Class RCDK::Util::Lang
In: lib/rcdk/util.rb
Parent: Object

Molecular language translation. Currently molfile, SMILES, and IUPAC nomenclature (read-only) are implemented.

Methods

Included Modules

Org::Openscience::Cdk Org::Openscience::Cdk::Io Java::Io Uk::Ac::Cam::Ch::Wwmm::Opsin

Public Class methods

Returns a String-based molfile by parsing the CDK molecule.

[Source]

    # File lib/rcdk/util.rb, line 87
87:       def self.get_molfile(molecule)
88:         writer = StringWriter.new
89:         
90:         @@mdl_writer.setWriter(writer)
91:         @@mdl_writer.writeMolecule(molecule)
92:         @@mdl_writer.close
93:         
94:         writer.toString
95:       end

Returns a SMILES string based on the structure of the indicated CDK molecule.

[Source]

     # File lib/rcdk/util.rb, line 104
104:       def self.get_smiles(molecule)
105:         @@smiles_generator.createSMILES(molecule)
106:       end

Returns a SMILES string by parsing the molfile string.

[Source]

     # File lib/rcdk/util.rb, line 109
109:       def self.molfile_to_smiles(molfile)
110:         get_smiles(read_molfile(molfile))
111:       end

Returns a CDK Molecule given the specified iupac_name.

[Source]

    # File lib/rcdk/util.rb, line 71
71:       def self.read_iupac(iupac_name)
72:         nts = NameToStructure.getInstance
73:         cml = nts.parseToCML(iupac_name)
74:         
75:         raise "Couldn't parse #{iupac_name}." unless cml
76:         
77:         string_reader = StringReader.new(cml.toXML)
78:         
79:         @@cml_reader = CMLReader.new unless @@cml_reader
80:         @@cml_reader.setReader(string_reader)
81:         
82:         chem_file = @@cml_reader.read(ChemFile.new)
83:         chem_file.getChemSequence(0).getChemModel(0).getSetOfMolecules.getMolecule(0)
84:       end

Returns a CDK Molecule given the String-based molfile molfile.

[Source]

    # File lib/rcdk/util.rb, line 63
63:       def self.read_molfile(molfile)
64:         reader = StringReader.new(molfile)
65:         
66:         @@mdl_reader.setReader(reader)
67:         @@mdl_reader.read(Molecule.new)
68:       end

Returns a CDK Molecule by parsing smiles.

[Source]

     # File lib/rcdk/util.rb, line 98
 98:       def self.read_smiles(smiles)
 99:         @@smiles_parser.parseSmiles(smiles)
100:       end

Returns a molfiles STRING by parsing smiles.

[Source]

     # File lib/rcdk/util.rb, line 114
114:       def self.smiles_to_molfile(smiles)
115:         get_molfile(read_smiles(smiles))
116:       end

[Validate]