lib/bio/db/pdb/pdb.rb in bio-1.0.0 vs lib/bio/db/pdb/pdb.rb in bio-1.1.0

@@ -2,30 +2,14 @@
 # = bio/db/pdb/pdb.rb - PDB database class for PDB file format
 #
 # Copyright:: Copyright (C) 2003-2006
 #             GOTO Naohisa <[e-mail]>
 #             Alex Gutteridge <[e-mail]>
-# License:: LGPL
+# License::   The Ruby License
 #
-#  $Id: pdb.rb,v 1.15 2006/02/20 13:00:43 ngoto Exp $
+#  $Id: pdb.rb,v 1.23 2007/07/10 10:44:46 ngoto Exp $
 #
-#--
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2 of the License, or (at your option) any later version.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#++
-#
 # = About Bio::PDB
 #
 # Please refer document of Bio::PDB class.
 #
 # = References
@@ -133,11 +117,11 @@
             end
           }
           m
         end
         def self.new(str)
-          String.new(str)
+          String.new(str.to_s)
         end
       end
 
       module Pdb_Real
         def self.[](fmt)
@@ -352,11 +336,11 @@
       #
       # Normally, it is automatically called and you don't explicitly
       # need to call it .
       #
       def do_parse
-        return self if @parsed
+        return self if @parsed or !@str
         str = @str
         each_symbol do |key, klass, ranges|
           #If we only have one range then pull that out
           #and store it in the hash
           if ranges.size <= 1 then
@@ -988,35 +972,83 @@
         def <=>(other)
           return serial <=> other.serial
         end
 
         def do_parse
-          return self if @parsed
+          return self if @parsed or !@str
           self.serial     = @str[6..10].to_i
-          self.name       = @str[12..15]
+          self.name       = @str[12..15].strip
           self.altLoc     = @str[16..16]
-          self.resName    = @str[17..19].rstrip
+          self.resName    = @str[17..19].strip
           self.chainID    = @str[21..21]
           self.resSeq     = @str[22..25].to_i
-          self.iCode      = @str[26..26]
+          self.iCode      = @str[26..26].strip
           self.x          = @str[30..37].to_f
           self.y          = @str[38..45].to_f
           self.z          = @str[46..53].to_f
           self.occupancy  = @str[54..59].to_f
           self.tempFactor = @str[60..65].to_f
-          self.segID      = @str[72..75]
-          self.element    = @str[76..77]
-          self.charge     = @str[78..79]
+          self.segID      = @str[72..75].to_s.rstrip
+          self.element    = @str[76..77].to_s.lstrip
+          self.charge     = @str[78..79].to_s.strip
           @parsed = true
           self
         end
 
+        def justify_atomname
+          atomname = self.name.to_s
+          return atomname[0, 4] if atomname.length >= 4
+          case atomname.length
+          when 0
+            return '    '
+          when 1
+            return ' ' + atomname + '  '
+          when 2
+            if /\A[0-9]/ =~ atomname then
+              return sprintf('%-4s', atomname)
+            elsif /[0-9]\z/ =~ atomname then
+              return sprintf(' %-3s', atomname)
+            end
+          when 3
+            if /\A[0-9]/ =~ atomname then
+              return sprintf('%-4s', atomname)
+            end
+          end
+          # ambiguous case for two- or three-letter name
+          elem = self.element.to_s.strip
+          if elem.size > 0 and i = atomname.index(elem) then
+            if i == 0 and elem.size == 1 then
+              return sprintf(' %-3s', atomname)
+            else
+              return sprintf('%-4s', atomname)
+            end
+          end
+          if self.kind_of?(HETATM) then
+            if /\A(B[^AEHIKR]|C[^ADEFLMORSU]|F[^EMR]|H[^EFGOS]|I[^NR]|K[^R]|N[^ABDEIOP]|O[^S]|P[^ABDMORTU]|S[^BCEGIMNR]|V|W|Y[^B])/ =~
+                atomname then
+              return sprintf(' %-3s', atomname)
+            else
+              return sprintf('%-4s', atomname)
+            end
+          else # ATOM
+            if /\A[CHONSP]/ =~ atomname then
+              return sprintf(' %-3s', atomname)
+            else
+              return sprintf('%-4s', atomname)
+            end
+          end
+          # could not be reached here
+          raise 'bug!'
+        end
+        private :justify_atomname
+
         def to_s
+          atomname = justify_atomname
           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,
+                  atomname,
                   self.altLoc,
                   self.resName,
                   self.chainID,
                   self.resSeq,
                   self.iCode,
@@ -1501,10 +1533,11 @@
           f.residue = ligand
           ligand.addAtom(f)
 
         when 'MODEL'
           c_atom = nil
+          cChain = nil
           if cModel.model_serial or cModel.chains.size > 0 then
             self.addModel(cModel)
           end
           cModel = Model.new(f.serial)
 
@@ -1639,11 +1672,11 @@
     # Example:
     # p pdb.record('HETATM')
     # p pdb.record['HETATM']
     #
     def record(name = nil)
-      name ? @hash[name] : @hash
+      name ? (@hash[name] || []) : @hash
     end
 
     #--
     # PDB original methods
     #Returns a hash of the REMARK records based on the remarkNum
@@ -1802,40 +1835,46 @@
       self.record('KEYWDS').collect { |f| f.keywds }.flatten
     end
 
     # Classification in "HEADER".
     def classification
-      self.record('HEADER').first.classification
+      f = self.record('HEADER').first
+      f ? f.classification : nil
     end
 
     # Get authors in "AUTHOR".
     def authors
-      self.record('AUTHOR').first.authorList
+      self.record('AUTHOR').collect { |f| f.authorList }.flatten
     end
 
     #--
     # Bio::DB methods
     #++
 
     # PDB identifier written in "HEADER". (e.g. 1A00)
     def entry_id
-      @id = self.record('HEADER').first.idCode unless @id
+      unless @id
+        f = self.record('HEADER').first
+        @id = f ? f.idCode : nil
+      end
       @id
     end
 
     # Same as <tt>Bio::PDB#entry_id</tt>.
     def accession
       self.entry_id
     end
 
     # Title of this entry in "TITLE".
     def definition
-      self.record('TITLE').first.title
+      f = self.record('TITLE').first
+      f ? f.title : nil
     end
 
     # Current modification number in "REVDAT".
     def version
-      self.record('REVDAT').first.modNum
+      f = self.record('REVDAT').first
+      f ? f.modNum : nil
     end
 
   end #class PDB
 
 end #module Bio