lazar 0.0.5 → 0.0.6

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Files changed (64) hide show
  1. checksums.yaml +4 -4
  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/Makefile +5 -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 +28 -0
  24. data/lib/SMARTS_InteLigand.txt +983 -0
  25. data/mongoid.yml +8 -0
  26. data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +13553 -0
  27. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv +436 -0
  28. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv +568 -0
  29. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv +87 -0
  30. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv +978 -0
  31. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv +1120 -0
  32. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv +1113 -0
  33. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv +850 -0
  34. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv +829 -0
  35. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Rat.csv +1198 -0
  36. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv +1505 -0
  37. data/test/data/EPAFHM.csv +618 -0
  38. data/test/data/EPAFHM.medi.csv +100 -0
  39. data/test/data/EPAFHM.mini.csv +22 -0
  40. data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv +581 -0
  41. data/test/data/FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv +1217 -0
  42. data/test/data/ISSCAN-multi.csv +59 -0
  43. data/test/data/LOAEL_log_mg_corrected_smiles.csv +568 -0
  44. data/test/data/LOAEL_log_mmol_corrected_smiles.csv +568 -0
  45. data/test/data/acetaldehyde.sdf +14 -0
  46. data/test/data/boiling_points.ext.sdf +11460 -0
  47. data/test/data/cpdb_100.csv +101 -0
  48. data/test/data/hamster_carcinogenicity.csv +86 -0
  49. data/test/data/hamster_carcinogenicity.mini.bool_float.csv +11 -0
  50. data/test/data/hamster_carcinogenicity.mini.bool_int.csv +11 -0
  51. data/test/data/hamster_carcinogenicity.mini.bool_string.csv +11 -0
  52. data/test/data/hamster_carcinogenicity.mini.csv +11 -0
  53. data/test/data/hamster_carcinogenicity.ntriples +618 -0
  54. data/test/data/hamster_carcinogenicity.sdf +2805 -0
  55. data/test/data/hamster_carcinogenicity.xls +0 -0
  56. data/test/data/hamster_carcinogenicity.yaml +352 -0
  57. data/test/data/hamster_carcinogenicity_with_errors.csv +88 -0
  58. data/test/data/kazius.csv +4070 -0
