bio 0.7.0 → 0.7.1

data/lib/bio/db/pdb/model.rb

@@ -1,8 +1,14 @@
 #
-# bio/db/pdb/model.rb - model class for PDB
+# = bio/db/pdb/model.rb - model class for PDB
 #
-#   Copyright (C) 2004 Alex Gutteridge <alexg@ebi.ac.uk>
+# Copyright:: Copyright (C) 2004, 2006
+#             Alex Gutteridge <alexg@ebi.ac.uk>
+#             Naohisa Goto <ng@bioruby.org>
+# License:: LGPL
 #
+#  $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
 #  modify it under the terms of the GNU Lesser General Public
 #  License as published by the Free Software Foundation; either
@@ -16,8 +22,12 @@
 #  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
+#++
+#
+# = Bio::PDB::Model
+#
+# Please refer Bio::PDB::Model.
 #
-#  $Id: model.rb,v 1.2 2005/09/26 13:00:08 k Exp $
 
 require 'bio/db/pdb'
 
@@ -25,82 +35,124 @@ module Bio
 
   class PDB
 
-    #Model class
+    # Bio::PDB::Model is a class to store a model.
+    #
+    # The object would contain some chains (Bio::PDB::Chain objects).
     class Model
       
       include Utils
       include AtomFinder
       include ResidueFinder
       include ChainFinder
+
+      include HetatmFinder
+      include HeterogenFinder
+
       include Enumerable
       include Comparable
       
-      attr_reader :model_serial, :structure, :solvent
-      attr_writer :model_serial
-      
-      def initialize(model_serial = nil, structure = nil)
-        
-        @model_serial = model_serial
-        
-        @structure    = structure
-        
-        @chains       = Array.new
-        @solvent      = Chain.new('',self)
+      # Creates a new Model object
+      def initialize(serial = nil, structure = nil)
         
+        @serial = serial
+        @structure = structure
+        @chains = []
+        @chains_hash = {}
+        @solvents = Chain.new('', self)
       end
-      
-      #Adds a chain
+
+      # chains in this model
+      attr_reader :chains
+
+      # (OBSOLETE) solvents (water, HOH) in this model
+      attr_reader :solvents
+
+      # serial number of this model. (Integer or nil)
+      attr_accessor :serial
+
+      # for backward compatibility
+      alias model_serial serial
+
+      # (reserved for future extension)
+      attr_reader :structure
+     
+      # Adds a chain to this model
       def addChain(chain)
-        raise "Expecting a Bio::PDB::Chain" if not chain.is_a? Bio::PDB::Chain
+        raise "Expecting a Bio::PDB::Chain" unless chain.is_a? Bio::PDB::Chain
         @chains.push(chain)
-        self        
+        if @chains_hash[chain.chain_id] then
+          $stderr.puts "Warning: chain_id #{chain.chain_id.inspect} is already used" if $VERBOSE
+        else
+          @chains_hash[chain.chain_id] = chain
+        end
+        self
+      end
+
+      # rehash chains hash
+      def rehash
+        begin
+          chains_bak = @chains
+          chains_hash_bak = @chains_hash
+          @chains = []
+          @chains_hash = {}
+          chains_bak.each do |chain|
+            self.addChain(chain)
+          end
+        rescue RuntimeError
+          @chains = chains_bak
+          @chains_hash = chains_hash_bak
+          raise
+        end
+        self
       end
       
-      #adds a solvent molecule
+      # (OBSOLETE) Adds a solvent molecule to this model
       def addSolvent(solvent)
-        raise "Expecting a Bio::PDB::Residue" if not solvent.is_a? Bio::PDB::Residue
-        @solvent.addResidue(solvent)
+        raise "Expecting a Bio::PDB::Residue" unless solvent.is_a? Bio::PDB::Residue
+        @solvents.addResidue(solvent)
       end
 
+      # (OBSOLETE) not recommended to use this method
       def removeSolvent
-        @solvent = nil
+        @solvents = nil
       end
 
-      #Chain iterator
-      def each
-        @chains.each{ |chain| yield chain }
+      # Iterates over each chain
+      def each(&x) #:yields: chain
+        @chains.each(&x)
       end
-      #Alias to override ChainFinder#each_chain
+      # Alias to override ChainFinder#each_chain
       alias each_chain each
      
-      #Sorts models based on serial number
+      # Operator aimed to sort models based on serial number
       def <=>(other)
-        return @mode_serial <=> other.model_serial
+        return @serial <=> other.model_serial
       end
       
-      #Keyed access to chains
+      # Keyed access to chains
       def [](key)
-        chain = @chains.find{ |chain| key == chain.id }
+        #chain = @chains.find{ |chain| key == chain.id }
+        @chains_hash[key]
       end
       
