bio-chembl 0.1.1

data/lib/bio-chembl/target.rb

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+require 'nokogiri'
+require 'bio-chembl/datamodel.rb'
+require 'bio-chembl/bioactivity.rb'
+
+module BioChEMBL
+  
+  # ChEMBL Target
+  #
+  # Data 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>
+  #
+  class Target
+    extend BioChEMBL::DataModel
+    
+    ATTRIBUTES = [
+      :chemblId,
+      :targetType,
+      :preferredName,
+      :proteinAccession,
+      :synonyms,
+      :organism,
+      :description,
+      :geneNames
+    ]
+
+    set_attr_accessors(ATTRIBUTES)
+    
+    def self.parse(str)
+      case str
+      when /^</
+        format = 'xml'
+      when /^\{/
+        format = 'json'
+      else
+        raise ArgumentError, "Unexpected file format: #{str.inspect}"
+      end
+      begin
+        eval "self.parse_#{format}(str)"
+      rescue
+        raise NoMethodError
+      end 
+    end 
+    
+    def self.parse_xml(str)
+      xml = Nokogiri::XML(str)
+      this = new  
+      eval set_attr_values(ATTRIBUTES)
+      this
+    end 
+
+    # XML
+    # <list><target> ...
+    def self.parse_list_xml(str)
+      xmls = Nokogiri::XML(str)
+      xmls.xpath("/list/target").map do |cpd|
+        self.parse_xml(cpd.to_s)
+      end
+    end
+    
+    def self.parse_json(str)
+      raise NotImplementedError
+    end
+
+    def self.parse_rdf(str)
+      raise NotImplementedError
+    end   
+    
+    def self.find(chemblId)
+      self.parse_xml(REST.new.targets(chemblId))
+    end
+    
+    def self.find_by_uniprot(uniprot_id)
+      self.parse_xml(REST.new.targets_uniprot(uniprot_id))      
+    end
+
+    def self.find_by_refseq(refseq_id)
+      self.parse_xml(REST.new.targets_refseq(refseq_id))            
+    end
+    
+    # bioactivities => [aBioactivity, ...]
+    def bioactivities
+      BioChEMBL::Bioactivity.parse_list_xml(REST.new.targets(chemblId, 'bioactivities'))
+    end
+    
+    # Resolve the target data by given ChEMBL ID => aTarget
+    def resolve
+      resolved = self.class.find(@chemblId)
+      ATTRIBUTES.each do |attr|
+        eval "@#{attr} = resolved.#{attr}"
+      end
+    end
+  end
+
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-chembl'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-chembl-assay.rb

