Module Bio::PDB::AtomFinder
In: lib/bio/db/pdb/utils.rb

methods to access atoms

XXX#each_residue must be defined.

Methods

atoms   each_atom   find_atom  

Public Instance methods

returns all atoms

[Source]

     # File lib/bio/db/pdb/utils.rb, line 329
329:     def atoms
330:       array = []
331:       self.each_residue { |residue| array.concat(residue.atoms) }
332:       return array
333:     end

iterates over each atom

[Source]

     # File lib/bio/db/pdb/utils.rb, line 324
324:     def each_atom(&x) #:yields: atom
325:       self.each_residue { |residue| residue.each(&x) }
326:     end

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

[Source]

     # File lib/bio/db/pdb/utils.rb, line 315
315:     def find_atom
316:       array = []
317:       self.each_atom do |atom|
318:         array.push(atom) if yield(atom)
319:       end
320:       return array
321:     end

[Validate]