-      #stringifies to chains
+      # stringifies to chains
       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 solvent
+        #  string << @solvent.to_s
+        #end
         if model_serial
-          string << "ENDMDL"
+          string << "ENDMDL\n"
         end
         return string
       end
       
     end #class Model
 
-  end
+  end #class PDB
 
-end
+end #module Bio

data/lib/bio/db/pdb/pdb.rb

@@ -1,9 +1,14 @@
 #
-# bio/db/pdb/pdb.rb - PDB database class for PDB file format
+# = bio/db/pdb/pdb.rb - PDB database class for PDB file format
 #
-#   Copyright (C) 2003,2004 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
-#   Copyright (C) 2004 Alex Gutteridge <alexg@ebi.ac.uk>
+# Copyright:: Copyright (C) 2003-2006
+#             GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+#             Alex Gutteridge <alexg@ebi.ac.uk>
+# License:: LGPL
 #
+#  $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
 #  modify it under the terms of the GNU Lesser General Public
 #  License as published by the Free Software Foundation; either
@@ -17,12 +22,20 @@
 #  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
+#++
 #
-#  $Id: pdb.rb,v 1.6 2005/12/18 17:37:14 ngoto Exp $
+# = About Bio::PDB
 #
-
-# *** CAUTION ***
-# This is pre-alpha version. Specs shall be changed frequently.
+# Please refer document of Bio::PDB class.
+#
+# = References
+#
+# * ((<URL:http://www.rcsb.org/pdb/>))
+# * PDB File Format Contents Guide Version 2.2 (20 December 1996)
+#   ((<URL:http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html>))
+#
+# = *** CAUTION ***
+# This is beta version. Specs shall be changed frequently.
 #
 
 require 'bio/db/pdb'
@@ -30,20 +43,37 @@ require 'bio/data/aa'
 
 module Bio
 
-  #This is the main PDB class which takes care of parsing, annotations
-  #and is the entry way to the co-ordinate data held in models
-  class PDB #< DB
+  # This is the main PDB class which takes care of parsing, annotations
+  # and is the entry way to the co-ordinate data held in models.
+  #
+  # There are many related classes.
+  #
+  # Bio::PDB::Model
+  # Bio::PDB::Chain
+  # Bio::PDB::Residue
+  # Bio::PDB::Heterogen
+  # Bio::PDB::Record::ATOM
+  # Bio::PDB::Record::HETATM
+  # Bio::PDB::Record::*
+  # Bio::PDB::Coordinate
+  # 
+  class PDB
 
     include Utils
     include AtomFinder
     include ResidueFinder
     include ChainFinder
     include ModelFinder
+
+    include HetatmFinder
+    include HeterogenFinder
+
     include Enumerable
 
+    # delimiter for reading via Bio::FlatFile
     DELIMITER = RS = nil # 1 file 1 entry
 
-    #Modules required by the field definitions
+    # Modules required by the field definitions
     module DataType
 
       Pdb_Continuation = nil
@@ -154,10 +184,20 @@ module Bio
       end #module ConstLikeMethod
     end #module DataType
 
+    # The ancestor of every single PDB record class.
+    # It inherits <code>Struct</code> class.
+    # Basically, each line of a PDB file corresponds to
+    # an instance of each corresponding child class.
+    # If continuation exists, multiple lines may correspond to
+    # single instance.
+    #
     class Record < Struct
       include DataType
       extend DataType::ConstLikeMethod
 
+      # Internal use only.
+      #
+      # parse filed definitions.
       def self.parse_field_definitions(ary)
         symbolhash = {}
         symbolary = []
@@ -192,7 +232,12 @@ module Bio
         [ symbolhash, symbolary, cont ]
       end
       private_class_method :parse_field_definitions
-      
+
+      # Creates new class by given field definition
+      # The difference from new_direct() is the class
+      # created by the method does lazy evaluation.
+      #
+      # Internal use only.
       def self.def_rec(*ary)
         symbolhash, symbolary, cont = parse_field_definitions(ary)
 
@@ -210,6 +255,7 @@ module Bio
         klass
       end #def self.def_rec
 
+      # creates new class which inherits given class.
       def self.new_inherit(klass)
         newklass = Class.new(klass)
         newklass.module_eval {
@@ -220,6 +266,9 @@ module Bio
         newklass
       end
 
+      # Creates new class by given field definition.
+      #
+      # Internal use only.
       def self.new_direct(*ary)
         symbolhash, symbolary, cont = parse_field_definitions(ary)
         if cont
@@ -242,11 +291,14 @@ module Bio
         klass
       end #def self.new_direct
 
+      # symbols
       def self.symbols
         #p self
         @symbols
       end
 
+      # Returns true if this record has a field type which allows 
+      # continuations.
       def self.continue?
         @cont
       end
@@ -265,8 +317,11 @@ module Bio
         end
       end
 
-      #Return original string for this record (usually just @str, but
-      #sometimes add on the continuation data from other lines
+      # Return original string (except that "\n" are truncated) 
+      # for this record (usually just @str, but
+      # sometimes add on the continuation data from other lines.
+      # Returns an array of string.
+      #
       def original_data
         if defined?(@cont_data) then
           [ @str, *@cont_data ]
@@ -275,7 +330,11 @@ module Bio
         end
       end
 
-      # initialize from the string
+      # initialize this record from the given string.
+      # <em>str</em> must be a line (in PDB format).
+      #
+      # You can add continuation lines later using
+      # <code>add_continuation</code> method.
       def initialize_from_string(str)
         @str = str
         @record_name = fetch_record_name(str)
@@ -283,8 +342,17 @@ module Bio
         self
       end
 
-      #Called when we need to access the data, takes the string
-      #and the array of FieldDefs and parses it out
+      #--
+      # Called when we need to access the data, takes the string
+      # and the array of FieldDefs and parses it out.
+      #++
+
+      # In order to speeding up processing of PDB file format,
+      # fields have not been parsed before calling this method.
+      #
+      # Normally, it is automatically called and you don't explicitly
+      # need to call it .
+      #
       def do_parse
         return self if @parsed
         str = @str
@@ -330,17 +398,19 @@ module Bio
         self
       end
 
+      # fetches record name
       def fetch_record_name(str)
         str[0..5].strip
       end
       private :fetch_record_name
 