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+require 'helper'
+require 'bio-chembl/chembl.rb'
+
+
+
+class TestBioChemblAssay < Test::Unit::TestCase
+  def setup
+    @xml = "<assay><chemblId>CHEMBL1217643</chemblId><assayType>B</assayType><journal>Bioorg. Med. Chem. Lett.</journal><assayOrganism>Homo sapiens</assayOrganism><assayStrain>Unspecified</assayStrain><assayDescription>Inhibition of human hERG</assayDescription><numBioactivities>1</numBioactivities></assay>"
+    @chemblId = "CHEMBL1217643"
+  end
+  
+  def test_assay_parser_xml
+    doc = BioChEMBL::Assay.parse_xml(@xml)
+    assert_equal("CHEMBL1217643", doc.chemblId)
+  end
+  
+  def test_assay_attributes
+    doc = BioChEMBL::Assay.parse_xml(@xml)
+    assert_equal(doc.class, BioChEMBL::Assay)
+  end
+
+  def test_assay_attributes
+    doc = BioChEMBL::Assay.parse_xml(@xml)
+    assert_equal("CHEMBL1217643", doc.chemblId)
+    assert_equal("B", doc.assayType)
+    assert_equal("Bioorg. Med. Chem. Lett.", doc.journal)
+    assert_equal("Homo sapiens", doc.assayOrganism)
+    assert_equal("Unspecified", doc.assayStrain)
+    assert_equal("Inhibition of human hERG", doc.assayDescription)
+    assert_equal("1", doc.numBioactivities)
+  end
+    
+
+  def test_assay_parse_json
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Assay.parse_json("")
+    }
+  end
+
+  
+  def test_assay_parse_rdf
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Assay.parse_rdf("")
+    }
+  end
+  
+  
+  def test_assay_parse
+    doc = BioChEMBL::Assay.parse(@xml)
+    assert_equal("CHEMBL1217643", doc.chemblId)
+  end
+
+  
+  def test_assay_resolve
+    doc = BioChEMBL::Assay.new
+    doc.chemblId = @chemblId
+    assert_equal(nil, doc.assayType)
+    doc.resolve
+    assert_equal("B", doc.assayType)
+  end
+end
+
+class TestBioChemblAssayClassMethods < Test::Unit::TestCase
+  def setup
+    @chemblId = "CHEMBL1217643"
+    @assay = BioChEMBL::Assay.find(@chemblId)
+  end
+
+  def test_find
+    assert_equal("CHEMBL1217643", @assay.chemblId)
+    assert_equal("B", @assay.assayType)
+  end
+
+  def test_bioactivities
+    docs = @assay.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., (2010) 20:15:4359", docs.first.reference)
+  end
+end
+
+
+class TestBioChemblBioactivity < Test::Unit::TestCase
+  def setup
+    @xml = "<list><bioactivity><parent__cmpd__chemblid>CHEMBL1214402</parent__cmpd__chemblid><ingredient__cmpd__chemblid>CHEMBL1214402</ingredient__cmpd__chemblid><target__chemblid>CHEMBL240</target__chemblid><target__confidence>9</target__confidence><target__name>HERG</target__name><reference>Bioorg. Med. Chem. Lett., (2010) 20:15:4359</reference><name__in__reference>26</name__in__reference><organism>Homo sapiens</organism><bioactivity__type>IC50</bioactivity__type><activity__comment>Unspecified</activity__comment><operator>=</operator><units>nM</units><assay__chemblid>CHEMBL1217643</assay__chemblid><assay__type>B</assay__type><assay__description>Inhibition of human hERG</assay__description><value>5900</value></bioactivity></list>"
+    @chemblId = "CHEMBL1214402"
+  end
+  
+  def test_bioactivity_new
+    ba = BioChEMBL::Bioactivity.new
+    assert_equal(BioChEMBL::Bioactivity, ba.class)
+    ba.reference = '11'
+    assert_equal('11', ba.reference)
+  end
+  
+  def test_bioactivities_parser_list_xml
+    docs = BioChEMBL::Bioactivity.parse_list_xml(@xml)
+    assert_equal("CHEMBL1214402", docs.first.parent__cmpd__chemblid)
+  end
+  
+  def test_bioactivity_attributes
+    docs = BioChEMBL::Bioactivity.parse_list_xml(@xml)
+    assert_equal(docs.first.class, BioChEMBL::Bioactivity)
+  end
+
+  def test_bioactivity_attributes
+    docs = BioChEMBL::Bioactivity.parse_list_xml(@xml)
+    doc = docs.first
+    assert_equal("CHEMBL1214402", doc.parent__cmpd__chemblid)
+    assert_equal("CHEMBL1214402", doc.ingredient__cmpd__chemblid)
+    assert_equal("CHEMBL240", doc.target__chemblid)
+    assert_equal("9", doc.target__confidence)
+    assert_equal("HERG", doc.target__name)
+    assert_equal("Bioorg. Med. Chem. Lett., (2010) 20:15:4359", doc.reference)
+    assert_equal("26", doc.name__in__reference)
+    assert_equal("Homo sapiens", doc.organism)
+    assert_equal("IC50", doc.bioactivity__type)
+    assert_equal("Unspecified", doc.activity__comment)
+    assert_equal("=", doc.operator)
+    assert_equal("nM", doc.units)
+    assert_equal("CHEMBL1217643", doc.assay__chemblid)
+    assert_equal("B", doc.assay__type)
+    assert_equal("Inhibition of human hERG", doc.assay__description)
+    assert_equal("5900", doc.value)
+  end
+    
+
+  def test_bioactivity_parse_json
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Bioactivity.parse_json("")
+    }
+  end
+
+  
+  
+  def test_bioactivity_parse_rdf
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Bioactivity.parse_rdf("")
+    }
+  end
+  
+  
+  def test_bioactivity_parse_xml
+    docs = BioChEMBL::Bioactivity.parse_list_xml(@xml)
+    assert_equal(Array, docs.class)
+    assert_equal(BioChEMBL::Bioactivity, docs.first.class)
+    assert_equal("CHEMBL1214402", docs.first.parent__cmpd__chemblid)
+  end
+
+end
+  

data/test/test_bio-chembl-assay.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-assay.rb

data/test/test_bio-chembl-chemblid.rb

@@ -0,0 +1,36 @@
+require 'helper'
+require 'bio-chembl/chembl.rb'
+
+
+
+class TestBioChemblChembId < Test::Unit::TestCase
+  def setup
+    @str = "CHEMBL1"
+    @chemblid = BioChEMBL::ChEMBLID.new(@str)
+  end
+  
+  def test_chemblid
+    assert_equal(@chemblid.class, BioChEMBL::ChEMBLID)
+    assert_equal(@chemblid, "CHEMBL1")
+    assert_equal(@chemblid.data_type, nil)
+  end
+  
+  def test_invalid_chembl_id
+    assert_raise(Exception) {
+      BioChEMBL::CHEMBLID.new("CHEMBLCHEMBL1")
+    }
+  end
+  
+  def test_chemblid_is_compound?
+    assert_equal(@chemblid.is_compound?, true)
+    assert_equal(@chemblid.data_type, Compound)
+  end
+  
+  def test_chemblid_is_target?
+    assert_equal(@chemblid.is_target?, false)    
+  end
+
+  def test_chemblid_is_assay?
+    assert_equal(@chemblid.is_assay?, false)    
+  end
+end

data/test/test_bio-chembl-chemblid.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-chemblid.rb

