lazar 0.9.3 → 1.0.0

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Files changed (88) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -4
  3. data/README.md +5 -15
  4. data/VERSION +1 -1
  5. data/ext/lazar/extconf.rb +1 -1
  6. data/ext/lazar/rinstall.R +9 -7
  7. data/java/CdkDescriptorInfo.class +0 -0
  8. data/java/CdkDescriptorInfo.java +3 -2
  9. data/java/CdkDescriptors.class +0 -0
  10. data/java/CdkDescriptors.java +28 -28
  11. data/java/Rakefile +3 -3
  12. data/java/{cdk-1.4.19.jar → cdk-2.0-SNAPSHOT.jar} +0 -0
  13. data/lazar.gemspec +6 -7
  14. data/lib/algorithm.rb +2 -11
  15. data/lib/caret.rb +96 -0
  16. data/lib/classification.rb +14 -22
  17. data/lib/compound.rb +21 -87
  18. data/lib/crossvalidation.rb +80 -279
  19. data/lib/dataset.rb +105 -174
  20. data/lib/feature.rb +11 -18
  21. data/lib/feature_selection.rb +42 -0
  22. data/lib/import.rb +122 -0
  23. data/lib/lazar.rb +14 -4
  24. data/lib/leave-one-out-validation.rb +46 -192
  25. data/lib/model.rb +319 -128
  26. data/lib/nanoparticle.rb +98 -0
  27. data/lib/opentox.rb +7 -4
  28. data/lib/overwrite.rb +24 -3
  29. data/lib/physchem.rb +11 -10
  30. data/lib/regression.rb +7 -137
  31. data/lib/rest-client-wrapper.rb +0 -6
  32. data/lib/similarity.rb +65 -0
  33. data/lib/substance.rb +8 -0
  34. data/lib/train-test-validation.rb +69 -0
  35. data/lib/validation-statistics.rb +223 -0
  36. data/lib/validation.rb +17 -100
  37. data/scripts/mg2mmol.rb +17 -0
  38. data/scripts/mirror-enm2test.rb +4 -0
  39. data/scripts/mmol2-log10.rb +32 -0
  40. data/test/compound.rb +4 -94
  41. data/test/data/EPAFHM.medi_log10.csv +92 -0
  42. data/test/data/EPAFHM.mini_log10.csv +16 -0
  43. data/test/data/EPAFHM_log10.csv +581 -0
  44. data/test/data/loael_log10.csv +568 -0
  45. data/test/dataset.rb +195 -133
  46. data/test/descriptor.rb +27 -18
  47. data/test/error.rb +2 -2
  48. data/test/experiment.rb +4 -4
  49. data/test/feature.rb +2 -3
  50. data/test/gridfs.rb +10 -0
  51. data/test/model-classification.rb +106 -0
  52. data/test/model-nanoparticle.rb +128 -0
  53. data/test/model-regression.rb +171 -0
  54. data/test/model-validation.rb +19 -0
  55. data/test/nanomaterial-model-validation.rb +55 -0
  56. data/test/setup.rb +8 -4
  57. data/test/validation-classification.rb +67 -0
  58. data/test/validation-nanoparticle.rb +133 -0
  59. data/test/validation-regression.rb +92 -0
  60. metadata +50 -121
  61. data/test/classification.rb +0 -41
  62. data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +0 -13553
  63. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv +0 -436
  64. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv +0 -568
  65. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv +0 -87
  66. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv +0 -978
  67. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv +0 -1120
  68. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv +0 -1113
  69. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv +0 -850
  70. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv +0 -829
  71. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Rat.csv +0 -1198
  72. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv +0 -1505
  73. data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv +0 -581
  74. data/test/data/FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv +0 -1217
  75. data/test/data/LOAEL_log_mg_corrected_smiles.csv +0 -568
  76. data/test/data/LOAEL_log_mmol_corrected_smiles.csv +0 -568
  77. data/test/data/boiling_points.ext.sdf +0 -11460
  78. data/test/data/cpdb_100.csv +0 -101
  79. data/test/data/hamster_carcinogenicity.ntriples +0 -618
  80. data/test/data/hamster_carcinogenicity.sdf +0 -2805
  81. data/test/data/hamster_carcinogenicity.xls +0 -0
