bio-chembl 0.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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+
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+ cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
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+ /opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl-compound.rb
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+ require 'helper'
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+ require 'bio-chembl/chembl.rb'
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+
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+ class TestBioChemblURI < Test::Unit::TestCase
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+ def setup
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+ @obj = BioChEMBL::REST::ChEMBL_URI
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+ end
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+
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+ def test_status
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+ assert_equal(@obj.status,
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+ "https://www.ebi.ac.uk/chemblws/status/")
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+ end
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+
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+ def test_compounds
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+ assert_equal(@obj.compounds('CHEMBL1'),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1')
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+ end
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+
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+ def test_compounds_image
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+ assert_equal(@obj.compounds('CHEMBL192', 'image'),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image')
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+ end
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+
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+ def test_compounds_image_params
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+ assert_equal(@obj.compounds('CHEMBL192', 'image', {:dimensions => 200}),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image?dimensions=200')
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+ end
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+
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+ def test_compounds_bioactivities
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+ assert_equal(@obj.compounds('CHEMBL1', 'bioactivities'),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1/bioactivities')
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+ end
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+
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+ def test_compounds_stdinchikey
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+ assert_equal(@obj.compounds_stdinchikey("QFFGVLORLPOAEC-SNVBAGLBSA-N"),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/stdinchikey/QFFGVLORLPOAEC-SNVBAGLBSA-N')
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+ end
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+
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+ def test_compounds_smiles
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+ assert_equal(@obj.compounds_smiles("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56"),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/smiles/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56')
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+ end
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+
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+ def test_compounds_substructure
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+ assert_equal(@obj.compounds_substructure("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56"),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/substructure/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56')
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+ end
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+
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+ def test_compounds_similarity
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+ assert_equal(@obj.compounds_similarity("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/70"),
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+ 'https://www.ebi.ac.uk/chemblws/compounds/similarity/COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/70')
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+ end
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+
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+ def test_targets_id
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+ assert_equal(@obj.targets("CHEMBL2477"),
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+ 'https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477')
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+ end
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+ def test_targets_bioactivities
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+ assert_equal(@obj.targets("CHEMBL2477", 'bioactivities'),
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+ 'https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477/bioactivities')
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+ end
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+ def test_targets
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+ # targets
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+ assert_equal(@obj.targets,
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+ 'https://www.ebi.ac.uk/chemblws/targets')
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+ end
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+
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+ def test_targets_uniprot
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+ assert_equal(@obj.targets_uniprot("Q13936"),
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+ 'https://www.ebi.ac.uk/chemblws/targets/uniprot/Q13936')
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+ end
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+
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+ def test_targets_refseq
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+ assert_equal(@obj.targets_refseq("NP_001128722"),
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+ 'https://www.ebi.ac.uk/chemblws/targets/refseq/NP_001128722')
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+ end
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+
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+ def test_assays
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+ assert_equal(@obj.assays("CHEMBL1217643"),
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+ 'https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643')
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+ end
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+ def test_assays_bioactivities
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+ assert_equal(@obj.assays("CHEMBL1217643", 'bioactivities'),
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+ 'https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643/bioactivities')
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+ end
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+
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+ end
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+
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+
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+ class TestBioChembl < Test::Unit::TestCase
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+ def setup
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+ @obj = BioChEMBL::REST.new
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+ end
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+
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+ def test_new
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+ assert(@obj)
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+ end
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+
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+ def test_uri_status
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+ assert_equal(@obj.uri.status,
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+ 'https://www.ebi.ac.uk/chemblws/status/')
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+ end
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+
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+ def test_status
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+ assert_equal(@obj.status, 'UP')
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+ end
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+
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+ def test_compounds
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+ doc = @obj.compounds('CHEMBL1')
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+ assert_equal(doc,
