lib/bio/db/pdb/pdb.rb in bio-1.2.1 vs lib/bio/db/pdb/pdb.rb in bio-1.3.0

@@ -4,11 +4,11 @@
 # Copyright:: Copyright (C) 2003-2006
 #             GOTO Naohisa <[e-mail]>
 #             Alex Gutteridge <[e-mail]>
 # License::   The Ruby License
 #
-#  $Id: pdb.rb,v 1.27 2007/12/28 14:43:44 ngoto Exp $
+#  $Id: pdb.rb,v 1.28 2008/04/01 10:36:44 ngoto Exp $
 #
 # = About Bio::PDB
 #
 # Please refer document of Bio::PDB class.
 #
@@ -1495,10 +1495,13 @@
               newChain = Chain.new(f.chainID, cModel)
               cModel.addChain(newChain)
               cChain = newChain
               chain = newChain
             end
+            # chain might be changed, clearing cResidue and cLigand
+            cResidue = nil
+            cLigand = nil
           end
         end
 
         case key
         when 'ATOM'
@@ -1548,10 +1551,12 @@
           ligand.addAtom(f)
 
         when 'MODEL'
           c_atom = nil
           cChain = nil
+          cResidue = nil
+          cLigand = nil
           if cModel.model_serial or cModel.chains.size > 0 then
             self.addModel(cModel)
           end
           cModel = Model.new(f.serial)
 
@@ -1807,16 +1812,20 @@
             # amino acid sequence
             a.collect! do |aa|
               #aa is three letter code: i.e. ALA
               #need to look up with Ala
               aa = aa.capitalize
-              (Bio::AminoAcid.three2one(aa) or 'X')
+              (begin
+                 Bio::AminoAcid.three2one(aa)
+               rescue ArgumentError
+                 nil
+               end || 'X')
             end
             seq = Bio::Sequence::AA.new(a.to_s)
           else
             # nucleic acid sequence
             a.collect! do |na|
-              na = na.strip
+              na = na.delete('^a-zA-Z')
               na.size == 1 ? na : 'n'
             end
             seq = Bio::Sequence::NA.new(a.to_s)
           end
           newHash[k] = seq