  82. data/test/data/hamster_carcinogenicity.yaml +0 -352
  83. data/test/dataset-long.rb +0 -114
  84. data/test/lazar-long.rb +0 -92
  85. data/test/lazar-physchem-short.rb +0 -31
  86. data/test/prediction_models.rb +0 -20
  87. data/test/regression.rb +0 -43
  88. data/test/validation.rb +0 -108
@@ -1,581 +0,0 @@
1
- STRUCTURE_SMILES,LC50_mmol
2
- O=C(OC(C2=CC=CC(OC3=CC=CC=C3)=C2)C#N)[C@H](C1=CC=C(OC(F)F)C=C1)[C@H](C)C,0.000000421
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- O=C(C(C1=CC=C(C=C1)Cl)C(C)C)OC(C2=CC=CC(=C2)OC3=CC=CC=C3)C#N,0.000012100
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- O=C([C@](C(C=C4OC)=C(C=C4OC)OC3)([H])[C@]3([H])O2)C(C=C5)=C2C1=C5O[C@@H]([C@@](C)=C)C1,0.000013200
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- C1=CC=C2C3=CC=CC=C3N(C2=C1)C=C,0.000016600
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- CC(C)=CC1C(C)(C)C1C(=O)OCC2=COC(CC3=CC=CC=C3)=C2,0.000018200
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- C1=CC=C(OC2=CC=CC=C2)C=C1COC(=O)C3C(C)(C)C3C=C(Cl)Cl,0.000040900
8
- CCOP(=S)(OCC)SCSC(C)(C)C,0.000046100
9
- CC[Sn](CC)(CC)CC,0.000046800
10
- OC1=C(C=C(C(=C1CC2=C(C(=CC(=C2Cl)Cl)Cl)O)Cl)Cl)Cl,0.000051600
11
- CCCC[Sn](CCCC)(CCCC)CCCC,0.000130000
12
- OC1=C(Br)C(Br)=C(Br)C(Br)=C1Br,0.000190000
13
- ClC1=CC(Cl)=C([N+]([O-])=O)C=C1[N+]([O-])=O,0.000192000
14
- O=C1C2=C(C=CC=C2)N=NN1CSP(=S)(OC)OC,0.000202000
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- ClCC1=CC=C(CCl)C=C1,0.000223000
16
- OC1=C(C=C(C=C1C(C)(C)C)C(C)(C)C)C(C)(C)C,0.000232000
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- CCOP(=S)(OC1=CC=C(C=C1)[N+](=O)[O-])C2=CC=CC=C2,0.000243000
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- C1=CC=CC=C1OC(=O)C2=CC=CC=C2C(=O)OC3=CC=CC=C3,0.000251000
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- NC1=CC=C(CCCCCCCCCC)C=C1,0.000266000
20
- C=CC=O,0.000303000
21
- CCCCCCCCCCCCCN,0.000328000
22
- Cl\C(Cl)=C(Cl)/C(Cl)=C(Cl)\Cl,0.000345000
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- [H][C@]1(CC2)C(C)(C)CCC[C@@](C)1[C@@H](CC[C@@](O)(C)C=C)C2=C,0.000413000
24
- C1=CC=CC=C1SSC2=CC=CC=C2,0.000504000
25
- CCCCCCCCCCCCN,0.000556000
26
- NC1=CC=C(CCCCCCCC)C=C1,0.000584000
27
- CCCCCCCCCC1=CC=C(O)C=C1,0.000635000
28
- C1=CC=C2C(=C1)C(=O)C(C)=CC2=O,0.000639000
29
- ClC1=CC=C(SCSP(=S)(OCC)OCC)C=C1,0.000700000
30
- ClC1=C([N+]([O-])=O)C(Cl)=C([N+]([O-])=O)C(Cl)=C1,0.000818000
31
- S=P(OC1=NC(=C(C=C1Cl)Cl)Cl)(OCC)OCC,0.000907000
32
- N1=C(C2=CC=CC=C2)C=CC=C1C3=CC=CC=C3,0.000908000
33
- OC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,0.000912000
34
- BrC(Br)C1=C(C(Br)Br)C=CC=C1,0.001040000
35
- O=C2N5[C@@]3([H])[C@@]1([H])[C@](C[C@]4([H])N(C7)CC[C@]34C6=C5C=CC=C6)([H])C7=CCO[C@]([H])1C2.O=C9N%12[C@@]%10([H])[C@@]8([H])[C@](C[C@]%11([H])N(C%14)CC[C@]%10%11C%13=C%12C=CC=C%13)([H])C%14=CCO[C@]([H])8C9.O=S(O)(O)=O,0.001110000
36
- C1=C(C=O)C=CC=C1OC2=CC(Cl)=C(Cl)C=C2,0.001120000
37
- OC1=CC=C(Cl)C=C1CC2=CC(Cl)=CC=C2O,0.001150000
38
- NC1=C(Cl)C(Cl)=CC(Cl)=C1Cl,0.001170000
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- CCCCCCCCCCCN,0.001230000
40
- C1=CC(C(C)(C)C)=CC=C1OC2=CC=CC(C=O)=C2,0.001450000
41
- C=C(CCl)C(Cl),0.001520000
42
- OC1=C(C=C(C=C1C(C)(C)C)C)C(C)(C)C,0.001650000
43
- OC(C1=CC=C(C=C1)Cl)(C2=CC=C(C=C2)Cl)C(Cl)(Cl)Cl,0.001670000
44
- CCCCCCCCOC1=CC=CC=C1NC(=O)C,0.001710000
45
- OC1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1,0.001770000
46
- CCCCCCCCCCCC(=O)C,0.001810000
47
- N1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl,0.001870000
48
- ClCC1=CC(C=C)=CC=C1,0.002030000
49
- C(CC(CC1CC23)C2)(C1)C3,0.002060000
50
- C=CCCCCCCC=C,0.002100000
51
- CCCCOC(=O)C1=CC=C(C(=O)OCCCC)C=C1,0.002120000
52
- Cl\C=C\CCl,0.002150000
53
- OC1=C(C=C(C=C1C(CC)C)[N+](=O)[O-])[N+](=O)[O-],0.002230000
