Class: Chem::SmilesMol

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

Constant Summary

Constants included from Molecule

Molecule::EpsHeader, Molecule::MDLCountLineFormat

Instance Attribute Summary collapse

Attributes included from Molecule

#name, #source

Attributes included from Graph

#adjacencies

Instance Method Summary collapse

Methods included from Molecule

#-, #assign_2d_geometry, #breadth_first_search, #canonical_ring, #composition, #connected?, #deep_dup, #delete, #delete_bond, #depth_first_search, #divide, #find_smallest_ring, #find_sssr, #induced_sub, #molecular_weight, #n_hydrogen, #oxidation_number, #save, #save_as_mdl, #save_as_pdf, #search_pubchem, #subset_in_composition?, #to_cansmi, #to_eps, #to_sybyl, #trim

Methods included from Graph

#adj_matrix, #adjacency_list, #adjacent_to, #clustering_coefficient, #connection, #each, #match_by_adj_mat, #match_by_ullmann, #match_exhaustively, #matchable, #matchable_old, #morgan

Constructor Details

#initialize ⇒ SmilesMol

Returns a new instance of SmilesMol.



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# File 'lib/chem/db/smiles/smiparser.rb', line 353

def initialize
  @nodes = []
  @edges = []
end

Instance Attribute Details

#edges ⇒ Object (readonly)

Returns the value of attribute edges.



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# File 'lib/chem/db/smiles/smiparser.rb', line 351

def edges
  @edges
end

#nodes ⇒ Object (readonly)

Returns the value of attribute nodes.



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# File 'lib/chem/db/smiles/smiparser.rb', line 351

def nodes
  @nodes
end

Instance Method Details

#join(from, to) ⇒ Object 



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# File 'lib/chem/db/smiles/smiparser.rb', line 358

def join from, to
  return if to.bond == '.'
  bond = SmilesBond.new

  case to.bond
  when '='
    bond.v = 2
  when '#'
    bond.v = 3
  else
    bond.v = 1
  end
  @edges.push([bond, from, to])
end