+      # fetches record name
       def self.fetch_record_name(str)
         str[0..5].strip
       end
       private_class_method :fetch_record_name
 
-      # If given str can be the continuation of the current record, then
+      # If given <em>str</em> can be the continuation of the current record,
       # then return the order number of the continuation associated with
       # the Pdb_Continuation field definition.
       # Otherwise, returns -1.
@@ -349,16 +419,20 @@ module Bio
       end
       private :fetch_cont
 
+      # Record name of this record, e.g. "HEADER", "ATOM".
       def record_name
-        @record_name or self.class.to_s.split(/\:\:/)[-1]
+        @record_name or self.class.to_s.split(/\:\:/)[-1].to_s.upcase
       end
       # keeping compatibility with old version
       alias record_type record_name
 
+      # Internal use only.
+      #
       # Adds continuation data to the record from str if str is
       # really the continuation of current record.
       # Returns self (= not nil) if str is the continuation.
       # Otherwaise, returns false.
+      #
       def add_continuation(str)
         #Check that this record can continue
         #and that str has the same type and definition
@@ -387,11 +461,19 @@ module Bio
         hash
       end
 
+      # same as Struct#inspect.
+      #
+      # Note that <code>do_parse</code> is automatically called
+      # before <code>inspect</code>.
+      #
+      # (Warning: The do_parse might sweep hidden bugs in PDB classes.)
       def inspect
-        #do_parse
+        do_parse
         super
       end
 
+      #--
+      #
       # definitions
       # contains all the rules for parsing each field
       # based on format V 2.2, 16-DEC-1996
@@ -405,13 +487,17 @@ module Bio
 
       # XXXXXX =
       #   new([ start, end, type of data, symbol to access ], ...)
+      #
+      #++
 
+      # HEADER record class
       HEADER = 
         def_rec([ 11, 50, Pdb_String, :classification ], #Pdb_String(40)
                 [ 51, 59, Pdb_Date,   :depDate ],
                 [ 63, 66, Pdb_IDcode, :idCode ]
                 )
 
+      # OBSLTE record class
       OBSLTE =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 12, 20, Pdb_Date,   :repDate ],
@@ -426,42 +512,50 @@ module Bio
                 [ 67, 70, Pdb_IDcode, :rIdCode ]
                 )
 
+      # TITLE record class
       TITLE =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 11, 70, Pdb_String, :title ]
                 )
         
+      # CAVEAT record class
       CAVEAT =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 12, 15, Pdb_IDcode, :idcode ],
                 [ 20, 70, Pdb_String, :comment ]
                 )
 
+      # COMPND record class
       COMPND =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 11, 70, Pdb_Specification_list, :compound ]
                 )
 
+      # SOURCE record class
       SOURCE =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 11, 70, Pdb_Specification_list, :srcName ]
                 )
 
+      # KEYWDS record class
       KEYWDS =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 11, 70, Pdb_List, :keywds ]
                 )
 
+      # EXPDTA record class
       EXPDTA =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 11, 70, Pdb_SList, :technique ]
                 )
 
+      # AUTHOR record class
       AUTHOR =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 11, 70, Pdb_List, :authorList ]
                 )
 
+      # REVDAT record class
       REVDAT =
         def_rec([  8, 10, Pdb_Integer,      :modNum  ],
                 [ 11, 12, Pdb_Continuation, nil      ],
@@ -474,6 +568,7 @@ module Bio
                 [ 61, 66, Pdb_LString(6),   :record  ]
                 )
 
+      # SPRSDE record class
       SPRSDE =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 12, 20, Pdb_Date,   :sprsdeDate ],
@@ -494,6 +589,7 @@ module Bio
       # 'REMARK' is defined below
       REMARK = nil
 
+      # DBREF record class
       DBREF =
         def_rec([  8, 11, Pdb_IDcode,    :idCode      ],
                 [ 13, 13, Pdb_Character, :chainID     ],
@@ -510,6 +606,7 @@ module Bio
                 [ 68, 68, Pdb_AChar,     :dbinsEnd    ]
                 )
         
+      # SEQADV record class
       SEQADV =
         def_rec([  8, 11, Pdb_IDcode,       :idCode   ],
                 [ 13, 15, Pdb_Residue_name, :resName  ],
@@ -523,6 +620,7 @@ module Bio
                 [ 50, 70, Pdb_LString,      :conflict ]
                 )
 
+      # SEQRES record class
       SEQRES =
         def_rec(#[  9, 10, Pdb_Integer,      :serNum ],
                 [  9, 10, Pdb_Continuation, nil      ],
@@ -543,6 +641,7 @@ module Bio
                 [ 68, 70, Pdb_Residue_name, :resName ]
                 )
       
+      # MODRS record class
       MODRES =
         def_rec([  8, 11, Pdb_IDcode,       :idCode ],
                 [ 13, 15, Pdb_Residue_name, :resName ],
@@ -553,6 +652,7 @@ module Bio
                 [ 30, 70, Pdb_String,       :comment ]
                 )
       
+      # HET record class
       HET =
         def_rec([  8, 10, Pdb_LString(3), :hetID ],
                 [ 13, 13, Pdb_Character,  :ChainID ],
@@ -562,18 +662,21 @@ module Bio
                 [ 31, 70, Pdb_String,     :text ]
                 )
       
+      # HETNAM record class
       HETNAM =
         def_rec([ 9, 10,  Pdb_Continuation, nil ],
                 [ 12, 14, Pdb_LString(3),   :hetID ],
                 [ 16, 70, Pdb_String,       :text ]
                 )
         
