Class: GlyDevKit::CDK

Inherits:
Object
  • Object
show all
Defined in:
lib/glydevkit/cdk.rb

Instance Method Summary collapse

Instance Method Details

#mol2svg(smiles, scale) ⇒ Object 



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# File 'lib/glydevkit/cdk.rb', line 23

def mol2svg(smiles,scale)
  
  begin
    sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance)
    molecule = sp.parseSmiles(smiles)

    sdg = StructureDiagramGenerator.new(molecule)
    sdg.generateCoordinates
    molecule = sdg.molecule
      
    depiction_gen = DepictionGenerator.new
    return depiction_gen.withSize(30, 30).depict(molecule).toSvgStr.sub(/width=\'30.0mm\' height=\'30.0mm\' /,"/width='#{30 * scale}.0mm' height='#{30 * scale}.0mm'")
  
  rescue => e
    puts e.message
  end
end

#sim(seq1, seq2, format) ⇒ Object 



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# File 'lib/glydevkit/cdk.rb', line 15

def sim(seq1,seq2,format)
  if format == "wurcs"
      Tanimoto.calculate(w2bit(seq1), w2bit(seq2))
  elsif format == "smiles"
      Tanimoto.calculate(smiles2bit(seq1), smiles2bit(seq2))
  end
end