bio-chembl 0.1.1

data/test/test_bio-chembl-compound.sh

@@ -0,0 +1,3 @@
+
+cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
+/opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl-compound.rb

data/test/test_bio-chembl-rest-client.rb

@@ -0,0 +1,188 @@
+require 'helper'
+require 'bio-chembl/chembl.rb'
+
+class TestBioChemblURI < Test::Unit::TestCase
+  def setup
+    @obj = BioChEMBL::REST::ChEMBL_URI
+  end
+  
+  def test_status
+    assert_equal(@obj.status,
+      "https://www.ebi.ac.uk/chemblws/status/")
+  end
+  
+  def test_compounds
+    assert_equal(@obj.compounds('CHEMBL1'), 
+      'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1')
+  end
+  
+  def test_compounds_image
+    assert_equal(@obj.compounds('CHEMBL192', 'image'), 
+       'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image')
+  end
+  
+  def test_compounds_image_params
+    assert_equal(@obj.compounds('CHEMBL192', 'image', {:dimensions => 200}), 
+      'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image?dimensions=200')
+  end
+  
+  def test_compounds_bioactivities
+    assert_equal(@obj.compounds('CHEMBL1', 'bioactivities'), 
+      'https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1/bioactivities')
+  end
+  
+  def test_compounds_stdinchikey
+    assert_equal(@obj.compounds_stdinchikey("QFFGVLORLPOAEC-SNVBAGLBSA-N"),
+      'https://www.ebi.ac.uk/chemblws/compounds/stdinchikey/QFFGVLORLPOAEC-SNVBAGLBSA-N')
+  end
+  
+  def test_compounds_smiles
+    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"),
+      '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')
+  end
+  
+  def test_compounds_substructure
+    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"),
+      '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') 
+  end
+  
+  def test_compounds_similarity
+    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"),
+      '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')
+  end
+   
+  def test_targets_id
+    assert_equal(@obj.targets("CHEMBL2477"),
+      'https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477')
+  end
+  def test_targets_bioactivities
+    assert_equal(@obj.targets("CHEMBL2477", 'bioactivities'),
+      'https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477/bioactivities')
+  end
+  def test_targets
+    # targets
+    assert_equal(@obj.targets,      
+      'https://www.ebi.ac.uk/chemblws/targets')
+  end
+  
+  def test_targets_uniprot
+    assert_equal(@obj.targets_uniprot("Q13936"),
+      'https://www.ebi.ac.uk/chemblws/targets/uniprot/Q13936')
+  end
+  
+  def test_targets_refseq
+    assert_equal(@obj.targets_refseq("NP_001128722"),
+      'https://www.ebi.ac.uk/chemblws/targets/refseq/NP_001128722')
+  end
+  
+  def test_assays
+    assert_equal(@obj.assays("CHEMBL1217643"),
+      'https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643')
+  end
+  def test_assays_bioactivities
+    assert_equal(@obj.assays("CHEMBL1217643", 'bioactivities'),
+      'https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643/bioactivities')
+  end
+
+end
+
+
+class TestBioChembl < Test::Unit::TestCase
+  def setup
+    @obj = BioChEMBL::REST.new    
+  end
+  
+  def test_new
+    assert(@obj)
+  end
+
+  def test_uri_status
+    assert_equal(@obj.uri.status, 
+      'https://www.ebi.ac.uk/chemblws/status/')
+  end
+  
+  def test_status
+    assert_equal(@obj.status, 'UP')
+  end
+
+  def test_compounds
+    doc = @obj.compounds('CHEMBL1')
+    assert_equal(doc, 
+      '<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>')
+  end
+  
+  def test_compounds_image
+#    assert_equal(@obj.compounds('CHEMBL192', 'image'), 
+#       '') # \x89PNG 
+  end
+  
+  def test_compounds_image_params
+#    assert_equal(@obj.compounds('CHEMBL192', 'image', {:dimensions => 200}), 
+#      '')
+  end
+  
+  def test_compounds_bioactivities
+    doc = @obj.compounds('CHEMBL1', 'bioactivities')
+    assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL1/)
+  end
+  
+  def test_compounds_stdinchikey
+    doc = @obj.compounds_stdinchikey("QFFGVLORLPOAEC-SNVBAGLBSA-N")
+    assert(doc =~ /<compound><chemblId>CHEMBL1201760/)
+    end
+  
+  def test_compounds_smiles
+    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")
+    assert(doc =~ /<list><compound><chemblId>CHEMBL1/)
+  end
+  
+  def test_compounds_substructure
+    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")
+    assert(doc, '<list/>')
+  end
+  
+  def test_compounds_similarity
+    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")
+    assert(doc =~ /<list><compound><chemblId>CHEMBL/)
+  end
+   
+  def test_targets_id
+    doc = @obj.targets("CHEMBL2477")
+    assert(doc =~ /<target><chemblId>CHEMBL2477/)
+  end
+
+  def test_targets_bioactivities
+    doc = @obj.targets("CHEMBL2477", 'bioactivities')
+    assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL/)
+  end
+
+  
+  def test_targets
+    doc = @obj.targets
+    assert(doc =~ /<list><target><chemblId>CHEMBL/)      
+  end
+  
+  def test_targets_uniprot
+    doc = @obj.targets_uniprot("Q13936")
+    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>')
+  end
+  
+  def test_targets_refseq_not_fount
+    assert_raise(Exception) {
+        @obj.targets_refseq("NP_001128722")
+    }
+  end
+  
+  def test_assays
+    doc = @obj.assays("CHEMBL1217643")
+    assert(doc =~ /<assay><chemblId>CHEMBL1217643/)
+  end
+
+  def test_assays_bioactivities
+    doc = @obj.assays("CHEMBL1217643", 'bioactivities')
+    assert(doc =~ /<list><bioactivity><parent__cmpd__chemblid>CHEMBL/)
+  end
+  
+end
+
+