54
- CCCCCCCCCCCC#N,0.002370000
55
- C1=C(C(=O)CBr)C(OC)=CC=C1OC,0.002550000
56
- OC1=C(I)C=C(I)C=C1I,0.002560000
57
- C1=CC=CC=C1OP(=O)(OC2=CC=CC=C2)OC3=CC=CC=C3,0.002660000
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- CCCCOC(=O)C=CC(=O)OCCCC,0.002760000
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- O=[C@](O)[C@@]3(C)[C@@]1([H])[C@@](CCC3)(C)[C@]2([H])C(C[C@](C=C)(C)CC2)=CC1,0.002880000
60
- BrC1=C(O)C(C=O)=CC(Br)=C1,0.003040000
61
- CC(C)(C)C1=CC=C(C=C)C=C1,0.003060000
62
- CCCCOC(=O)C1=CC=CC(C(=O)OCCCC)=C1,0.003230000
63
- C#CC(O)CCCCC,0.003270000
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- C1=CC=C(C(=O)OCCCC)C(=C1)C(=O)OCCCC,0.003590000
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- ClC1=C(O)C(Cl)=CC(=C1)C(C2=CC(Cl)=C(O)C(=C2)Cl)(C)C,0.003630000
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- O=C(NC)OC1=CC=CC(C2)=C1OC2(C)C,0.003810000
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- CCCCCCNCCCCCC,0.004210000
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- [O-][N+](=O)C1=CC=C([N+]([O-])=O)C=C1,0.004220000
69
- ClC(Cl)C1=C(Cl)C=CC=C1Cl,0.004220000
70
- BrCCCCCCCC,0.004340000
71
- OC1=C(Cl)C(Cl)=C(Cl)C=C1Cl,0.004440000
72
- CC(C=NOC(=O)NC)(SC)C,0.004520000
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- CCOC(=O)C(Cl)C(=O)OCC,0.004880000
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- C1(C=O)=C(O)C=CC(Cl)=C1,0.004920000
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- O=[C@](O)[C@@]1(C)[C@]([C@]([C@]([H])2CC3)(C)CCC1)([H])CCC2=C\C3=C(C)/C,0.004930000
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- OC1=C(O)C=C(Cl)C(Cl)=C1,0.004970000
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- OC1=C(O)C(Cl)=C(Cl)C(Cl)=C1Cl,0.005120000
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- C1(C=O)=CC(C(F)(F)F)=CC=C1,0.005310000
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- C1=CC(F)=CC=C1OC2=CC=C(F)C=C2,0.005480000
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- C=CCO,0.005510000
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- C1=CC=CC(O)=C1C(=O)OC2=CC=CC=C2,0.005510000
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- C1(C=O)=C(F)C(F)=C(F)C(F)=C1F,0.005610000
83
- C1=CC(O)=CC=C1/N=N/C2=CC=CC=C2,0.006000000
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- ClC(C(Cl)(Cl)Cl)(Cl)Cl,0.006000000
85
- CCCCCCCCCCC(=O)C,0.006400000
86
- OC(CC/C=C(C)/CC/C=C(C)\C)(C)C=C,0.006430000
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- C1(C=O)=C(O)C=CC(Br)=C1,0.006460000
88
- CCCCCCCCCCN,0.006550000
89
- C1=CC=CC=C1C(=O)CC(=O)C,0.006780000
90
- C(O)C#CCCCCCCC,0.006940000
91
- O=[C@](O)[C@@]3(C)[C@@]2([H])[C@@](CCC3)(C)C1=C(CC2)C=[C@@]([C@@H](C)C)C=C1,0.006990000
92
- C=CC(=O)OCCCCCC,0.007100000
93
- IC(I)I,0.007420000
94
- CC(C)(C)SSC(C)(C)C,0.007680000
95
- C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2,0.007690000
96
- C=C(C)C(=O)OCC=C,0.007850000
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- O=[C@](O)[C@@]3(C)[C@@]1([H])[C@@](CCC3)(C)[C@]2([H])C(C=[C@@]([C@@H](C)C)CC2)=CC1,0.007870000
98
- BrCCCCCCC,0.008210000
99
- N#CCC#N,0.008480000
100
- OC1=C(C)C=C([N+]([O-])=O)C=C1[N+]([O-])=O,0.008730000
101
- CCCCCCCCCC(=O)C,0.008810000
102
- C1=CC=CC2C3=CC=CC=C3OC1=2,0.008920000
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- C1=C(C(=O)C)C(Cl)=C(Cl)C(Cl)=C1,0.008950000
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- C1=CC=CC(N)=C1C(=O)C2=CC=C(Cl)C=C2,0.009150000
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- CNC(=O)OC1=CC(C)=C(N(C)C)C=C1,0.009360000
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- C=CC(=O)OC1CCCCC1,0.009600000
107
- CCOP(OCC)(=S)SCCSCC,0.009950000
108
- O=CC1=C(Cl)C=C(Cl)C=C1,0.010300000
109
- BrCCCBr,0.010400000
110
- CCOC(=O)CCCCCCCCC(=O)OCC,0.010500000
111
