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/hamster_carcinogenicity.sdf ADDED
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1639
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1643
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1644
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1673
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1730
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1758
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2473
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2477
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2479
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2480
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2481
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2495
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2498
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2499
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2511
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2513
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2515
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2517
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2518
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2519
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2531
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2532
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2533
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2560
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2561
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2562
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2564
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2565
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2566
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2567
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2568
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2595
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2597
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2598
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2599
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2600
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2601
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2619
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2623
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2625
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2626
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2627
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2649
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2650
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2652
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2655
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2675
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2676
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2677
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2679
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2680
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2681
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2725
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2726
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2728
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2730
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2731
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2732
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2760
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2761
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2762
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2763
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2764
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2765
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2766
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2767
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2768
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2769
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2782
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2783
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2784
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2785
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2786
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2787
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2788
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2789
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2790
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2802
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2803
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2804
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2805
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