[BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb, 1.3, 1.4 pdb.rb, 1.4, 1.5 residue.rb, 1.2, 1.3

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv28178

Modified Files:
	atom.rb pdb.rb residue.rb 
Log Message:
more changes

(does not correctly work now!)


Index: atom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/atom.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** atom.rb	16 Dec 2005 19:23:02 -0000	1.3
--- atom.rb	18 Dec 2005 15:09:46 -0000	1.4
***************
*** 93,99 ****
        end
  
!       def record_type
          'ATOM'
        end
      end #class Atom
  
--- 93,102 ----
        end
  
!       def record_name
          'ATOM'
        end
+       def record_type
+         record_name
+       end
      end #class Atom
  
***************
*** 102,106 ****
      # Since HetAtm inherits Atom class, please refer Atom class for usage.
      class HetAtm < Atom
!       def record_type
          'HETATM'
        end
--- 105,109 ----
      # Since HetAtm inherits Atom class, please refer Atom class for usage.
      class HetAtm < Atom
!       def record_name
          'HETATM'
        end

Index: residue.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** residue.rb	26 Sep 2005 13:00:08 -0000	1.2
--- residue.rb	18 Dec 2005 15:09:46 -0000	1.3
***************
*** 88,92 ****
        #Adds an atom to this residue
        def addAtom(atom)
!         raise "Expecting Bio::PDB::Atom" if not atom.is_a? Bio::PDB::Atom
          @atoms.push(atom)
          self
--- 88,92 ----
        #Adds an atom to this residue
        def addAtom(atom)
!         raise "Expecting ATOM or HETATM" unless atom.is_a? Bio::PDB::Record::ATOM
          @atoms.push(atom)
          self

Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** pdb.rb	16 Dec 2005 19:23:03 -0000	1.4
--- pdb.rb	18 Dec 2005 15:09:46 -0000	1.5
***************
*** 51,55 ****
        module Pdb_Integer
          def self.new(str)
!           str.strip.to_i
          end
        end
--- 51,55 ----
        module Pdb_Integer
          def self.new(str)
!           str.to_i
          end
[...1773 lines suppressed...]
!                 newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
                                           chain)
                  chain.addResidue(newResidue)
                else
!                 newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
!                                          chain, true)
                  chain.addLigand(newResidue)
                end
                
!               atom = f
!               f.residue = newResidue
                newResidue.addAtom(atom)
                cResidue = newResidue
!              
              end
            end
! 
!         when 'MODEL'
            if cModel.model_serial
              self.addModel(cModel)