Class: Chem::KEGG::KCF

Inherits:
Object
  • Object
show all
Includes:
Molecule, Enumerable
Defined in:
lib/chem/db/kcf.rb

Constant Summary

Constants included from Molecule

Molecule::DESCRIPTORNAME, Molecule::ELEMNUM, Molecule::EpsHeader, Molecule::MDLCountLineFormat, Molecule::MDLHeaderLine2Format

Instance Attribute Summary

Attributes included from Molecule

#cdk2atom, #cdk_mol, #name, #ob_mol, #source

Attributes included from Graph

#adjacencies, #edges, #nodes

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Molecule

#-, #adjacent_index, #assign_2d_geometry, #bit_mat, #box_size, #breadth_first_search, #canonical_ring, #cdk_BCUT, #cdk_CPSA, #cdk_RotatableBondsCount, #cdk_calc_descriptor, #cdk_calc_descriptors, #cdk_find_all_rings, #cdk_fingerprint, #cdk_gasteiger_marsili_partial_charges, #cdk_generate_2D, #cdk_generate_randomly, #cdk_generate_vicinity, #cdk_hose_code, #cdk_hueckel, #cdk_mcs, #cdk_properties, #cdk_rule_of_file, #cdk_save_as, #cdk_setup, #cdk_sssr, #cdk_wiener_numbers, #cdk_xlogp, #composition, #connected?, #deep_dup, #delete, #delete_bond, #depth_first_search, #divide, #f_dfs, #find_smallest_ring, #find_sssr, #fingerprint, #generate_pubchem_subskey, #hilight, #induced_sub, #match, #match_by_ullmann, #method_missing, #molecular_weight, #n_hydrogen, #ob_export_as, #ob_save_as, #oxidation_number, #pubchem_subskeys, #remove_hydrogens!, #save, #save_as_mdl, #save_as_pdf, #subset_in_composition?, #to_cansmi, #to_eps, #to_inchi, #to_sybyl, #typ_str, #use_open_babel

Methods included from Graph

#adjacent_to, #clustering_coefficient, #each, #morgan, #terminal_nodes

Constructor Details

#initialize(input) ⇒ KCF

Returns a new instance of KCF.



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# File 'lib/chem/db/kcf.rb', line 60

def initialize input
  @nodes = []
  @edges = []
  hash = {}
  while ! /\/\/\//.match(line = input.readline)
    case line[0...12]
    when 'ENTRY       '
    when 'ATOM        '
      line.split[1].to_i.times do |n|
        atom = KCFAtom.new input.readline

        hash[atom.atom_id] = atom
        @nodes.push(atom)
      end
    when 'BOND        '
      line.split[1].to_i.times do |n|
        bond = KCFBond.new input.readline
        @edges.push([bond, hash[line[16...19].to_i], hash[line[19...23].to_i]])
      end
    end
  end
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Chem::Molecule

Class Method Details

.open(filename) ⇒ Object 



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# File 'lib/chem/db/kcf.rb', line 83

def KCF.open filename
  @input = File.open(filename)
  KCF.new(@input)
end