data/test/test_bio-chembl-rest-client.sh

@@ -0,0 +1,3 @@
+
+cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
+/opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl-rest-client.rb

data/test/test_bio-chembl-target.rb

@@ -0,0 +1,114 @@
+require 'helper'
+require 'bio-chembl/chembl.rb'
+
+
+
+class TestBioChemblTarget < Test::Unit::TestCase
+  def setup
+    @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>"
+    @chemblId = "CHEMBL1785"
+  end
+
+  def test_target_parser_xml
+    doc = BioChEMBL::Target.parse_xml(@xml)
+    assert_equal(doc.chemblId, "CHEMBL1785")
+  end
+  
+  def test_target_attributes
+    doc = BioChEMBL::Target.parse_xml(@xml)
+    assert_equal(doc.class, BioChEMBL::Target)
+  end
+
+  def test_target_attributes
+    doc = BioChEMBL::Target.parse_xml(@xml)
+    assert_equal("CHEMBL1785", doc.chemblId)
+    assert_equal("PROTEIN", doc.targetType)
+    assert_equal("Endothelin receptor ET-B", doc.preferredName)
+    assert_equal("P24530", doc.proteinAccession)
+    assert_equal("Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR", doc.synonyms)
+    assert_equal("Homo sapiens", doc.organism)
+    assert_equal("Endothelin B receptor", doc.description)
+    assert_equal("EDNRB; ETRB", doc.geneNames)
+  end
+    
+  def test_target_synonyms_to_array
+    doc = BioChEMBL::Target.parse_xml(@xml)
+    assert_equal("Endothelin B receptor; Endothelin receptor non-selective type; ET-B; ET-BR", doc.synonyms)
+    synonyms = BioChEMBL.to_array(doc.synonyms)
+    assert_equal(4, synonyms.size)
+    assert_equal("Endothelin B receptor", synonyms[0])
+  end
+
+  def test_target_geneNames_to_array
+    doc = BioChEMBL::Target.parse_xml(@xml)
+    assert_equal("EDNRB; ETRB", doc.geneNames)
+    geneNames = BioChEMBL.to_array(doc.geneNames)
+    assert_equal(2, geneNames.size)
+    assert_equal("EDNRB", geneNames[0])
+  end
+  
+  def test_target_parse_json
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Target.parse_json("")
+    }
+  end
+
+  
+  def test_target_parse_rdf
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Target.parse_rdf("")
+    }
+  end
+  
+  
+  def test_target_parse
+    doc = BioChEMBL::Target.parse(@xml)
+    assert_equal("CHEMBL1785", doc.chemblId)
+  end
+
+  
+  def test_target_resolve
+    doc = BioChEMBL::Target.new
+    doc.chemblId = @chemblId
+    assert_equal(doc.targetType, nil)
+    doc.resolve
+    assert_equal(doc.targetType, "PROTEIN")
+  end
+  
+end 
+
+class TestBioChemblTargetClassMethods < Test::Unit::TestCase
+  def setup
+    @chemblId = "CHEMBL2477"
+    @target = BioChEMBL::Target.find(@chemblId)
+    @uniprot_id = "Q13936"
+    @refseq_id = "NP_001128722"
+  end
+
+  def test_find
+    assert_equal(@target.chemblId, "CHEMBL2477")
+    assert_equal(@target.targetType, "PROTEIN")
+  end
+  
+  def test_find_by_uniprot
+    @target = BioChEMBL::Target.find_by_uniprot(@uniprot_id)
+    assert_equal(@target.chemblId, "CHEMBL1940")
+    assert_equal(@target.targetType, "PROTEIN")
+  end
+  
+  def test_find_by_refseq
+#    @target = BioChEMBL::Target.find_by_refseq(@refseq_id)
+#    p @target
+#    assert_equal(@target.chemblId, "CHEMBL2477")
+#    assert_equal(@target.targetType, "PROTEIN")
+  end
+
+  def test_bioactivities
+     docs = @target.bioactivities
+     assert_equal(Array, docs.class)
+     assert_equal(BioChEMBL::Bioactivity, docs.first.class)
+     assert_equal("Homo sapiens", docs.first.organism)
+     assert_equal("Bioorg. Med. Chem. Lett., (1998) 8:13:1703", docs.first.reference)
+  end
+  
+end