+      # HETSYN record class
       HETSYN =
         def_rec([  9, 10, Pdb_Continuation, nil ],
                 [ 12, 14, Pdb_LString(3),   :hetID ],
                 [ 16, 70, Pdb_SList,        :hetSynonyms ]
                 )
       
+      # FORMUL record class
       FORMUL =
         def_rec([  9, 10, Pdb_Integer,    :compNum ],
                 [ 13, 15, Pdb_LString(3), :hetID ],
@@ -582,6 +685,7 @@ module Bio
                 [ 20, 70, Pdb_String,     :text ]
                 )
       
+      # HELIX record class
       HELIX =
         def_rec([  8, 10, Pdb_Integer,      :serNum ],
                 #[ 12, 14, Pdb_LString(3),   :helixID ],
@@ -599,6 +703,7 @@ module Bio
                 [ 72, 76, Pdb_Integer,      :length ]
                 )
 
+      # SHEET record class
       SHEET =
         def_rec([  8, 10, Pdb_Integer,      :strand ],
                 #[ 12, 14, Pdb_LString(3),   :sheetID ],
@@ -625,6 +730,7 @@ module Bio
                 [ 70, 70, Pdb_AChar,        :prevICode ]
                 )
       
+      # TURN record class
       TURN =
         def_rec([  8, 10, Pdb_Integer,      :seq ],
                 #[ 12, 14, Pdb_LString(3),   :turnId ],
@@ -640,6 +746,7 @@ module Bio
                 [ 41, 70, Pdb_String,       :comment ]
                 )
         
+      # SSBOND record class
       SSBOND =
         def_rec([  8, 10, Pdb_Integer,    :serNum   ],
                 [ 12, 14, Pdb_LString(3), :pep1     ], # "CYS"
@@ -654,6 +761,7 @@ module Bio
                 [ 67, 72, Pdb_SymOP,      :sym2     ]
                 )
 
+      # LINK record class
       LINK =
         def_rec([ 13, 16, Pdb_Atom,         :name1 ],
                 [ 17, 17, Pdb_Character,    :altLoc1 ],
@@ -671,6 +779,7 @@ module Bio
                 [ 67, 72, Pdb_SymOP,        :sym2 ]
                 )
         
+      # HYDBND record class
       HYDBND =
         def_rec([ 13, 16, Pdb_Atom,         :name1 ],
                 [ 17, 17, Pdb_Character,    :altLoc1 ],
@@ -693,6 +802,7 @@ module Bio
                 [ 67, 72, Pdb_SymOP,        :sym2 ]
                 )
         
+      # SLTBRG record class
       SLTBRG =
         def_rec([ 13, 16, Pdb_Atom,          :atom1 ],
                 [ 17, 17, Pdb_Character,     :altLoc1 ],
@@ -710,6 +820,7 @@ module Bio
                 [ 67, 72, Pdb_SymOP,         :sym2 ]
                 )
       
+      # CISPEP record class
       CISPEP =
         def_rec([  8, 10, Pdb_Integer,     :serNum ],
                 [ 12, 14, Pdb_LString(3),  :pep1 ],
@@ -724,6 +835,7 @@ module Bio
                 [ 54, 59, Pdb_Real('6.2'), :measure ]
                 )
       
+      # SITE record class
       SITE =
         def_rec([  8, 10, Pdb_Integer,      :seqNum    ],
                 [ 12, 14, Pdb_LString(3),   :siteID    ],
@@ -746,6 +858,7 @@ module Bio
                 [ 61, 61, Pdb_AChar,        :iCode4    ]
                 )
       
+      # CRYST1 record class
       CRYST1 =
         def_rec([  7, 15, Pdb_Real('9.3'), :a ],
                 [ 16, 24, Pdb_Real('9.3'), :b ],
@@ -757,6 +870,8 @@ module Bio
                 [ 67, 70, Pdb_Integer,     :z ]
                 )
       
+      # ORIGX1 record class
+      #
       # ORIGXn n=1, 2, or 3
       ORIGX1 =
         def_rec([ 11, 20, Pdb_Real('10.6'), :On1 ],
@@ -765,9 +880,13 @@ module Bio
                 [ 46, 55, Pdb_Real('10.5'), :Tn ]
                 )
       
+      # ORIGX2 record class
       ORIGX2 = new_inherit(ORIGX1)
+      # ORIGX3 record class
       ORIGX3 = new_inherit(ORIGX1)
 
+      # SCALE1 record class
+      #
       # SCALEn n=1, 2, or 3
       SCALE1 =
         def_rec([ 11, 20, Pdb_Real('10.6'), :Sn1 ],
@@ -776,9 +895,13 @@ module Bio
                 [ 46, 55, Pdb_Real('10.5'), :Un ]
                 )
       
+      # SCALE2 record class
       SCALE2 = new_inherit(SCALE1)
+      # SCALE3 record class
       SCALE3 = new_inherit(SCALE1)
       
+      # MTRIX1 record class
+      #
       # MTRIXn n=1,2, or 3
       MTRIX1 =
         def_rec([  8, 10, Pdb_Integer,      :serial ],
@@ -789,9 +912,12 @@ module Bio
                 [ 60, 60, Pdb_Integer,      :iGiven ]
                 )
       
+      # MTRIX2 record class
       MTRIX2 = new_inherit(MTRIX1)
+      # MTRIX3 record class
       MTRIX3 = new_inherit(MTRIX1)
 
