[BioRuby-cvs] bioruby/lib/bio/db/pdb chain.rb, 1.5, 1.6 model.rb, 1.6, 1.7 pdb.rb, 1.12, 1.13 residue.rb, 1.9, 1.10

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv26464

Modified Files:
	chain.rb model.rb pdb.rb residue.rb 
Log Message:
Added Bio::PDB::Record::ATOM#to_s and modified Bio::PDB::*.to_s.

Note that Bio::PDB#to_s and Bio::PDB::{Model,Chain,Residue,Heterogen}#to_s is still imcomplete.
Note that Bio::PDB::Record::ATOM#to_s (and Bio::PDB::Record::HETATM#to_s)
may return invalid data when giving inordinary data.



Index: residue.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** residue.rb	9 Jan 2006 11:22:36 -0000	1.9
--- residue.rb	20 Jan 2006 13:54:08 -0000	1.10
***************
*** 143,149 ****
        # Stringifies each atom
        def to_s
!         string = ""
!         @atoms.each{ |atom| string << atom.to_s << "\n" }
!         return string
        end
  
--- 143,147 ----
        # Stringifies each atom
        def to_s
!         @atoms.join('')
        end
  

Index: model.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/model.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** model.rb	9 Jan 2006 11:22:36 -0000	1.6
--- model.rb	20 Jan 2006 13:54:08 -0000	1.7
***************
*** 140,144 ****
          string = ""
          if model_serial
!           string = "MODEL     #{model_serial}" #Should use proper formatting
          end
          @chains.each{ |chain| string << chain.to_s }
--- 140,144 ----
          string = ""
          if model_serial
!           string = "MODEL     #{model_serial}\n" #Should use proper formatting
          end
          @chains.each{ |chain| string << chain.to_s }
***************
*** 147,151 ****
          #end
          if model_serial
!           string << "ENDMDL"
          end
          return string
--- 147,151 ----
          #end
          if model_serial
!           string << "ENDMDL\n"
          end
          return string

Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** pdb.rb	8 Jan 2006 12:59:04 -0000	1.12
--- pdb.rb	20 Jan 2006 13:54:08 -0000	1.13
***************
*** 1010,1013 ****
--- 1010,1031 ----
            self
          end
+ 
+         def to_s
+           sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s%-2s\n",
+                   self.record_name,
+                   self.serial, 
+                   self.name,
+                   self.altLoc,
+                   self.resName,
+                   self.chainID,
+                   self.resSeq,
+                   self.iCode,
+                   self.x, self.y, self.z,
+                   self.occupancy,
+                   self.tempFactor,
+                   self.segID,
+                   self.element,
+                   self.charge)
+         end
        end #class ATOM
  
***************
*** 1577,1581 ****
        string = ""
        @models.each{ |model| string << model.to_s }
!       string << "END"
        return string
      end
--- 1595,1599 ----
        string = ""
        @models.each{ |model| string << model.to_s }
!       string << "END\n"
        return string
      end

Index: chain.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/chain.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** chain.rb	9 Jan 2006 11:22:36 -0000	1.5
--- chain.rb	20 Jan 2006 13:54:08 -0000	1.6
***************
*** 186,190 ****
        # Stringifies each residue
        def to_s
!         @residues.join('') + "TER\n"
        end
  
--- 186,190 ----
        # Stringifies each residue
        def to_s
!         @residues.join('') + "TER\n" + @heterogens.join('')
        end