data/test/test_bio-chembl-compound.rb

@@ -0,0 +1,125 @@
+require 'helper'
+require 'bio-chembl/chembl.rb'
+
+
+
+class TestBioChemblCompound < Test::Unit::TestCase
+  def setup
+    @xml = "<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>"
+    @chemblId = "CHEMBL1"
+  end
+  
+  def test_compound_parser_xml
+    doc = BioChEMBL::Compound.parse_xml(@xml)
+    assert_equal(doc.chemblId, "CHEMBL1")
+  end
+  
+  def test_compound_attributes
+    doc = BioChEMBL::Compound.parse_xml(@xml)
+    assert_equal(doc.class, BioChEMBL::Compound)
+  end
+
+  def test_compound_attributes
+    doc = BioChEMBL::Compound.parse_xml(@xml)
+    assert_equal(doc.chemblId, "CHEMBL1")
+    assert_equal(doc.knownDrug, "No")
+    assert_equal(doc.medChemFriendly, "Yes")
+    assert_equal(doc.passesRuleOfThree, "No")
+    assert_equal(doc.molecularFormula, "C32H32O8")
+    assert_equal(doc.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_equal(doc.stdInChiKey, "GHBOEFUAGSHXPO-XZOTUCIWSA-N")
+    assert_equal(doc.numRo5Violations, "1")
+    assert_equal(doc.rotatableBonds, "2")
+    assert_equal(doc.molecularWeight, "544.59167")
+    assert_equal(doc.alogp, "3.627")
+    assert_equal(doc.acdLogp, "7.669")
+    assert_equal(doc.acdLogd, "7.669")
+  end
+    
+
+  def test_compound_parse_json
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Compound.parse_json("")
+    }
+  end
+
+  
+  def test_compound_parse_rdf
+    assert_raise(NotImplementedError) {
+      BioChEMBL::Compound.parse_rdf("")
+    }
+  end
+  
+  
+  def test_compound_parse
+    doc = BioChEMBL::Compound.parse(@xml)
+    assert_equal("CHEMBL1", doc.chemblId)
+  end
+
+  
+  def test_compound_resolve
+    doc = BioChEMBL::Compound.new
+    doc.chemblId = @chemblId
+    assert_equal(doc.knownDrug, nil)
+    doc.resolve
+    assert_equal(doc.knownDrug, "No")
+  end
+end
+
+class TestBioChemblCompoundClassMethods < Test::Unit::TestCase
+  def setup
+    @chemblId = "CHEMBL1"
+    @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"
+    @stdinchikey = "QFFGVLORLPOAEC-SNVBAGLBSA-N"
+    @warfarine = "CC(=O)CC(C1=C(O)c2ccccc2OC1=O)c3ccccc3"
+    @warfarine70 = "CC(=O)CC(C1=C(O)c2ccccc2OC1=O)c3ccccc3/70"
+  end
+
+  def test_find
+    doc = BioChEMBL::Compound.find(@chemblId)
+    assert_equal(doc.chemblId, "CHEMBL1")
+    assert_equal(doc.knownDrug, "No")
+  end
+
+  def test_find_by_smiles
+    uri = BioChEMBL::REST::ChEMBL_URI.compounds_smiles(@smiles)
+    assert_equal(uri, "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")
+    xml = BioChEMBL::REST.new.compounds_smiles(@smiles)
+    assert_equal(xml, "<list><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></list>")
+    doc = BioChEMBL::Compound.find_by_smiles(@smiles)
+    assert_equal(doc.class, BioChEMBL::Compound)
+    assert_equal("CHEMBL1", doc.chemblId)
+  end
+
+  def test_find_all_by_smiles
+    uri = BioChEMBL::REST::ChEMBL_URI.compounds_smiles(@smiles)
+    assert_equal(uri, "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")
+    xml = BioChEMBL::REST.new.compounds_smiles(@smiles)
+    assert_equal(xml, "<list><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></list>")
+    docs = BioChEMBL::Compound.find_all_by_smiles(@smiles)
+    assert_equal(docs.class, Array)
+    assert_equal(docs.first.class, BioChEMBL::Compound)
+    assert_equal("CHEMBL1", docs.first.chemblId)
+  end
+
+  def test_find_by_stdinchikey
+    doc = BioChEMBL::Compound.find_by_stdinchikey(@stdinchikey)
+    assert_equal(doc.class, BioChEMBL::Compound)
+    assert_equal("CHEMBL1201760", doc.chemblId)
+  end
+
+  def test_find_all_by_substructure
+    docs = BioChEMBL::Compound.find_all_by_substructure(@warfarine)
+    assert_equal(docs.class, Array)
+    assert_equal(docs.first.class, BioChEMBL::Compound)
+    assert_equal("CHEMBL149194", docs.first.chemblId)
+  end
+
+  def test_find_all_by_similarity
+    docs = BioChEMBL::Compound.find_all_by_similarity(@warfarine70)
+    assert_equal(docs.class, Array)
+    assert_equal(docs.first.class, BioChEMBL::Compound)
+    assert_equal("CHEMBL313331", docs.first.chemblId)
+  end
+
+end