bio-chembl

    BioChEMBL::REST::ChEMBL_URI.status
     #=> "https://www.ebi.ac.uk/chemblws/status/" 
    BioChEMBL::REST::ChEMBL_URI.compounds("CHEMBL1") 
     #=> "https://www.ebi.ac.uk/chemblws/compounds/CHEMBL1"
    BioChEMBL::REST::ChEMBL_URI.targets("CHEMBL2477") 
     #=> "https://www.ebi.ac.uk/chemblws/targets/CHEMBL2477"
    BioChEMBL::REST::ChEMBL_URI.assays("CHEMBL1217643") 
     #=> "https://www.ebi.ac.uk/chemblws/assays/CHEMBL1217643"

    api = BioChEMBL::REST.new
    compound = api.compounds("CHEMBL1")
    targst   = api.targets("CHEMBL2477")
    assay    = api.assays("CHEMBL1217643")

   BioChEMBL::REST.up? #=> true/false

    cpd = BioChEMBL::Compound.find("CHEMBL1")
    cpd.chemblId #=> "CHEMBL1"
    cpd.slimes
   
    smiles = "CC(=O)CC(C1=C(O)c2ccccc2OC1=O)c3ccccc3"
    cpds = BioChEMBL::Compound.find_all_by_smiles(smiles)
    cpds = BioChEMBL::Compound.find_all_by_substructure(smiles)
    cpds = BioChEMBL::Compound.find_all_by_similarity(smiles + "/70")

    cpd.bioactivities[0].parent_compound.chemblId #=> "CHEMBL1"
    
    xml = BioChEMBL::REST.new.compounds("CHEMBL1") 
    cpd = BioChEMBL::Compound.parse_xml(xml)

    target = BioChEMBL::Target.find("CHEMBL1785")
    target.chemblId #=> "CHEMBL1785"
    target.targetType #=> "PROTEIN"
    target.geneNames #=> "EDNRB; ETRB"
    
    BioChEMBL.to_array(target.geneNames) #=> ["EDNRB", "ETRB"]
    synonyms = BioChEMBL.to_array(target.synonyms)
    synosyms[0] #=> "Endothelin B receptor"

    target = BioChEMBL::Target.find_by_uniprot("Q13936")
    
    target.bioactivities[0].target.chemblId #=> "CHEMBL1785"
    
    xml = BioChEMBL::REST.new.targets("CHEMBL1785")     
    target = BioChEMBL::Target.parse_xml(xml)

    assay = BioChEMBL::Assay.find("CHEMBL1217643")
    assay.chemblId #=> "CHEMBL1217643"
    
    assay.bioactivities[0].assay.chemblId #=> "CHEMBL1217643"
    assay.bioactivities[0].target
    assay.bioactivities[0].parent_compound
    
    xml = BioChEMBL::REST.new.assays("CHEMBL1217643") 
    assay = BioChEMBL::Assay.parse_xml(xml)

    cpd.bioactivities[0].parent_compound.chemblId
    target.bioactivities[0].target.chemblId
    assay.bioactivities[0].assay.chemblId
    assay.bioactivities[0].target
    assay.bioactivities[0].parent_compound

    require 'bio-chembl'
    # 1. Use UniProt accession to get target details
    puts "
    # =========================================================
    # 1. Use UniProt accession to get target details
    # =========================================================
    "
    
  	accession = "Q00534"
  	target = BioChEMBL::Target.find_by_uniprot(accession)
  	
  	puts "Target description:  #{target.description}"
  	puts "Target CHEMBLID:     #{target.chemblId}"
  	
  
    # 2. Get all bioactivties for target CHEMBL_ID
    puts "
	# =========================================================
	# 2. Get all bioactivties for target CHEMBL_ID
	# =========================================================
	"

	bioactivities = target.bioactivities
	
	puts "Bioactivity count:           #{bioactivities.size}"
	puts "Bioactivity count (IC50's):  #{bioactivities.find_all {|x| x.bioactivity__type =~ /IC50/}.size}"


	# 3. Get compounds with high binding affinity (IC50 < 100)
	puts "
	# =========================================================
	# 3. Get compounds with high binding affinity (IC50 < 100)
	# =========================================================
	"

	bioactivities.find_all {|x| x.bioactivity__type =~ /IC50/ and x.value.to_i < 100 }.each do |ba|
	  compound = ba.parent_compound
	  print "Compound CHEMBLID: #{compound.chemblId}"
	  puts "  #{compound.smiles}"
	end
	
	# 4. Get assay details for Ki actvity types
	puts "
	# =========================================================
	# 4. Get assay details for Ki actvity types
	# =========================================================
	"
	
	bioactivities.find_all {|x| x.bioactivity__type =~ /Ki/i }.each do |ba|
	  assay = ba.assay
	  print "Assay CHEMBLID:  #{assay.chemblId}"
	  puts "  #{assay.assayDescription}"
	end

	require 'bio-chembl/chembldb.rb'
	
	ActiveRecord::Base.establish_connection( {:adapter => 'mysql', 
    	                                      :host => 'localhost',
        	                                  :port => 3306,
            	                              :username => 'chembl', 
                	                          :password => '', 
                    	                      :socket => '/tmp/mysql.sock',
                        	                  :database => 'chembl_14'} )
                        	                  
  	accession = "Q00534"
	target = BioChEMBL::ChEMBLDB::Target.find_by_protein_accession(accession)
	puts "Target description:  #{target.description}"
	puts "Target CHEMBLID:     #{target.chembl_id}"
	
	# ChEMBL ID
	chembl_id = "CHEMBL1"
	chemblid = BioChEMBL::ChEMBLDB::ChemblIdLookup.find(chembl_id)
	chemblid.entity_type 
	compound = chemblid.entity
	
	# Compound
	compound = BioChEMBL::ChEMBLDB::Molecule.find_by_chembl_id(chembl_id)
	activities = compound.compound_records.map {|x| x.activities }.flatten
	
	# Target
	target = BioChEMBL::ChEMBLDB::Target.find_by_chembl_id(chembl_id)
	activities = target.assays.map {|x| x.activities }.flatten
	
	# Assay
	assay = BioChEMBL::ChEMBLDB::Assay.find_by_chembl_id(chembl_id)
	activities = assay.activities

    require 'bio-chembl'