  59. data/test/data/multi_cell_call.csv +1067 -0
  60. data/test/data/multi_cell_call_no_dup.csv +1057 -0
  61. data/test/data/multicolumn.csv +8 -0
  62. data/test/data/rat_feature_dataset.csv +1179 -0
  63. data/test/data/wrong_dataset.csv +8 -0
  64. metadata +108 -8
data/test/data/ISSCAN-multi.csv ADDED
@@ -0,0 +1,59 @@
1
+ SMILES,ISSCAN
2
+ CC(CCl)Cl,1
3
+ C(Br)(Br)Br,1
4
+ C=C(C)CCl,1
5
+ O=Cc1ccco1,1
6
+ COC34(C(COC(N)=O)C=1C(=O)C(N)=C(C)C(=O)C=1N4(CC2NC23)),1
7
+ CC(N)Cc1ccccc1.CC(N)Cc1ccccc1,1
8
+ Cc1cc(ccc1(N))C(=C2C=CC(=N)C=C2)c3ccc(N)cc3,1
9
+ Oc1ccc(cc1)c2ccccc2,1
10
+ CC(C)C=O,1
11
+ N#CC(C#N)=Cc1ccccc1Cl,1
12
+ Nc1ccc(cc1(N))[N+](=O)[O-],2
13
+ NC(CCC(=O)NNc1ccc(CO)cc1)C(O)=O,2
14
+ c1ccc2c(c1)nc(s2)SSc4nc3ccccc3s4,2
15
+ C=CC=O,2
16
+ CC(=O)Nc3cccc2Cc1ccccc1c23,2
17
+ Cc1cccc2cccnc12,2
18
+ Cc1ccc2ncccc2(c1),2
19
+ CBr,2
20
+ Nc1cc(ccc1(C(=O)O))[N+](=O)[O-],2
21
+ C1N2CN3CN1CN(C2)C3,2
22
+ O=[N+]([O-])c2cccc1ccccc12,2
23
+ Oc1cccc2cccnc12,2
24
+ O=CC(=C(C(=O)O)Cl)Cl,2
25
+ CC1CN(N=O)C(=O)NC1(=O),2
26
+ O1C2C1C3C4C2C5C3C6(C4(C(C5(C6(Cl)Cl)Cl)Cl)Cl)Cl,2
27
+ OCCNc1ccc(cc1[N+](=O)[O-])N(CCO)CCO,2
28
+ Cc1cc(N)ccc1(N).OS(=O)(=O)O,2
29
+ CC(O)CCl,2
30
+ O=[N+]([O-])C(Cl)(Cl)Cl,2
31
+ Cc1ccc(cc1)S(=O)(=O)NC(=O)NN2CCCCCC2,2
32
+ c1cc2ccc3cccc4ccc(c1)c2c34,2
33
+ CC(=O)Nc1ccc(cc1)C(=O)CCl,2
34
+ FC(F)Cl,2
35
+ CN(N=O)c1ccc(cc1)[N+](=O)[O-],2
36
+ C=CC,2
37
+ Oc4c(cc1cc(ccc1c4(N=Nc2ccc(c3ccccc23)S(=O)(=O)[O-]))S(=O)(=O)[O-])S(=O)(=O)[O-],0
38
+ CC=NN(C)C=O,0
39
+ Nc2ccc(N=Nc1ccccc1)c(N)n2,0
40
+ Cc3cc(C)c(N=Nc1cc(c2ccccc2(c1(O)))S(=O)(=O)[O-])c(c3)S(=O)(=O)[O-],0
41
+ [O-]c1ccccc1c2ccccc2,0
42
+ NNC(N)=O,0
43
+ CNNCc1ccc(cc1)C(=O)NC(C)C,0
44
+ c1cc(c(cc1c2ccc(c(c2Cl)Cl)Cl)Cl)Cl,0
45
+ CCN(Cc1cccc(c1)S(=O)(=O)[O-])c2ccc(cc2)C(=C3C=CC(C=C3)=[N+](CC)Cc4cccc(c4)S(=O)(=O)[O-])c5ccc(cc5)S(=O)(=O)[O-],0
46
+ COC(=O)C(c1ccccc1)C2CCCCN2,0
47
+ CCCCC(CC)COS(=O)(=O)[O-],0
48
+ Nc1ccccc1,0
49
+ Cc1cccc(N)c1,0
50
+ CN(C)CCN(Cc1cccs1)c2ccccn2,0
51
+ CN(C)CCOC(C)(c1ccccc1)c2ccccn2,0
52
+ Cc1cc(C)c(cc1(C))N=Nc3c(O)c(cc2cc(ccc23)S(=O)(=O)[O-])S(=O)(=O)[O-],0
53
+ Cc1ccccc1(N),0
54
+ CCC1(C(=O)N=C([O-])NC1(=O))c2ccccc2,0
55
+ Nc5cc(cc6cc(c(N=Nc1ccc(cc1(O))c4ccc(N=Nc2c(O)c3c(N)cc(cc3(cc2S(=O)(=O)[O-]))S(=O)(=O)[O-])c(O)[c-]4)c(O)c56)S(=O)(=O)[O-])S(=O)(=O)[O-],0
56
+ O=C1[N-]S(=O)(=O)c2ccccc12,0
57
+ CN(C)c1ccc(cc1)C(c2ccc(cc2)N(C)C)=C3C=CC(C=C3)=[N+](C)C,0