+      # TVECT record class
       TVECT =
         def_rec([  8, 10, Pdb_Integer,      :serial ],
                 [ 11, 20, Pdb_Real('10.5'), :t1 ],
@@ -800,11 +926,13 @@ module Bio
                 [ 41, 70, Pdb_String,       :text ]
                 )
 
+      # MODEL record class
       MODEL =
         def_rec([ 11, 14, Pdb_Integer, :serial ]
                 )
         # ChangeLog: model_serial are changed to serial
       
+      # ATOM record class
       ATOM =
         new_direct([  7, 11, Pdb_Integer,      :serial ],
                    [ 13, 16, Pdb_Atom,         :name ],
@@ -823,6 +951,7 @@ module Bio
                    [ 79, 80, Pdb_LString(2),   :charge ]
                    )
 
+      # ATOM record class
       class ATOM
 
         include Utils
@@ -830,11 +959,21 @@ module Bio
 
         # for backward compatibility
         alias occ  occupancy
+        # for backward compatibility
         alias bfac tempFactor
 
         # residue the atom belongs to.
         attr_accessor :residue
 
+        # SIGATM record
+        attr_accessor :sigatm
+
+        # ANISOU record
+        attr_accessor :anisou
+
+        # TER record
+        attr_accessor :ter
+
         #Returns a Coordinate class instance of the xyz positions
         def xyz
           Coordinate[ x, y, z ]
@@ -870,8 +1009,27 @@ module Bio
           @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
       SIGATM =
         def_rec([  7, 11, Pdb_Integer,      :serial ],
                 [ 13, 16, Pdb_Atom,         :name ],
@@ -890,6 +1048,7 @@ module Bio
                 [ 79, 80, Pdb_LString(2),   :charge ]
                 )
 
+      # ANISOU record class
       ANISOU =
         def_rec([  7, 11, Pdb_Integer,      :serial ],
                 [ 13, 16, Pdb_Atom,         :name ],
@@ -909,6 +1068,13 @@ module Bio
                 [ 79, 80, Pdb_LString(2),   :charge ]
                 )
 
+      # ANISOU record class
+      class ANISOU
+        # SIGUIJ record
+        attr_accessor :siguij
+      end #class ANISOU
+
+      # SIGUIJ record class
       SIGUIJ =
         def_rec([  7, 11, Pdb_Integer,      :serial ],
                 [ 13, 16, Pdb_Atom,         :name ],
@@ -928,6 +1094,7 @@ module Bio
                 [ 79, 80, Pdb_LString(2),   :charge ]
                 )
 
+      # TER record class
       TER =
         def_rec([  7, 11, Pdb_Integer,      :serial ],
                 [ 18, 20, Pdb_Residue_name, :resName ],
@@ -954,12 +1121,19 @@ module Bio
       #             [ 79, 80, Pdb_LString(2),   :charge ]
       #             )
 
+      # HETATM record class
       HETATM = new_inherit(ATOM)
 
+      # HETATM record class.
+      # It inherits ATOM class.
+      class HETATM; end
+
+      # ENDMDL record class
       ENDMDL =
         def_rec([  2,  1, Pdb_Integer, :serial ] # dummy field (always 0)
                 )
 
+      # CONECT record class
       CONECT =
         def_rec([  7, 11, Pdb_Integer, :serial ],
                 [ 12, 16, Pdb_Integer, :serial ],
@@ -974,6 +1148,7 @@ module Bio
                 [ 57, 61, Pdb_Integer, :serial ]
                 )
 
+      # MASTER record class
       MASTER =
         def_rec([ 11, 15, Pdb_Integer, :numRemark ],
                 [ 16, 20, Pdb_Integer, "0" ],
@@ -989,27 +1164,32 @@ module Bio
                 [ 66, 70, Pdb_Integer, :numSeq ]
                 )
 
+      # JRNL record classes
       class Jrnl < self
         # subrecord of JRNL
         # 13, 16
+        # JRNL AUTH record class
         AUTH =
           def_rec([ 13, 16, Pdb_String,       :sub_record ], # "AUTH"
                   [ 17, 18, Pdb_Continuation, nil ],
                   [ 20, 70, Pdb_List,         :authorList ]
                   )
 
+        # JRNL TITL record class
         TITL =
           def_rec([ 13, 16, Pdb_String,       :sub_record ], # "TITL"
                   [ 17, 18, Pdb_Continuation, nil ],
                   [ 20, 70, Pdb_LString,      :title ]
                   )
 
+        # JRNL EDIT record class
         EDIT =
           def_rec([ 13, 16, Pdb_String,       :sub_record ], # "EDIT"
                   [ 17, 18, Pdb_Continuation, nil ],
                   [ 20, 70, Pdb_List,         :editorList ]
                   )
 
+        # JRNL REF record class
         REF =
           def_rec([ 13, 16, Pdb_String,       :sub_record ], # "REF"
                   [ 17, 18, Pdb_Continuation, nil ],
@@ -1020,12 +1200,14 @@ module Bio
                   [ 63, 66, Pdb_Integer,      :year ]
                   )
 
+        # JRNL PUBL record class
         PUBL =
           def_rec([ 13, 16, Pdb_String,       :sub_record ], # "PUBL"
                   [ 17, 18, Pdb_Continuation, nil ],
                   [ 20, 70, Pdb_LString,      :pub ]
                   )
 
+        # JRNL REFN record class
         REFN =
           def_rec([ 13, 16, Pdb_String,     :sub_record ], # "REFN"
                   [ 20, 23, Pdb_LString(4), "ASTM" ], 
@@ -1037,21 +1219,25 @@ module Bio
                   )
 
