[BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.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-serv30006

Modified Files:
	pdb.rb 
Log Message:
changed logics

It might work correctly, but would stil have many bugs.


Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** pdb.rb	18 Dec 2005 15:09:46 -0000	1.5
--- pdb.rb	18 Dec 2005 17:37:14 -0000	1.6
***************
*** 1196,1205 ****
      }
  
-     #Aha! Our entry into the world of PDB parsing, we initialise a PDB
-     #object with the whole PDB file as a string
-     #each PDB has an array of the lines of the original file
-     #a bit memory-tastic! A hash of records and an array of models
-     #also has an id
      def initialize(str)
  
        @data = str.split(/[\r\n]+/)
--- 1196,1205 ----
      }
  
      def initialize(str)
+       #Aha! Our entry into the world of PDB parsing, we initialise a PDB
+       #object with the whole PDB file as a string
+       #each PDB has an array of the lines of the original file
+       #a bit memory-tastic! A hash of records and an array of models
+       #also has an id
  
        @data = str.split(/[\r\n]+/)
***************
*** 1236,1252 ****
          end
  
!         #The meat of the atom parsing - could be speeded up I think
          case key
!         when 'ATOM', 'HETATM'
  
            #Each model has a special solvent chain
            #any chain id with the solvent is lost
            #I can fix this if really needed
!           if key == 'HETATM' and f.resName == 'HOH'
              solvent =   Residue.new(f.resName, f.resSeq, f.iCode,
                                      cModel.solvent, true)
!             solvent_atom = f
              f.residue = solvent
!             solvent.addAtom(solvent_atom)
              cModel.addSolvent(solvent)
              
--- 1236,1278 ----
          end
  
!         # Do something for ATOM and HETATM
          case key
!         when 'ATOM'
!           residueID = "#{f.resSeq}#{f.iCode.strip}".strip
!           #p f
! 
!           if f.chainID == cChain.id
!             chain = cChain
!           elsif !(chain = cModel[f.chainID])
!             #If we don't have chain, add a new chain
!             newChain = Chain.new(f.chainID, cModel)
!             cModel.addChain(newChain)
!             cChain = newChain
!             chain = newChain
!           end
! 
!           if !newChain and residueID == cResidue.id
!             residue = cResidue
!           elsif newChain or !(residue = chain[residueID])
!             newResidue = Residue.new(f.resName, f.resSeq, f.iCode, chain)
!             chain.addResidue(newResidue)
!             cResidue = newResidue
!             residue = newResidue
!           end
! 
!           f.residue = residue
!           residue.addAtom(f)
! 
!         when 'HETATM'
  
            #Each model has a special solvent chain
            #any chain id with the solvent is lost
            #I can fix this if really needed
!           if f.resName == 'HOH'
              solvent =   Residue.new(f.resName, f.resSeq, f.iCode,
                                      cModel.solvent, true)
!             #p solvent
              f.residue = solvent
!             solvent.addAtom(f)
              cModel.addSolvent(solvent)
              
***************
*** 1257,1317 ****
              #numbers for HETATMS
              residueID = "#{f.resSeq}#{f.iCode.strip}".strip
!             if key == 'HETATM'
!               residueID = "LIGAND" + residueID
!             end
!             
!             #If this atom is part of the current residue then add it to
!             #the current residue straight away
!             if f.chainID == cChain.id and residueID == cResidue.id
!               
!               #If we have this chain and residue just add the atom
!               atom = f
!               f.residue = cResidue
!               cResidue.addAtom(atom)
  
!             elsif !cModel[f.chainID]
!               
!               #If we don't have anyhting, add a new chain, residue and atom
!               newChain   = Chain.new(f.chainID, cModel)
                cModel.addChain(newChain)
!               
!               if key == 'ATOM'
!                 newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
!                                          newChain)
!                 newChain.addResidue(newResidue)
!               else
!                 newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
!                                          newChain, true)
!                 newChain.addLigand(newResidue)
!               end
!               atom = f
!               f.residue = newResidue
!               newResidue.addAtom(atom)
!               
!               cChain   = newChain
!               cResidue = newResidue
! 
!             elsif !cModel[f.chainID][residueID]
  
!               #If we have the chain (but not the residue)
!               #make a new residue, add it and add the atom
!               chain = cModel[f.chainID]
!               
!               if key == 'ATOM'
!                 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
  
--- 1283,1313 ----
              #numbers for HETATMS
              residueID = "#{f.resSeq}#{f.iCode.strip}".strip
!             residueID = "LIGAND" + residueID
!             #p f
!             #p residueID
  
!             if f.chainID == cChain.id
!               chain = cChain
!             elsif !(chain = cModel[f.chainID])
!               #If we don't have chain, add a new chain
!               newChain = Chain.new(f.chainID, cModel)
                cModel.addChain(newChain)
!               cChain = newChain
!               chain = newChain
!             end
  
!             if !newChain and residueID == cResidue.id
!               residue = cResidue
!             elsif newChain or !(residue = chain[residueID])
!               newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
!                                        chain, true)
!               chain.addLigand(newResidue)
                cResidue = newResidue
!               residue = newResidue
              end
+ 
+             f.residue = residue
+             residue.addAtom(f)
+             
            end