Class: Chem::SmilesMol

Inherits:

Object

• Object
• Chem::SmilesMol

Includes:

Molecule, Enumerable

Defined in:

lib/chem/db/smiles/smiparser.rb

Constant Summary

Constants included from Molecule

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

Instance Attribute Summary

• #edges ⇒ Object readonly

  Returns the value of attribute edges.

• #nodes ⇒ Object readonly

  Returns the value of attribute nodes.

Attributes included from Molecule

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

Attributes included from Graph

#adjacencies

Instance Method Summary

• #initialize ⇒ SmilesMol constructor

  A new instance of SmilesMol.

• #join(from, to) ⇒ Object

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 ⇒ SmilesMol

Returns a new instance of SmilesMol.

# File 'lib/chem/db/smiles/smiparser.rb', line 355

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

Dynamic Method Handling

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

Instance Attribute Details

#edges ⇒ Object (readonly)

Returns the value of attribute edges.

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

def edges
  @edges
end

#nodes ⇒ Object (readonly)

Returns the value of attribute nodes.

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

def nodes
  @nodes
end

Instance Method Details

#join(from, to) ⇒ Object

# File 'lib/chem/db/smiles/smiparser.rb', line 360

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

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