Class: Chem::Sybyl::SybylMolecule

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

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(filename) ⇒ SybylMolecule

def charge?


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# File 'lib/chem/db/sybyl.rb', line 120

def initialize filename
  @nodes = []
  @edges = []
  File.open(filename) do |input|
    input.read.split("\[email protected]").each do |line|
      ary = line.split("\n")
      case ary[0]
      when /<TRIPOS>MOLECULE/
        parse_mol ary
      when /<TRIPOS>ATOM/
        ary[1..-1].each{|line| @nodes.push(SybylAtom.new(line))}
      when /<TRIPOS>BOND/
        ary[1..-1].each do |line|
          bond = SybylBond.new(line)
          @edges.push([bond, @nodes[bond.e - 1], @nodes[bond.b - 1]])
        end
      end
    end
  end
end

Dynamic Method Handling

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

Instance Method Details

#n_atomsObject


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# File 'lib/chem/db/sybyl.rb', line 117

def n_atoms ;  @n_atoms ||= @count_line[0..4].to_i ;                end

#n_bondsObject


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# File 'lib/chem/db/sybyl.rb', line 118

def n_bonds ;  @n_bonds ||= @count_line[5..10].to_i ;               end