module Bio::PDB::AtomFinder

methods to access atoms

XXX#each_residue must be defined.

Public Instance Methods

atoms() click to toggle source

returns all atoms

    # File lib/bio/db/pdb/utils.rb
331 def atoms
332   array = []
333   self.each_residue { |residue| array.concat(residue.atoms) }
334   return array
335 end

each_atom() { |atom| ... } click to toggle source

iterates over each atom

    # File lib/bio/db/pdb/utils.rb
326 def each_atom(&x) #:yields: atom
327   self.each_residue { |residue| residue.each(&x) }
328 end

find_atom() { |atom| ... } click to toggle source

returns an array containing all atoms for which given block is not false (similar to Enumerable#find_all).

    # File lib/bio/db/pdb/utils.rb
317 def find_atom
318   array = []
319   self.each_atom do |atom|
320     array.push(atom) if yield(atom)
321   end
322   return array
323 end