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+ '<compound><chemblId>CHEMBL1</chemblId><knownDrug>No</knownDrug><medChemFriendly>Yes</medChemFriendly><passesRuleOfThree>No</passesRuleOfThree><molecularFormula>C32H32O8</molecularFormula><smiles>COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56</smiles><stdInChiKey>GHBOEFUAGSHXPO-XZOTUCIWSA-N</stdInChiKey><numRo5Violations>1</numRo5Violations><rotatableBonds>2</rotatableBonds><molecularWeight>544.59167</molecularWeight><alogp>3.627</alogp><acdLogp>7.669</acdLogp><acdLogd>7.669</acdLogd></compound>')
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+ end
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+
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+ def test_compounds_image
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+ # assert_equal(@obj.compounds('CHEMBL192', 'image'),
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+ # '') # \x89PNG
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+ end
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+
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+ def test_compounds_image_params
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+ # assert_equal(@obj.compounds('CHEMBL192', 'image', {:dimensions => 200}),
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+ # '')
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+ end
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+
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+ def test_compounds_bioactivities
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+ doc = @obj.compounds('CHEMBL1', 'bioactivities')
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+ assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL1/)
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+ end
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+
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+ def test_compounds_stdinchikey
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+ doc = @obj.compounds_stdinchikey("QFFGVLORLPOAEC-SNVBAGLBSA-N")
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+ assert(doc =~ /<compound><chemblId>CHEMBL1201760/)
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+ end
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+
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+ def test_compounds_smiles
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+ doc = @obj.compounds_smiles("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56")
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+ assert(doc =~ /<list><compound><chemblId>CHEMBL1/)
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+ end
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+
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+ def test_compounds_substructure
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+ doc = @obj.compounds_substructure("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56")
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+ assert(doc, '<list/>')
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+ end
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+
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+ def test_compounds_similarity
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+ doc = @obj.compounds_similarity("COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56/70")
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+ assert(doc =~ /<list><compound><chemblId>CHEMBL/)
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+ end
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+
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+ def test_targets_id
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+ doc = @obj.targets("CHEMBL2477")
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+ assert(doc =~ /<target><chemblId>CHEMBL2477/)
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+ end
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+
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+ def test_targets_bioactivities
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+ doc = @obj.targets("CHEMBL2477", 'bioactivities')
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+ assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL/)
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+ end
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+
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+
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+ def test_targets
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+ doc = @obj.targets
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+ assert(doc =~ /<list><target><chemblId>CHEMBL/)
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+ end
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+
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+ def test_targets_uniprot
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+ doc = @obj.targets_uniprot("Q13936")
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+ assert_equal(doc, '<target><chemblId>CHEMBL1940</chemblId><targetType>PROTEIN</targetType><preferredName>Voltage-gated L-type calcium channel alpha-1C subunit</preferredName><proteinAccession>Q13936</proteinAccession><synonyms>Voltage-dependent L-type calcium channel subunit alpha-1C; Calcium channel, L type, alpha-1 polypeptide, isoform 1, cardiac muscle; Voltage-gated calcium channel subunit alpha Cav1.2</synonyms><organism>Homo sapiens</organism><description>Voltage-dependent L-type calcium channel subunit alpha-1C</description><geneNames>CACNA1C; CACH2; CACN2; CACNL1A1; CCHL1A1</geneNames></target>')
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+ end
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+
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+ def test_targets_refseq_not_fount
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+ assert_raise(Exception) {
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+ @obj.targets_refseq("NP_001128722")
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+ }
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+ end
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+
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+ def test_assays
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+ doc = @obj.assays("CHEMBL1217643")
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+ assert(doc =~ /<assay><chemblId>CHEMBL1217643/)
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+ end
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+
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+ def test_assays_bioactivities
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+ doc = @obj.assays("CHEMBL1217643", 'bioactivities')
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+ assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL/)
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+ end
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+
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+ end
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+
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+
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+
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+ cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
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+ /opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl-rest-client.rb
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+ require 'helper'
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+ require 'bio-chembl/chembl.rb'
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+
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+
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+
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+ class TestBioChemblTarget < Test::Unit::TestCase
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+ def setup
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+ @xml = "<target><chemblId>CHEMBL1785</chemblId><targetType>PROTEIN</targetType><preferredName>Endothelin receptor ET-B</preferredName><proteinAccession>P24530</proteinAccession><synonyms>Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR</synonyms><organism>Homo sapiens</organism><description>Endothelin B receptor</description><geneNames>EDNRB; ETRB</geneNames></target>"
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+ @chemblId = "CHEMBL1785"
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+ end
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+
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+ def test_target_parser_xml
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+ doc = BioChEMBL::Target.parse_xml(@xml)
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+ assert_equal(doc.chemblId, "CHEMBL1785")
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+ end
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+
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+ def test_target_attributes
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+ doc = BioChEMBL::Target.parse_xml(@xml)
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+ assert_equal(doc.class, BioChEMBL::Target)
