lazar 0.0.7 → 0.0.9

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Files changed (61) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +3 -0
  3. data/README.md +2 -1
  4. data/VERSION +1 -1
  5. data/ext/lazar/extconf.rb +15 -76
  6. data/ext/lazar/rinstall.R +9 -0
  7. data/lazar.gemspec +7 -7
  8. data/lib/classification.rb +5 -78
  9. data/lib/compound.rb +201 -44
  10. data/lib/crossvalidation.rb +224 -121
  11. data/lib/dataset.rb +83 -93
  12. data/lib/error.rb +1 -1
  13. data/lib/experiment.rb +99 -0
  14. data/lib/feature.rb +2 -54
  15. data/lib/lazar.rb +47 -34
  16. data/lib/leave-one-out-validation.rb +205 -0
  17. data/lib/model.rb +131 -76
  18. data/lib/opentox.rb +2 -2
  19. data/lib/overwrite.rb +37 -0
  20. data/lib/physchem.rb +133 -0
  21. data/lib/regression.rb +117 -189
  22. data/lib/rest-client-wrapper.rb +4 -5
  23. data/lib/unique_descriptors.rb +6 -7
  24. data/lib/validation.rb +63 -69
  25. data/test/all.rb +2 -2
  26. data/test/classification.rb +41 -0
  27. data/test/compound.rb +116 -7
  28. data/test/data/LOAEL_log_mg_corrected_smiles.csv +567 -567
  29. data/test/data/LOAEL_log_mmol_corrected_smiles.csv +566 -566
  30. data/test/data/LOAEL_mmol_corrected_smiles.csv +568 -0
  31. data/test/data/batch_prediction.csv +25 -0
  32. data/test/data/batch_prediction_inchi_small.csv +4 -0
  33. data/test/data/batch_prediction_smiles_small.csv +4 -0
  34. data/test/data/hamster_carcinogenicity.json +3 -0
  35. data/test/data/loael.csv +568 -0
  36. data/test/dataset-long.rb +5 -8
  37. data/test/dataset.rb +31 -11
  38. data/test/default_environment.rb +11 -0
  39. data/test/descriptor.rb +26 -41
  40. data/test/error.rb +1 -3
  41. data/test/experiment.rb +301 -0
  42. data/test/feature.rb +22 -10
  43. data/test/lazar-long.rb +43 -23
  44. data/test/lazar-physchem-short.rb +19 -16
  45. data/test/prediction_models.rb +20 -0
  46. data/test/regression.rb +43 -0
  47. data/test/setup.rb +3 -1
  48. data/test/test_environment.rb +10 -0
  49. data/test/validation.rb +92 -26
  50. metadata +64 -38
  51. data/lib/SMARTS_InteLigand.txt +0 -983
  52. data/lib/bbrc.rb +0 -165
  53. data/lib/descriptor.rb +0 -247
  54. data/lib/neighbor.rb +0 -25
  55. data/lib/similarity.rb +0 -58
  56. data/mongoid.yml +0 -8
  57. data/test/descriptor-long.rb +0 -26
  58. data/test/fminer-long.rb +0 -38
  59. data/test/fminer.rb +0 -52
  60. data/test/lazar-fminer.rb +0 -50
  61. data/test/lazar-regression.rb +0 -27
data/test/lazar-regression.rb DELETED
@@ -1,27 +0,0 @@
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- require_relative "setup.rb"
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-
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- class LazarRegressionTest < MiniTest::Test
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-
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- def test_weighted_average
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- training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
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- model = Model::LazarRegression.create training_dataset
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- compound = Compound.from_smiles "CC(C)(C)CN"
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- prediction = model.predict compound
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- assert_equal 13.6, prediction[:value].round(1)
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- assert_equal 0.83, prediction[:confidence].round(2)
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- assert_equal 1, prediction[:neighbors].size
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- end
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-
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- def test_weighted_average_with_relevant_fingerprints
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- training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
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- model = Model::LazarRegression.create training_dataset
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- model.update(:prediction_algorithm => "OpenTox::Algorithm::Regression.weighted_average_with_relevant_fingerprints")
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- compound = Compound.from_smiles "CC(C)(C)CN"
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- prediction = model.predict compound
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- p prediction
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- #assert_equal 13.6, prediction[:value].round(1)
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- #assert_equal 0.83, prediction[:confidence].round(2)
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- #assert_equal 1, prediction[:neighbors].size
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- end
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-
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- end