         # default or unknown record
-        # ''
+        #
         Default =
           def_rec([ 13, 16, Pdb_String, :sub_record ]) # ""
         
+        # definitions (hash)
         Definition = create_definition_hash
       end #class JRNL
 
+      # REMARK record classes for REMARK 1
       class Remark1 < self
         # 13, 16
+        # REMARK 1 REFERENCE record class
         EFER =
           def_rec([  8, 10, Pdb_Integer,    :remarkNum ],  # "1"
                   [ 12, 20, Pdb_String,     :sub_record ], # "REFERENCE"
                   [ 22, 70, Pdb_Integer,    :refNum ]
                   )
         
+        # REMARK 1 AUTH record class
         AUTH =
           def_rec([  8, 10, Pdb_Integer,      :remarkNum ],  # "1"
                   [ 13, 16, Pdb_String,       :sub_record ], # "AUTH"
@@ -1059,6 +1245,7 @@ module Bio
                   [ 20, 70, Pdb_List,         :authorList ]
                   )
         
+        # REMARK 1 TITL record class
         TITL =
           def_rec([  8, 10, Pdb_Integer,      :remarkNum ],  # "1"
                   [ 13, 16, Pdb_String,       :sub_record ], # "TITL"
@@ -1066,6 +1253,7 @@ module Bio
                   [ 20, 70, Pdb_LString,      :title ]
                   )
         
+        # REMARK 1 EDIT record class
         EDIT =
           def_rec([  8, 10, Pdb_Integer,      :remarkNum ],  # "1"
                   [ 13, 16, Pdb_String,       :sub_record ], # "EDIT"
@@ -1073,6 +1261,7 @@ module Bio
                   [ 20, 70, Pdb_LString,      :editorList ]
                   )
         
+        # REMARK 1 REF record class
         REF =
           def_rec([  8, 10, Pdb_Integer,      :remarkNum ],  # "1"
                   [ 13, 16, Pdb_LString(3),   :sub_record ], # "REF"
@@ -1084,6 +1273,7 @@ module Bio
                   [ 63, 66, Pdb_Integer,      :year ]
                   )
         
+        # REMARK 1 PUBL record class
         PUBL =
           def_rec([  8, 10, Pdb_Integer,      :remarkNum ],  # "1"
                   [ 13, 16, Pdb_String,       :sub_record ], # "PUBL"
@@ -1091,6 +1281,7 @@ module Bio
                   [ 20, 70, Pdb_LString,      :pub ]
                   )
         
+        # REMARK 1 REFN record class
         REFN =
           def_rec([  8, 10, Pdb_Integer,    :remarkNum ],  # "1"
                   [ 13, 16, Pdb_String,     :sub_record ], # "REFN"
@@ -1102,14 +1293,17 @@ module Bio
                   [ 68, 70, Pdb_LString(4), :coden ]
                   )
         
+        # default (or unknown) record class for REMARK 1
         Default =
           def_rec([  8, 10, Pdb_Integer,    :remarkNum ],  # "1"
                   [ 13, 16, Pdb_String,     :sub_record ]  # ""
                   )
 
+        # definitions (hash)
         Definition = create_definition_hash
       end #class Remark1
 
+      # REMARK record classes for REMARK 2
       class Remark2 < self
         # 29, 38 == 'ANGSTROMS.'
         ANGSTROMS = 
@@ -1135,16 +1329,21 @@ module Bio
                   )
       end #class Remark2
       
+      # REMARK record class for REMARK n (n>=3)
       RemarkN =
         def_rec([  8, 10, Pdb_Integer, :remarkNum ],
                 [ 12, 70, Pdb_LString, :text ]
                 )
 
+      # default (or unknown) record class
       Default = def_rec([ 8, 70, Pdb_LString, :text ])
 
+      # definitions (hash)
       Definition = create_definition_hash
 
-      # because END is a reserved word of Ruby, it is separately
+      # END record class.
+      #
+      # Because END is a reserved word of Ruby, it is separately
       # added to the hash
       End = 
         def_rec([  2,  1, Pdb_Integer, :serial ]) # dummy field (always 0)
@@ -1195,6 +1394,7 @@ module Bio
       'TER'    => true,
     }
 
+    # Creates a new Bio::PDB object from given <em>str</em>.
     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
@@ -1211,9 +1411,11 @@ module Bio
       cont = false
 
       #Empty current model
-      cModel   = Bio::PDB::Model.new
-      cChain   = Bio::PDB::Chain.new
-      cResidue = Bio::PDB::Residue.new
+      cModel    = Model.new
+      cChain    = nil #Chain.new
+      cResidue  = nil #Residue.new
+      cLigand   = nil #Heterogen.new
+      c_atom    = nil
 
       #Goes through each line and replace that line with a PDB::Record
       @data.collect! do |line|
@@ -1236,87 +1438,107 @@ module Bio
         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
+        if key == 'ATOM' or key == 'HETATM' then
+          if cChain and 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)
-            
           else
-
-            #Make residue we add 'LIGAND' to the id if it's a HETATM
-            #I think this is neccessary because some PDB files reuse
-            #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
+            if chain = cModel[f.chainID]
+              cChain = chain unless cChain
+            else
+              # If we don't have chain, add a new chain
               newChain = Chain.new(f.chainID, cModel)
               cModel.addChain(newChain)
               cChain = newChain
               chain = newChain
             end
+          end
+        end
+
+        case key
+        when 'ATOM'
+          c_atom = f
+          residueID = Residue.get_residue_id_from_atom(f)
 