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+ end
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+
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+ def test_target_attributes
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+ doc = BioChEMBL::Target.parse_xml(@xml)
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+ assert_equal("CHEMBL1785", doc.chemblId)
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+ assert_equal("PROTEIN", doc.targetType)
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+ assert_equal("Endothelin receptor ET-B", doc.preferredName)
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+ assert_equal("P24530", doc.proteinAccession)
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+ assert_equal("Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR", doc.synonyms)
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+ assert_equal("Homo sapiens", doc.organism)
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+ assert_equal("Endothelin B receptor", doc.description)
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+ assert_equal("EDNRB; ETRB", doc.geneNames)
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+ end
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+
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+ def test_target_synonyms_to_array
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+ doc = BioChEMBL::Target.parse_xml(@xml)
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+ assert_equal("Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR", doc.synonyms)
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+ synonyms = BioChEMBL.to_array(doc.synonyms)
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+ assert_equal(4, synonyms.size)
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+ assert_equal("Endothelin B receptor", synonyms[0])
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+ end
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+
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+ def test_target_geneNames_to_array
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+ doc = BioChEMBL::Target.parse_xml(@xml)
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+ assert_equal("EDNRB; ETRB", doc.geneNames)
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+ geneNames = BioChEMBL.to_array(doc.geneNames)
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+ assert_equal(2, geneNames.size)
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+ assert_equal("EDNRB", geneNames[0])
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+ end
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+
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+ def test_target_parse_json
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+ assert_raise(NotImplementedError) {
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+ BioChEMBL::Target.parse_json("")
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+ }
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+ end
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+
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+
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+ def test_target_parse_rdf
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+ assert_raise(NotImplementedError) {
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+ BioChEMBL::Target.parse_rdf("")
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+ }
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+ end
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+
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+
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+ def test_target_parse
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+ doc = BioChEMBL::Target.parse(@xml)
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+ assert_equal("CHEMBL1785", doc.chemblId)
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+ end
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+
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+
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+ def test_target_resolve
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+ doc = BioChEMBL::Target.new
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+ doc.chemblId = @chemblId
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+ assert_equal(doc.targetType, nil)
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+ doc.resolve
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+ assert_equal(doc.targetType, "PROTEIN")
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+ end
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+
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+ end
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+
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+ class TestBioChemblTargetClassMethods < Test::Unit::TestCase
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+ def setup
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+ @chemblId = "CHEMBL2477"
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+ @target = BioChEMBL::Target.find(@chemblId)
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+ @uniprot_id = "Q13936"
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+ @refseq_id = "NP_001128722"
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+ end
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+
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+ def test_find
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+ assert_equal(@target.chemblId, "CHEMBL2477")
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+ assert_equal(@target.targetType, "PROTEIN")
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+ end
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+
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+ def test_find_by_uniprot
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+ @target = BioChEMBL::Target.find_by_uniprot(@uniprot_id)
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+ assert_equal(@target.chemblId, "CHEMBL1940")
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+ assert_equal(@target.targetType, "PROTEIN")
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+ end
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+
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+ def test_find_by_refseq
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+ # @target = BioChEMBL::Target.find_by_refseq(@refseq_id)
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+ # p @target
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+ # assert_equal(@target.chemblId, "CHEMBL2477")
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+ # assert_equal(@target.targetType, "PROTEIN")
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+ end
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+
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+ def test_bioactivities
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+ docs = @target.bioactivities
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+ assert_equal(Array, docs.class)
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+ assert_equal(BioChEMBL::Bioactivity, docs.first.class)
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+ assert_equal("Homo sapiens", docs.first.organism)
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+ assert_equal("Bioorg. Med. Chem. Lett., (1998) 8:13:1703", docs.first.reference)
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+ end
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+
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+ end
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+
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+ cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
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+ /opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl-target.rb
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+ require 'helper'
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+ require 'bio-chembl/chembl.rb'
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+
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+ class TestBioChEMBL < Test::Unit::TestCase
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+ def test_website
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+ assert_equal("https://www.ebi.ac.uk/chembl/", BioChEMBL.website)
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+ end
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+ end
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+
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+
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+ cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
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+ /opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl.rb
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-chembl
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+ version: !ruby/object:Gem::Version
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+ prerelease: false
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+ segments:
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+ - 0
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+ - 1
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+ - 1
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+ version: 0.1.1
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+ platform: ruby
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+ authors:
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+ - Mitsuteru Nakao
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+
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+ date: 2012-07-22 00:00:00 +09:00
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+ default_executable:
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: shoulda
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+ prerelease: false
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+ requirement: &id001 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 0
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+ version: "0"
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+ type: :development
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+ version_requirements: *id001
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ prerelease: false
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+ requirement: &id002 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 3
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+ - 12
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+ version: "3.12"
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+ type: :development
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+ version_requirements: *id002
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ prerelease: false
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+ requirement: &id003 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 1
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+ - 0
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+ - 0
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+ version: 1.0.0
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+ type: :development
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+ version_requirements: *id003
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ prerelease: false
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+ requirement: &id004 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 1
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+ - 8
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+ - 3
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+ version: 1.8.3
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+ type: :development
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+ version_requirements: *id004
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+ - !ruby/object:Gem::Dependency
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+ name: bio
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+ prerelease: false
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+ requirement: &id005 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 1
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+ - 4
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+ - 2
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+ version: 1.4.2
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+ type: :development
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+ version_requirements: *id005
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ prerelease: false
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+ requirement: &id006 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 3
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+ - 12
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+ version: "3.12"
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+ type: :development
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+ version_requirements: *id006
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+ - !ruby/object:Gem::Dependency
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+ name: curb
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+ prerelease: false
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+ requirement: &id007 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 0
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+ version: "0"
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+ type: :development
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+ version_requirements: *id007
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+ - !ruby/object:Gem::Dependency
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+ name: nokogiri
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+ prerelease: false
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+ requirement: &id008 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ segments:
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+ - 1
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+ - 5
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+ - 5
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+ version: 1.5.5
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+ type: :development
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+ version_requirements: *id008
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+ description: BioRuby plugin for ChEMBL REST API Client, Parser and Container classes
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+ email: mitsuteru.nakao@gmail.com
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+ executables: []
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+
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+ extensions: []
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+
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+ extra_rdoc_files:
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+ - LICENSE.txt
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+ - README.md
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+ files:
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+ - .document
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+ - .project
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+ - .travis.yml
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+ - Gemfile
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+ - Gemfile.lock
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+ - LICENSE.txt
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+ - README.md
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+ - Rakefile
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+ - VERSION
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+ - bio-chembl.gemspec
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+ - lib/bio-chembl.rb
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+ - lib/bio-chembl/assay.rb
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+ - lib/bio-chembl/bioactivity.rb
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+ - lib/bio-chembl/chembl.rb
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+ - lib/bio-chembl/chemblid.rb
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+ - lib/bio-chembl/compound.rb
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+ - lib/bio-chembl/datamodel.rb
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+ - lib/bio-chembl/rest_api_server.rb
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+ - lib/bio-chembl/rest_client.rb
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+ - lib/bio-chembl/target.rb
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+ - test/helper.rb
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+ - test/test_bio-chembl-assay.rb
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+ - test/test_bio-chembl-assay.sh
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+ - test/test_bio-chembl-chemblid.rb
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+ - test/test_bio-chembl-chemblid.sh
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+ - test/test_bio-chembl-compound.rb
170
+ - test/test_bio-chembl-compound.sh
171
+ - test/test_bio-chembl-rest-client.rb
172
+ - test/test_bio-chembl-rest-client.sh
173
+ - test/test_bio-chembl-target.rb
174
+ - test/test_bio-chembl-target.sh
175
+ - test/test_bio-chembl.rb
176
+ - test/test_bio-chembl.sh
177
+ has_rdoc: true
178
+ homepage: http://github.com/nakao/bio-chembl
179
+ licenses:
180
+ - MIT
181
+ post_install_message:
182
+ rdoc_options: []
183
+
184
+ require_paths:
185
+ - lib
186
+ required_ruby_version: !ruby/object:Gem::Requirement
187
+ none: false
188
+ requirements:
189
+ - - ">="
190
+ - !ruby/object:Gem::Version
191
+ segments:
192
+ - 0
193
+ version: "0"
194
+ required_rubygems_version: !ruby/object:Gem::Requirement
195
+ none: false
196
+ requirements:
197
+ - - ">="
198
+ - !ruby/object:Gem::Version
199
+ segments:
200
+ - 0
201
+ version: "0"
202
+ requirements: []
203
+
204
+ rubyforge_project:
205
+ rubygems_version: 1.3.7
206
+ signing_key:
207
+ specification_version: 3
208
+ summary: ChEMBL REST API Client, Parser and Container
209
+ test_files: []
210
+