- OC1=C(O)C=C(Cl)C=C1,0.010900000
112
- C1(C=O)=C(F)C=CC=C1,0.010900000
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- C1=CC=C2C=CC=C3C2=C1CC3,0.011200000
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- C1=CC(C=O)=CC(OC)=C1OCCCCCC,0.011300000
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- C1=CC=CC=C1CCCCC,0.011500000
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- C1=CC=CC=C1OC2=CC=C([N+](=O)[O-])C=C2,0.012300000
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- CSC(C)=NOC(=O)NC,0.013000000
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- CCCCOC(=O)CCCCC(=O)OCCCC,0.014100000
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- [Na+].O.O.[O-]C1=C([N+]([O-])=O)C=C([N+]([O-])=O)C2=CC=CC=C12,0.014500000
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- CCCSCCCCSCCC,0.014500000
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- C1(C=O)=C(O)C=C(OC)C=C1OC,0.014700000
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- CCCCCCCCCN,0.015000000
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- O=C1OC2=CC=CC=C2C(O)=C1CC3=C(O)C4=CC=CC=C4OC3=O,0.015200000
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- CCCCCCCCCCO,0.015200000
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- NC1=CC=C(OCCCCCC)C=C1,0.015600000
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- ClC1=CC=C(C=O)C=C1,0.015600000
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- C#CC(O)CCCC,0.015700000
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- C1=CC=CC=C1C2=CC(=O)C3=CC=CC=C3O2,0.015700000
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- C(C1C=CC(=CC=1)O)(CC)(C)C,0.015800000
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- C1(C=O)=C(O)C(OC)=CC=C1,0.015800000
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- C1=CC(Cl)=CC2N=C(S)SC1=2,0.015900000
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- C=CC(=O)OCC(C)C,0.016400000
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- ClC1=C(Cl)C=C(Cl)C=C1,0.016500000
134
- CCCSSCCC,0.017000000
135
- BrC1=C(Br)C=CC=C1,0.017200000
136
- ClCC#N,0.017800000
137
- CC1=CC(Cl)=C(Cl)C=C1,0.018100000
138
- OC1=C([N+](=O)[O-])C=CC([N+]([O-])=O)=C1,0.018200000
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- C1=C(I)C(O)=C(I)C=C1C#N,0.018300000
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- NC1=C(Cl)C(Cl)=C(Cl)C=C1,0.018500000
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- C1(CC)=CC=CC(CC)=C1N(COC)C(=O)CCl,0.018500000
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- N1=C(Br)NC(Br)=C1Br,0.020100000
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- C1=CC=CC=C1OC(=O)C2=C(O)C=C(N)C=C2,0.020800000
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- ClC1=CC=C([N+](=O)[O-])C=C1C=O,0.020900000
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- C1=CC=CC=C1OC2=CC=CC=C2,0.023500000
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157
- OC1=C(C=C(C=C1Cl)Cl)Cl,0.024800000
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- C=CC(=O)OCC(O)C,0.026000000
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- C1(C)(C)CCCC(C)=C1C=CC(C)=O,0.026500000
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- S=P(OC1=NC(=NC(=C1)C)C(C)C)(OCC)OCC,0.030700000
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- O=C(C(=NOC(=O)NC)SC)N(C)C,0.030900000
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- CC(=O)CCCCCCCC,0.030900000
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177
- CC(C)=CC=C(C)C,0.034300000
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- C1=C(/C=C/C=O)C=CC(N(C)C)=C1,0.036700000
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- ClC(C(Cl)Cl)(Cl)Cl,0.037200000
183
- CC(C)CC=O,0.037700000
184
- CCCCCCCCC#N,0.037700000
185
- C1(Br)=CSC=C1,0.038000000
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