58
+ C13(C4(C2(C5(C(C1(C2(Cl)Cl)Cl)(C3(C(C45Cl)(Cl)Cl)Cl)Cl)Cl)Cl)Cl)Cl,0
59
+ CCOCCc1c(nc(N)[n+]2[nH]cnc12)c3ccccc3,0
data/test/data/LOAEL_log_mg_corrected_smiles.csv ADDED
@@ -0,0 +1,568 @@
1
+ SMILES,LOAEL_log_mg_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+]',3.57275546515422
3
+ 'O1C(=O)C(O)=C(O)C1C(O)CO',3.48444220764241
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',2.69897000433602
5
+ 'c(cccc1)(c1)C(C)C',2.66464197555613
6
+ 'O=C(OCCCC)c(c(ccc1)C(=O)OCCCC)c1',2.77815125038364
7
+ 'O=C(OCC)c(c(ccc1)C(=O)OCC)c1',3.64689362416774
8
+ 'O=C(OC(OC(OC1C)C)C1)C',2.09691001300806
9
+ 'Oc(c(ccc1)C)c1C',0.778151250383644
10
+ 'Oc(ccc(c1C)C)c1',1.14612803567824
11
+ 'O=C(OCC)C=C',2.39445168082622
12
+ 'c(cccc1)(c1)CC',2.61066016308988
13
+ 'OCCO',2.39794000867204
14
+ 'c(ccc1C(=O)OCC(=O)OCC)cc1C(=O)OCC',3.39794000867204
15
+ 'O=C',1.91381385238372
16
+ 'O=C(O)C=CC(=O)O',3.03382569395331
17
+ 'OCC(O)CO',3.83777776955373
18
+ 'O=C(OC)c(ccc(O)c1)c1',3.17609125905568
19
+ 'O=C(OCCC)c(ccc(O)c1)c1',3.17609125905568
20
+ 'CC(CCC(=O)(O))C3CCC4C2CCC1CC(O)CCC1(C)C2CCC34C',2.69897000433602
21
+ 'OC(C(CCC1C)C(C)C)C1',2.77305469336426
22
+ 'O=C(O)C(=C)C',2.39445168082622
23
+ 'O=C(OC)c(c(O)ccc1)c1',2.55630250076729
24
+ 'Oc(cccc1)c1',2.53655844257153
25
+ 'O=C(OCCC)c(cc(O)c(O)c1O)c1',2.93651374247889
26
+ 'OCC(O)C1C(O)=C(O)C(=O)O1',3.19145101446490
27
+ 'c(cccc1)(c1)C=C',1.32221929473392
28
+ 'O=Cc(occ1)c1',1.77815125038364
29
+ 'NCCNc1cccc2ccccc12',1.89762709129044
30
+ 'CN(C)(C)CCCl',2.43933269383026
31
+ 'O=C(Nc(ccc(c1)C(=O)CCl)c1)C',3.19865708695442
32
+ 'c(ccc(c1)Cl)(c1)C(c(ccc(c2)Cl)c2)C(Cl)(Cl)Cl',1.50514997831991
33
+ 'CC(Oc1cc(Cl)c(Cl)cc1Cl)C(=O)(O)',0.939519252618618
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',3.32221929473392
35
+ 'O=N(=O)C(C=C1)=CC(OCCO)=C1NCCO',2.35983548233989
36
+ 'Cc1cccc(CC)c1N(C(=O)CCl)COCC',1.69897000433602
37
+ 'C1=C(C(=CC=C1OC2=CC=C(C=C2Cl)C(F)(F)F)[N+](=O)[O-])C(=O)[O-].[Na+]',2.25527250510331
38
+ 'CCc1cccc(CC)c1N(COC)C(=O)CCl',1.17609125905568
39
+ 'O=C(Nc(ccc(OCC)c1N)c1)C',3.07371835034612
40
+ 'Oc(ccc(N)c1)c1',2.83632411570675
41
+ 'CC(N)CC(=CC=C1)C=C1',0.698970004336019
42
+ 'O(c(ccc(c1)C=CC)c1)C',2.53655844257153
43
+ 'COc1ccc(N)cc1',2.67577834167409
44
+ 'O=C(O)c(c(N)ccc1)c1',3.43949059038968
45
+ 'Clc2cccc(c2)c1ccccc1',0.602059991327962
46
+ 'O=C(NC(C(=O)OC)Cc(cccc1)c1)C(N)CC(=O)O',2.16731733474818
