RubyGems - lazar - Versions diffs - 0.0.1 - Mend

lazar 0.0.1

Files changed (98) hide show

checksums.yaml +7 -0
data/.gitignore +10 -0
data/.yardopts +4 -0
data/Gemfile +2 -0
data/LICENSE +674 -0
data/README.md +44 -0
data/Rakefile +1 -0
data/VERSION +1 -0
data/ext/lazar/extconf.rb +87 -0
data/java/CdkDescriptorInfo.class +0 -0
data/java/CdkDescriptorInfo.java +22 -0
data/java/CdkDescriptors.class +0 -0
data/java/CdkDescriptors.java +141 -0
data/java/Jmol.jar +0 -0
data/java/JoelibDescriptorInfo.class +0 -0
data/java/JoelibDescriptorInfo.java +15 -0
data/java/JoelibDescriptors.class +0 -0
data/java/JoelibDescriptors.java +60 -0
data/java/Rakefile +15 -0
data/java/cdk-1.4.19.jar +0 -0
data/java/joelib2.jar +0 -0
data/java/log4j.jar +0 -0
data/lazar.gemspec +29 -0
data/lib/SMARTS_InteLigand.txt +983 -0
data/lib/algorithm.rb +21 -0
data/lib/bbrc.rb +165 -0
data/lib/classification.rb +107 -0
data/lib/compound.rb +254 -0
data/lib/crossvalidation.rb +187 -0
data/lib/dataset.rb +334 -0
data/lib/descriptor.rb +247 -0
data/lib/error.rb +66 -0
data/lib/feature.rb +97 -0
data/lib/lazar-model.rb +170 -0
data/lib/lazar.rb +69 -0
data/lib/neighbor.rb +25 -0
data/lib/opentox.rb +22 -0
data/lib/overwrite.rb +119 -0
data/lib/regression.rb +199 -0
data/lib/rest-client-wrapper.rb +98 -0
data/lib/similarity.rb +58 -0
data/lib/unique_descriptors.rb +120 -0
data/lib/validation.rb +114 -0
data/mongoid.yml +8 -0
data/test/all.rb +5 -0
data/test/compound.rb +100 -0
data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +13553 -0
data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv +436 -0
data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv +568 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv +87 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv +978 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv +1120 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv +1113 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv +850 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv +829 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Rat.csv +1198 -0
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv +1505 -0
data/test/data/EPAFHM.csv +618 -0
data/test/data/EPAFHM.medi.csv +100 -0
data/test/data/EPAFHM.mini.csv +22 -0
data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv +581 -0
data/test/data/FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv +1217 -0
data/test/data/ISSCAN-multi.csv +59 -0
data/test/data/LOAEL_log_mg_corrected_smiles.csv +568 -0
data/test/data/LOAEL_log_mmol_corrected_smiles.csv +568 -0
data/test/data/acetaldehyde.sdf +14 -0
data/test/data/boiling_points.ext.sdf +11460 -0
data/test/data/cpdb_100.csv +101 -0
data/test/data/hamster_carcinogenicity.csv +86 -0
data/test/data/hamster_carcinogenicity.mini.bool_float.csv +11 -0
data/test/data/hamster_carcinogenicity.mini.bool_int.csv +11 -0
data/test/data/hamster_carcinogenicity.mini.bool_string.csv +11 -0
data/test/data/hamster_carcinogenicity.mini.csv +11 -0
data/test/data/hamster_carcinogenicity.ntriples +618 -0
data/test/data/hamster_carcinogenicity.sdf +2805 -0
data/test/data/hamster_carcinogenicity.xls +0 -0
data/test/data/hamster_carcinogenicity.yaml +352 -0
data/test/data/hamster_carcinogenicity_with_errors.csv +88 -0
data/test/data/kazius.csv +4070 -0
data/test/data/multi_cell_call.csv +1067 -0
data/test/data/multi_cell_call_no_dup.csv +1057 -0
data/test/data/multicolumn.csv +8 -0
data/test/data/rat_feature_dataset.csv +1179 -0
data/test/data/wrong_dataset.csv +8 -0
data/test/dataset-long.rb +117 -0
data/test/dataset.rb +199 -0
data/test/descriptor-long.rb +26 -0
data/test/descriptor.rb +83 -0
data/test/error.rb +24 -0
data/test/feature.rb +65 -0
data/test/fminer-long.rb +38 -0
data/test/fminer.rb +52 -0
data/test/lazar-fminer.rb +50 -0
data/test/lazar-long.rb +72 -0
data/test/lazar-physchem-short.rb +27 -0
data/test/setup.rb +6 -0
data/test/validation.rb +41 -0
metadata +212 -0

