(C=CC(=C1)SC2=CC=CC=C2)NC(=NC(=O)OC)NC(=O)OC',4.04773898332238
556
+ 'CC1CCC2=C3N1C=C(C(=O)C3=CC(=C2)F)C(=O)O',2.81499362006104
557
+ 'COC(=O)NC1=NC2=C(N1)C=C(C=C2)S(=O)C3=CC=CC=C3',5.1977587356423
558
+ 'CC1(C2CC3C(C(=O)C(=C(N)O)C(=O)C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)N(C)C)O',3.47171656401627
559
+ 'C1CN(CCN1CCCC(=O)C2=CC=C(C=C2)F)C3=CC=CC=N3',4.03795195940707
560
+ 'CC(C)NCC(COC1=CC=CC2=C1C3=CC=CC=C3N2)O',4.62967091273678
561
+ 'C1=CC(=CC=C1C(C#N)C2=C(C=CC(=C2Cl)N3C(=O)NC(=O)C=N3)Cl)Cl',4.24854678350451
562
+ 'CC1C=CC=C2COC3C2(C(C=C(C3O)C)C(=O)OC4CC(CC=C(C1OC5CC(C(C(O5)C)OC6CC(C(C(O6)C)NC(=O)C)OC)OC)C)OC7(C4)C=CC(C(O7)C(C)C)C)O',5.55635182416848
563
+ 'COP(=S)(OC)Oc1ccc(SC)c(C)c1',5.79134448028095
564
+ 'C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl',4.56054897737691
565
+ 'C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl',4.86157897304089
566
+ 'CC(N(C)C)CN(C(=CC=C3)C1=C3)C(=CC=C2)C(=C2)S1',4.23385066979149
567
+ 'C1=C(C=C(C(=C1Cl)N)Cl)[N+](=O)[O-]',2.93578881098946
568
+ 'c(cccc1)(c1)C=C',2.41559561343340
data/test/data/acetaldehyde.sdf ADDED
@@ -0,0 +1,14 @@
1
+
2
+
3
+
4
+ 3 2 0 0 0 0 0 0 0 0 1 V2000
5
+ 2.3030 -0.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6
+ 1.1515 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7
+ 0.0000 -0.6656 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8
+ 1 2 1 0 0 0 0
9
+ 2 3 2 0 0 0 0
10
+ M END
11
+ > <ActivityOutcome_CPDBAS_Hamster>
12
+ active
13
+
14
+ $$$$