47
+ 'n1c2ccc(Cl)cc2ncc1Oc3ccc(OC(C)C(=O)OCC)cc3',0.568201724066995
48
+ 'COC(=O)NS(=O)(=O)c1ccc(N)cc1',2.25527250510331
49
+ 'S=P(OC)(OC)SCN1N=Nc2ccccc2C1(=O)',-0.443697499232713
50
+ 'CNC(=O)Oc1ccccc1OC(C)C',1.69897000433602
51
+ 'CC(C)(C)C(=O)C(Oc1ccc(Cl)cc1)n2cncn2',1.39794000867204
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',2.85733249643127
53
+ 'c(c(cccc1)c1)(cccc2)c2',2.39794000867204
54
+ 'BrC(Cl)Cl',2.11394335230684
55
+ 'ClC(Cl)C(Cl)(Cl)SN2C(=O)C1CC=CCC1C2(=O)',1.07918124604762
56
+ 'O=C(Oc(c(c(ccc1)cc2)c1)c2)NC',1.19312459835446
57
+ 'CC1=C(SCCO1)C(=O)Nc2ccccc2',1.47712125471966
58
+ 'ClC1CC2C(C1Cl)C3(Cl)C(=C(Cl)C2(Cl)C3(Cl)Cl)Cl',-0.568636235841013
59
+ 'O=C(O)CCl',1.47712125471966
60
+ 'ClC(=CC=C1N)C=C1',0.778151250383644
61
+ 'CC(C)OC(=O)C(O)(c1ccc(Cl)cc1)c2ccc(Cl)cc2',0.954242509439325
62
+ 'n1c(OC)nc(C)nc1NC(=O)NS(=O)(=O)c2ccccc2Cl',1.39794000867204
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',2.8668778143375
64
+ 'S=P(OCC)(OCC)Oc1ccc2C(C)=C(Cl)C(=O)Oc2c1',-0.0969100130080564
65
+ 'CNP(=O)(OC)Oc1ccc(cc1Cl)C(C)(C)C',0.602059991327962
66
+ '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',3.20411998265593
67
+ 'n1c(N)nc(N)nc1NC2CC2',1.17609125905568
68
+ 'COC(=O)c1c(Cl)c(Cl)c(C(=O)OC)c(Cl)c1Cl',2.69897000433602
69
+ 'O=C(O)C(Cl)(Cl)C',1.44978684698577
70
+ 'Nc1cc(N)c(O)cc1',1.39794000867204
71
+ 'FC(F)(Cl)Cl',2.17609125905568
72
+ 'ClCCl',1.69897000433602
73
+ 'O=P(OC)(OC)OC=C(Cl)Cl',0.361727836017593
74
+ 'OC(c1ccc(Cl)cc1)(c2ccc(Cl)cc2)C(Cl)(Cl)Cl',1.30102999566398
75
+ 'ClC4=C(Cl)C5(Cl)C3C1CC(C2OC12)C3C4(Cl)C5(Cl)Cl',-1.30102999566398
76
+ 'CN(=C1C(C=C2)=CC=C2)N(C)C(=C1)C(C=C3)=CC=C3',2.09691001300806
77
+ 'O=C(NC(=O)c(c(F)ccc1)c1F)Nc(ccc(c2)Cl)c2',0.903089986991944
78
+ 'CC1=C(C)S(=O)(=O)CCS1(=O)=O',1
79
+ 'O=C(NC)CSP(OC)(OC)=S',-0.602059991327962
80
+ 'COc1ccc(N)c(OC)c1',2.44090908206522
81
+ 'COP(=O)OC',2
82
+ 'CC(=C(N(=O)=O)C=C1N(=O)=O)C=C1',1.53147891704226
83
+ 'CN(C)C(=O)C(c1ccccc1)c2ccccc2',1.47712125471966
84
+ 'N(c(cccc1)c1)c(cccc2)c2',1.49136169383427
85
+ 'C(C=C1)(=N(C=C1)CC2)C(N2=C3)=CC=C3',-0.236572006437063
86
+ 'CCOP(=S)(OCC)SCCSCC',-1
87
+ 'NC(=S)NNC(N)=S',2.97634997900327
88
+ 'O=C(N(C)C)Nc(ccc(c1Cl)Cl)c1',0.778151250383644
89
+ 'O=P(O)(O)CCCl',2.17609125905568
90
+ 'O=C(OCC)C(O1)C1(c(cccc2)c2)C',2.24303804868629
91
+ 'COC(=O)NC(=NC1=C2)NC1=CC(=C2)SC(C=C3)=CC=C3',1.17609125905568