-            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)
+          if cResidue and residueID == cResidue.id
+            residue = cResidue
+          else
+            if residue = chain.get_residue_by_id(residueID)
+              cResidue = residue unless cResidue
+            else
+              # add a new residue
+              newResidue = Residue.new(f.resName, f.resSeq, f.iCode, chain)
+              chain.addResidue(newResidue)
               cResidue = newResidue
               residue = newResidue
             end
+          end
+          
+          f.residue = residue
+          residue.addAtom(f)
+
+        when 'HETATM'
+          c_atom = f
+          residueID = Heterogen.get_residue_id_from_atom(f)
 
-            f.residue = residue
-            residue.addAtom(f)
-            
+          if cLigand and residueID == cLigand.id
+            ligand = cLigand
+          else
+            if ligand = chain.get_heterogen_by_id(residueID)
+              cLigand = ligand unless cLigand
+            else
+              # add a new heterogen
+              newLigand = Heterogen.new(f.resName, f.resSeq, f.iCode, chain)
+              chain.addLigand(newLigand)
+              cLigand = newLigand
+              ligand = newLigand
+              #Each model has a special solvent chain. (for compatibility)
+              if f.resName == 'HOH'
+                cModel.addSolvent(newLigand)
+              end
+            end
           end
 
+          f.residue = ligand
+          ligand.addAtom(f)
+
         when 'MODEL'
-          if cModel.model_serial
+          c_atom = nil
+          if cModel.model_serial or cModel.chains.size > 0 then
             self.addModel(cModel)
           end
-          model_serial = line[6,5]
-          cModel = Model.new(model_serial)
+          cModel = Model.new(f.serial)
+
+        when 'TER'
+          if c_atom
+            c_atom.ter = f
+          else
+            #$stderr.puts "Warning: stray TER?"
+          end
+        when 'SIGATM'
+          if c_atom
+            #$stderr.puts "Warning: duplicated SIGATM?" if c_atom.sigatm
+            c_atom.sigatm = f
+          else
+            #$stderr.puts "Warning: stray SIGATM?"
+          end
+        when 'ANISOU'
+          if c_atom
+            #$stderr.puts "Warning: duplicated ANISOU?" if c_atom.anisou
+            c_atom.anisou = f
+          else
+            #$stderr.puts "Warning: stray ANISOU?"
+          end
+        when 'SIGUIJ'
+          if c_atom and c_atom.anisou
+            #$stderr.puts "Warning: duplicated SIGUIJ?" if c_atom.anisou.siguij
+            c_atom.anisou.siguij = f
+          else
+            #$stderr.puts "Warning: stray SIGUIJ?"
+          end
+
+        else
+          c_atom = nil
+
         end
         f
       end #each
@@ -1325,34 +1547,54 @@ module Bio
       @data.compact!
     end #def initialize
 
-    attr_reader :data, :hash
+    # all records in this entry as an array.
+    attr_reader :data
+
+    # all records in this entry as an hash accessed by record names.
+    attr_reader :hash
 
-    #Adds a Bio::Model to the current strucutre
+    # models in this entry (array).
+    attr_reader :models
+
+    # Adds a <code>Bio::Model</code> object to the current strucutre.
+    # Adds a model to the current structure.
+    # Returns self.
     def addModel(model)
       raise "Expecting a Bio::PDB::Model" if not model.is_a? Bio::PDB::Model
       @models.push(model)
       self
     end
     
-    #Iterates over the models
+    # Iterates over each model.
+    # Iterates over each of the models in the structure.
+    # Returns <code>self</code>.
     def each
       @models.each{ |model| yield model }
+      self
     end
-    #Alias needed for Bio::PDB::ModelFinder
+    # Alias needed for Bio::PDB::ModelFinder
     alias each_model each
     
-    #Provides keyed access to the models based on serial number
-    #returns nil if it's not there (should it raise an exception?)
+    # Provides keyed access to the models based on serial number
+    # returns nil if it's not there 
     def [](key)
       @models.find{ |model| key == model.model_serial }
     end
-    
+    #--
+    # (should it raise an exception?)
+    #++
+
+    #--
     #Stringifies to a list of atom records - we could add the annotation
     #as well if needed
+    #++
+
+    # Returns a string of Bio::PDB::Models. This propogates down the heirarchy
+    # till you get to Bio::PDB::Record::ATOM which are outputed in PDB format
     def to_s
       string = ""
       @models.each{ |model| string << model.to_s }
-      string << "END"
+      string << "END\n"
       return string
     end
     
@@ -1389,12 +1631,30 @@ module Bio
     end
     private :make_grouping
 
-    def record(name)
-      @hash[name]
+    # Gets all records whose record type is _name_.
+    # Returns an array of <code>Bio::PDB::Record::*</code> objects.
+    #
+    # if _name_ is nil, returns hash storing all record data.
+    #
+    # Example:
+    # p pdb.record('HETATM')
+    # p pdb.record['HETATM']
+    #
+    def record(name = nil)
+      name ? @hash[name] : @hash
     end
 
+    #--
     # PDB original methods
     #Returns a hash of the REMARK records based on the remarkNum
+    #++
+
+    # Gets REMARK records.
+    # If no arguments, it returns all REMARK records as a hash.
+    # If remark number is specified, returns only corresponding REMARK records.
+    # If number == 1 or 2 ("REMARK   1" or "REMARK   2"), returns an array
+    # of Bio::PDB::Record instances. Otherwise, returns an array of strings.
+    #
     def remark(nn = nil)
       unless defined?(@remark)
         h = make_hash(self.record('REMARK'), :remarkNum)
@@ -1409,7 +1669,11 @@ module Bio
       nn ? @remark[nn] : @remark
     end
 
