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::EpsHeader, Molecule::MDLCountLineFormat

Instance Attribute Summary

Attributes included from Molecule

#name, #source

Attributes included from Graph

#adjacencies, #edges, #nodes

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(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("\n@").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

Instance Method Details

#n_atoms ⇒ Object 



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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_bonds ⇒ Object 



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

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