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.
bioruby · Jan 20, 2006 · f1625af · f1625af
1 parent cb6c0e6
commit f1625af
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Showing 4 changed files with 27 additions and 11 deletions.
diff --git a/lib/bio/db/pdb/chain.rb b/lib/bio/db/pdb/chain.rb
@@ -6,7 +6,7 @@
 #             Naohisa Goto <ng@bioruby.org>
 # License:: LGPL
 # 
-#  $Id: chain.rb,v 1.5 2006/01/09 11:22:36 ngoto Exp $
+#  $Id: chain.rb,v 1.6 2006/01/20 13:54:08 ngoto Exp $
 #
 #--
 #  This library is free software; you can redistribute it and/or
@@ -185,7 +185,7 @@ def <=>(other)
 
       # Stringifies each residue
       def to_s
-        @residues.join('') + "TER\n"
+        @residues.join('') + "TER\n" + @heterogens.join('')
       end
 
       # gets an amino acid sequence of this chain from ATOM records

diff --git a/lib/bio/db/pdb/model.rb b/lib/bio/db/pdb/model.rb
@@ -6,7 +6,7 @@
 #             Naohisa Goto <ng@bioruby.org>
 # License:: LGPL
 #
-#  $Id: model.rb,v 1.6 2006/01/09 11:22:36 ngoto Exp $
+#  $Id: model.rb,v 1.7 2006/01/20 13:54:08 ngoto Exp $
 #
 #--
 #  This library is free software; you can redistribute it and/or
@@ -139,14 +139,14 @@ def [](key)
       def to_s
         string = ""
         if model_serial
-          string = "MODEL     #{model_serial}" #Should use proper formatting
+          string = "MODEL     #{model_serial}\n" #Should use proper formatting
         end
         @chains.each{ |chain| string << chain.to_s }
         #if solvent
         #  string << @solvent.to_s
         #end
         if model_serial
-          string << "ENDMDL"
+          string << "ENDMDL\n"
         end
         return string
       end

diff --git a/lib/bio/db/pdb/pdb.rb b/lib/bio/db/pdb/pdb.rb
@@ -6,7 +6,7 @@
 #             Alex Gutteridge <alexg@ebi.ac.uk>
 # License:: LGPL
 #
-#  $Id: pdb.rb,v 1.12 2006/01/08 12:59:04 ngoto Exp $
+#  $Id: pdb.rb,v 1.13 2006/01/20 13:54:08 ngoto Exp $
 #
 #--
 #  This library is free software; you can redistribute it and/or
@@ -1009,6 +1009,24 @@ def do_parse
           @parsed = true
           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
 
       # SIGATM record class
@@ -1576,7 +1594,7 @@ def [](key)
     def to_s
       string = ""
       @models.each{ |model| string << model.to_s }
-      string << "END"
+      string << "END\n"
       return string
     end
 

diff --git a/lib/bio/db/pdb/residue.rb b/lib/bio/db/pdb/residue.rb
@@ -6,7 +6,7 @@
 #              Naohisa Goto <ng@bioruby.org>
 # License:: LGPL
 #
-#  $Id: residue.rb,v 1.9 2006/01/09 11:22:36 ngoto Exp $
+#  $Id: residue.rb,v 1.10 2006/01/20 13:54:08 ngoto Exp $
 #
 #--
 #  This library is free software; you can redistribute it and/or
@@ -142,9 +142,7 @@ def <=>(other)
 
       # Stringifies each atom
       def to_s
-        string = ""
-        @atoms.each{ |atom| string << atom.to_s << "\n" }
-        return string
+        @atoms.join('')
       end
 
       # Always returns false.