92
+ 'CN1C=C(c2ccccc2)C(=O)C(c3cc(C(F)(F)F)ccc3)=C1',1.39794000867204
93
+ 'c1cc(C(F)(F)F)cc(Cl)c1NC(C(C)C)C(=O)OC(C(#N))c2cccc(Oc3ccccc3)c2',0.397940008672038
94
+ 'S=P(OCC)(Sc1ccccc1)CC',0.198657086954423
95
+ 'n1c(C)nc(OC)nc1NC(=O)NS(=O)(=O)c2ccsc2C(=O)OC',1.39794000867204
96
+ 'C(C(C(C(C1Cl)Cl)Cl)Cl)(C1Cl)Cl',0.698970004336019
97
+ 'O=N(=O)N(CN1N(=O)=O)CN(C1)N(=O)=O',0.176091259055681
98
+ 'O=C(N=C(N(C1(=O))C)N(C)C)N1C(CCCC2)C2',1.69897000433602
99
+ 'n(c(c(ccc1)cc2)c1O)c2',2.15533603746506
100
+ 'c1cc(Cl)cc(Cl)c1C(OCC=C)Cn2cncc2',1.60205999132796
101
+ 'COc1cccc(OC)c1C(=O)Nc2onc(C(C)(CC)CC)c2',1.70500795933334
102
+ 'n1c(OC)cc(OC)nc1NC(=O)NS(=O)(=O)Cc2ccccc2C(=O)OC',2.48995847942483
103
+ 'CCOC(=O)CC(SP(=S)(OC)OC)C(=O)OCC',1.69897000433602
104
+ 'CN(C)(CCC1)CC1',2.17609125905568
105
+ 'O=P(SCCCC)(SCCCC)SCCCC',0.0969100130080564
106
+ 'COCC(=O)N(C(C)C(=O)OC)c1c(C)cccc1C',1.79588001734408
107
+ 'S=P(OC)(OC)SCN1C(=O)SC(OC)=N1',0.301029995663981
108
+ 'CNC(=O)ON=C(C)SC',1
109
+ 'COP(=S)(OC)Oc1ccc(cc1)N(=O)(=O)',-0.602059991327962
110
+ 'O=C1N(N)C(SC)=NN=C1C(C)(C)C',1.17609125905568
111
+ 'COP(=O)(OC)OC(Br)C(Cl)(Cl)Br',0.301029995663981
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',1.85733249643127
113
+ 'O=N(=O)c(ccc(c1N)C)c1',0.903089986991944
114
+ 'O=N(=O)c(c(N)ccc1N)c1',1.93951925261862
115
+ 'O=C(O)C(=C(N)C=C1N(=O)=O)C=C1',3.07371835034612
116
+ 'O=N(=O)c(c(c(ccc1)cc2)c1)c2',2.21748394421391
117
+ 'c12c(N=Nc3ccccc3)c(O)ccc1cc(S(=O)(=O)O)cc2',2.25527250510331
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320
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327
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368
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370
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385
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392
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399
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402
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410
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418
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419
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420
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428
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439
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