data/test/test_bio-chembl-target.sh

@@ -0,0 +1,3 @@
+
+cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
+/opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl-target.rb

data/test/test_bio-chembl.rb

@@ -0,0 +1,9 @@
+require 'helper'
+require 'bio-chembl/chembl.rb'
+
+class TestBioChEMBL < Test::Unit::TestCase
+  def test_website
+    assert_equal("https://www.ebi.ac.uk/chembl/", BioChEMBL.website)
+  end
+end
+

data/test/test_bio-chembl.sh

@@ -0,0 +1,3 @@
+
+cd /Users/mitsuteru/Applications/biogems/bioruby-chembl/
+/opt/local/bin/ruby1.9 -I lib -I test test/test_bio-chembl.rb

metadata

@@ -0,0 +1,210 @@
+--- !ruby/object:Gem::Specification 
+name: bio-chembl
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 1
+  version: 0.1.1
+platform: ruby
+authors: 
+- Mitsuteru Nakao
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-07-22 00:00:00 +09:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: rdoc
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
+  type: :development
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 8
+        - 3
+        version: 1.8.3
+  type: :development
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: bio
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 4
+        - 2
+        version: 1.4.2
+  type: :development
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: rdoc
+  prerelease: false
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
+  type: :development
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: curb
+  prerelease: false
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id007
+- !ruby/object:Gem::Dependency 
+  name: nokogiri
+  prerelease: false
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 5
+        - 5
+        version: 1.5.5
+  type: :development
+  version_requirements: *id008
+description: BioRuby plugin for ChEMBL REST API Client, Parser and Container classes
+email: mitsuteru.nakao@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.md
+files: 
+- .document
+- .project
+- .travis.yml
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bio-chembl.gemspec
+- lib/bio-chembl.rb
+- lib/bio-chembl/assay.rb
+- lib/bio-chembl/bioactivity.rb
+- lib/bio-chembl/chembl.rb
+- lib/bio-chembl/chemblid.rb
+- lib/bio-chembl/compound.rb
+- lib/bio-chembl/datamodel.rb
+- lib/bio-chembl/rest_api_server.rb
+- lib/bio-chembl/rest_client.rb
+- lib/bio-chembl/target.rb
+- test/helper.rb
+- test/test_bio-chembl-assay.rb
+- test/test_bio-chembl-assay.sh
+- test/test_bio-chembl-chemblid.rb
+- test/test_bio-chembl-chemblid.sh
+- test/test_bio-chembl-compound.rb
+- test/test_bio-chembl-compound.sh
+- test/test_bio-chembl-rest-client.rb
+- test/test_bio-chembl-rest-client.sh
+- test/test_bio-chembl-target.rb
+- test/test_bio-chembl-target.sh
+- test/test_bio-chembl.rb
+- test/test_bio-chembl.sh
+has_rdoc: true
+homepage: http://github.com/nakao/bio-chembl
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: ChEMBL REST API Client, Parser and Container
+test_files: []
+