Class: BioChEMBL::Compound

Inherits:
Object
  • Object
show all
Extended by:
DataModel
Defined in:
lib/bio-chembl/compound.rb

Overview

ChEMBL Compound Data Container and Parser

XML Data string <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>

Usage “‘cpd = BioChEMBL::Compound.find(“CHEMBL1”)

cpd.chemblId #=> "CHEMLB1"
cpd.smiles

cpd2 = BioChEMBL::Compound.find_all_by_smiles(cpd.smile)

cpd3 = BioChEMBL::Compound.parse(xml)

“‘

Constant Summary collapse

ATTRIBUTES = 
[ 
  :chemblId, 
  :knownDrug,
  :medChemFriendly,
  :passesRuleOfThree,
  :molecularFormula,
  :smiles,
  :stdInChiKey,
  :species,
  :numRo5Violations,
  :rotatableBonds,
  :molecularWeight,
  :alogp,
  :acdAcidicPka,
  :acdLogp,
  :acdLogd 
]

Class Method Summary collapse

Instance Method Summary collapse

Methods included from DataModel

set_attr_accessors, set_attr_values

Constructor Details

#initialize(chemblId = nil) ⇒ Compound

new



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# File 'lib/bio-chembl/compound.rb', line 144

def initialize(chemblId = nil)
  @chemblId = chemblId
end

Class Method Details

.find(chemblId) ⇒ Object

Compound.find(chemblId) Find a compound data by a ChEMBL ID



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# File 'lib/bio-chembl/compound.rb', line 108

def self.find(chemblId)
  self.parse_xml(REST.new.compounds(chemblId))
end

.find_all_by_similarity(smiles_with_similarity) ⇒ Object

Compound.find_similarity(smiles_with_similarity) Search compounds by a SMILES with similarity



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# File 'lib/bio-chembl/compound.rb', line 138

def self.find_all_by_similarity(smiles_with_similarity)
  self.parse_list_xml(REST.new.compounds_similarity(smiles_with_similarity))
end

.find_all_by_smiles(smiles) ⇒ Object

Compound.find_all_by_smiles(smiles) Find compounds by a SMILES.



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# File 'lib/bio-chembl/compound.rb', line 120

def self.find_all_by_smiles(smiles)
  self.parse_list_xml(REST.new.compounds_smiles(smiles))
end

.find_all_by_substructure(smiles) ⇒ Object

Compound.find_all_by_substructure(smiles) Substructure Search by a SMILES



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# File 'lib/bio-chembl/compound.rb', line 132

def self.find_all_by_substructure(smiles)
  self.parse_list_xml(REST.new.compounds_substructure(smiles))
end

.find_by_smiles(smiles) ⇒ Object

Compound.find_by_smiles(smiles) Find a compound data by a SMILES



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# File 'lib/bio-chembl/compound.rb', line 114

def self.find_by_smiles(smiles)
  self.find_all_by_smiles(smiles).first
end

.find_by_stdinchikey(stdinchikey) ⇒ Object

Compound.find_by_stdinchikey(stdinchikey) Find a compound data by a StdInChiKey



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# File 'lib/bio-chembl/compound.rb', line 126

def self.find_by_stdinchikey(stdinchikey)
  self.parse_xml(REST.new.compounds_stdinchikey(stdinchikey))
end

.parse(str) ⇒ Object

BioChEMBL::Compound.parse(doc)



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# File 'lib/bio-chembl/compound.rb', line 61

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

.parse_json(str) ⇒ Object

JSON

Raises:

  • (NotImplementedError) 


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# File 'lib/bio-chembl/compound.rb', line 96

def self.parse_json(str)
  raise NotImplementedError
end

.parse_list_xml(str) ⇒ Object

XML <list><compound> …



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# File 'lib/bio-chembl/compound.rb', line 88

def self.parse_list_xml(str)
  xmls = Nokogiri::XML(str)
  xmls.xpath("/list/compound").map do |cpd|
    self.parse_xml(cpd.to_s)
  end
end

.parse_rdf(str) ⇒ Object

RDF

Raises:

  • (NotImplementedError) 


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# File 'lib/bio-chembl/compound.rb', line 101

def self.parse_rdf(str)
  raise NotImplementedError
end

.parse_xml(str) ⇒ Object

XML <compound>



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# File 'lib/bio-chembl/compound.rb', line 79

def self.parse_xml(str)
  xml = Nokogiri::XML(str)
  this = new  
  eval set_attr_values(ATTRIBUTES)
  this
end

Instance Method Details

#resolve ⇒ Object

Resolve the compound data by given ChEMBL ID



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# File 'lib/bio-chembl/compound.rb', line 149

def resolve
  resolved = self.class.find(@chemblId)
  ATTRIBUTES.each do |attr|
    eval "@#{attr} = resolved.#{attr}"
  end
end