data/test/data/EPAFHM.medi.csv ADDED Viewed

@@ -0,0 +1,100 @@
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+"CC#N",4.01E+01
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+"IC(I)I",7.42E-03
+"[N+](C)(C)(C)C.[Cl-]",4.22E+00
+"CC(C)(C)O",8.65E+01
+"C(F)(F)(F)CO",1.19E+00
+"CC(=O)C(C)(C)C",8.69E-01
+"ClC(C(Cl)Cl)(Cl)Cl",3.72E-02
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+"CCC(O)(C)CC",6.58E+00
+"C#CC(O)(C)CC",1.24E+01
+"C1CCCC(C#C)(O)C1",2.06E+00
+"CCCCOCCOP(=O)(OCCOCCCC)OCCOCCCC",2.81E-02
+"CCCCOCCOP(=O)(OCCOCCCC)OCCOCCCC",1.81E-02
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+"OC(C)CN",3.36E+01
+"ClC(CCl)Cl",6.12E-01
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+"CC(=O)OC",4.82E+00
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+"ClC(Cl)C1=C(Cl)C=CC=C1Cl",4.22E-03
+"C1=CC=C2C=CC=C3C2=C1CC3",1.12E-02
+"CC1=CNC2=C1C=CC=C2",6.74E-02
+"C1=CC=CC=C1OC(=O)C2=CC=CC=C2C(=O)OC3=CC=CC=C3",2.51E-04
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+"C1=CC=C(C(=O)OCCCC)C(=C1)C(=O)OCCCC",3.5900E-03
+"CCC1=C(Br)C(Br)=C(Br)C(Br)=C1Br",
+"O=C1C2=C(C=CC=C2)N=NN1CSP(=S)(OC)OC",2.02E-04
+"C1=CC=CC=C1NC(=O)C2=C(O)C=CC=C2",1.85E-02
+"Cl\C(Cl)=C(Cl)/C(Cl)=C(Cl)\Cl",3.45E-04
+"OC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl",9.12E-04
+"OC1=C(C=C(C=C1Cl)Cl)Cl",2.48E-02
+"OC1=CC(C(F)(F)F)=C([N+]([O-])=O)C=C1",4.41E-02
+"C1(N)=CC=CC=C1C(=O)N",2.90E+00
+"C1(N)=CC=CC=C1C(=O)N",2.50E+00
+"OC1=C([N+]([O-])=O)C=CC=C1",1.15E+00

data/test/data/EPAFHM.mini.csv ADDED Viewed

@@ -0,0 +1,22 @@
+"STRUCTURE_SMILES","LC50_mmol"
+"C1=CC(C=O)=CC(OC)=C1OCCCCCC",1.13E-02
+"C1(OC)=C([N+]([O-])=O)C(C=O)=CC(Br)=C1O",2.66E-01
+"CCCCCCCCOC(=O)C1=CC=CC(C(=O)OCCCCCCCC)=C1",
+"C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2",7.69E-03
+"CC1=C(NC=O)C=CC=C1Cl",2.75E-01
+"CCCCOC(=O)C1=CC=CC(C(=O)OCCCC)=C1",3.23E-03
+"C(C1=CC=CC=C1)(C2=CC=CC=C2)(O)C#C",5.33E-02
+"CCCSCCSCCC",4.22E-02
+"CCCCCCCCOC(=O)C1=CC=C(C(=O)OCCCCCCCC)C=C1",
+"OCCCCOC(=O)C1=CC=CC=C1C(=O)OCCCCOC(=O)C2=CC=CC=C2C(=O)OCCCCO",
+"CCCSCCCCSCCC",1.45E-02
+"C1([N+](=O)[O-])=CC=C(C)C=C1OP(=O)(OC2=C([N+](=O)[O-])C=CC(C)=C2)OC3=C([N+]([O-])=O)C=CC(C)=C3",
+"C1=C([N+]([O-])=O)C=CC=C1P(=O)(C2=CC([N+](=O)[O-])=CC=C2)C3=CC([N+](=O)[O-])=CC=C3",
+"ClCCOC(=O)NC1CCCCC1",1.70E-01
+"O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC",2.08E+00
+"OC1=C(C=C(C=C1)[N+](=O)[O-])[N+](=O)[O-]",5.92E-02
+"NC(=O)OCC",5.88E+01
+"[O-]C(C1=CC=CC=C1O)=O.[Na+]",1.25E+01
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+"CC[N+](CC)(CC)CC1(=CC=CC=C1).[Cl-]",7.07E-01
+"OCCCCCCCC\C=C/CCCCCCCC",

data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv ADDED Viewed

@@ -0,0 +1,581 @@
+STRUCTURE_SMILES,LC50_mmol
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