[BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb, 1.7, 1.8 residue.rb, 1.5, 1.6

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv12116

Modified Files:
	pdb.rb residue.rb 
Log Message:
HeteroCompound is renamed to Heterogen.


Index: residue.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** residue.rb	4 Jan 2006 13:01:09 -0000	1.5
--- residue.rb	4 Jan 2006 14:01:14 -0000	1.6
***************
*** 141,145 ****
      end #class Residue
  
!     class HeteroCompound < Residue
  
        # Creates residue id from an ATOM (or HETATM) object.
--- 141,145 ----
      end #class Residue
  
!     class Heterogen < Residue
  
        # Creates residue id from an ATOM (or HETATM) object.
***************
*** 166,170 ****
          true
        end
!     end #class HeteroCompound
  
    end #class PDB
--- 166,170 ----
          true
        end
!     end #class Heterogen
  
    end #class PDB

Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** pdb.rb	4 Jan 2006 13:01:09 -0000	1.7
--- pdb.rb	4 Jan 2006 14:01:14 -0000	1.8
***************
*** 1215,1219 ****
        cChain    = Chain.new
        cResidue  = Residue.new
!       #cCompound = HeteroCompound.new
  
        #Goes through each line and replace that line with a PDB::Record
--- 1215,1219 ----
        cChain    = Chain.new
        cResidue  = Residue.new
!       #cCompound = Heterogen.new
  
        #Goes through each line and replace that line with a PDB::Record
***************
*** 1271,1276 ****
            #I can fix this if really needed
            if f.resName == 'HOH'
!             solvent =   HeteroCompound.new(f.resName, f.resSeq, f.iCode,
!                                            cModel.solvent)
              #p solvent
              f.residue = solvent
--- 1271,1276 ----
            #I can fix this if really needed
            if f.resName == 'HOH'
!             solvent =   Heterogen.new(f.resName, f.resSeq, f.iCode,
!                                       cModel.solvent)
              #p solvent
              f.residue = solvent
***************
*** 1280,1284 ****
            else
  
!             residueID = HeteroCompound.get_residue_id_from_atom(f)
              #p f
              #p residueID
--- 1280,1284 ----
            else
  
!             residueID = Heterogen.get_residue_id_from_atom(f)
              #p f
              #p residueID
***************
*** 1297,1301 ****
                residue = cResidue
              elsif newChain or !(residue = chain[residueID])
!               newResidue = HeteroCompound.new(f.resName, f.resSeq, f.iCode,
                                                chain)
                chain.addLigand(newResidue)
--- 1297,1301 ----
                residue = cResidue
              elsif newChain or !(residue = chain[residueID])
!               newResidue = Heterogen.new(f.resName, f.resSeq, f.iCode,
                                                chain)
                chain.addLigand(newResidue)