-    #Returns a hash of journal entries
+    # Gets JRNL records.
+    # If no arguments, it returns all JRNL records as a hash.
+    # If sub record name is specified, it returns only corresponding records
+    # as an array of Bio::PDB::Record instances.
+    #
     def jrnl(sub_record = nil)
       unless defined?(@jrnl)
         @jrnl = make_hash(self.record('JRNL'), :sub_record)
@@ -1417,8 +1681,18 @@ module Bio
       sub_record ? @jrnl[sub_record] : @jrnl
     end
 
+    #--
     #Finding methods - just grabs the record with the appropriate id
     #or returns and array of all of them
+    #++
+
+    # Gets HELIX records.
+    # If no arguments are given, it returns all HELIX records.
+    # (Returns an array of <code>Bio::PDB::Record::HELIX</code> instances.)
+    # If <em>helixID</em> is given, it only returns records
+    # corresponding to given <em>helixID</em>.
+    # (Returns an <code>Bio::PDB::Record::HELIX</code> instance.)
+    #
     def helix(helixID = nil)
       if helixID then
         self.record('HELIX').find { |f| f.helixID == helixID }
@@ -1427,6 +1701,13 @@ module Bio
       end
     end
 
+    # Gets TURN records.
+    # If no arguments are given, it returns all TURN records. 
+    # (Returns an array of <code>Bio::PDB::Record::TURN</code> instances.)
+    # If <em>turnId</em> is given, it only returns a record
+    # corresponding to given <em>turnId</em>.
+    # (Returns an <code>Bio::PDB::Record::TURN</code> instance.)
+    #
     def turn(turnId = nil)
       if turnId then
         self.record('TURN').find { |f| f.turnId == turnId }
@@ -1435,6 +1716,11 @@ module Bio
       end
     end
 
+    # Gets SHEET records.
+    # If no arguments are given, it returns all SHEET records
+    # as an array of arrays of <code>Bio::PDB::Record::SHEET</code> instances.
+    # If <em>sheetID</em> is given, it returns an array of
+    # <code>Bio::PDB::Record::SHEET</code> instances.
     def sheet(sheetID = nil)
       unless defined?(@sheet)
         @sheet = make_grouping(self.record('SHEET'), :sheetID)
@@ -1446,11 +1732,20 @@ module Bio
       end
     end
 
+    # Gets SSBOND records.
     def ssbond
       self.record('SSBOND')
     end
 
-    #Get seqres - we get this to return a nice Bio::Seq object
+    #--
+    # Get seqres - we get this to return a nice Bio::Seq object
+    #++
+    
+    # Amino acid or nucleic acid sequence of backbone residues in "SEQRES".
+    # If <em>chainID</em> is given, it returns corresponding sequence
+    # as an array of string.
+    # Otherwise, returns a hash which contains all sequences.
+    #
     def seqres(chainID = nil)
       unless defined?(@seqres)
         h = make_hash(self.record('SEQRES'), :chainID)
@@ -1458,14 +1753,27 @@ module Bio
         h.each do |k, a|
           a.collect! { |f| f.resName }
           a.flatten!
-          a.collect!{ |aa|
-            #aa is three letter code: i.e. ALA
-            #need to look up with Ala
-            aa = aa.capitalize
-            aa = AminoAcid.names.invert[aa]
-            aa = 'X' if aa.nil? 
-          }
-          newHash[k] = Bio::Sequence::AA.new(a.to_s)
+          # determine nuc or aa?
+          tmp = Hash.new(0)
+          a[0,13].each { |x| tmp[x.to_s.strip.size] += 1 }
+          if tmp[3] >= tmp[1] then
+            # 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')
+            end
+            seq = Bio::Sequence::AA.new(a.to_s)
+          else
+            # nucleic acid sequence
+            a.collect! do |na|
+              na = na.strip
+              na.size == 1 ? na : 'n'
+            end
+            seq = Bio::Sequence::NA.new(a.to_s)
+          end
+          newHash[k] = seq
         end
         @seqres = newHash
       end
@@ -1476,6 +1784,10 @@ module Bio
       end
     end
 
+    # Gets DBREF records.
+    # Returns an array of Bio::PDB::Record::DBREF objects.
+    #
+    # If <em>chainID</em> is given, it returns corresponding DBREF records.
     def dbref(chainID = nil)
       if chainID then
         self.record('DBREF').find_all { |f| f.chainID == chainID }
@@ -1484,28 +1796,38 @@ module Bio
       end
     end
 
+    # Keywords in "KEYWDS".
+    # Returns an array of string.
     def keywords
       self.record('KEYWDS').collect { |f| f.keywds }.flatten
     end
 
+    # Classification in "HEADER".
     def classification
       self.record('HEADER').first.classification
     end
 
+    #--
     # Bio::DB methods
+    #++
+
+    # PDB identifier written in "HEADER". (e.g. 1A00)
     def entry_id
       @id = self.record('HEADER').first.idCode unless @id
       @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
     end
 
+    # Current modification number in "REVDAT".
     def version
       self.record('REVDAT').first.modNum
     end
@@ -1514,169 +1836,3 @@ module Bio
 
 end #module Bio
 
-=begin
-
-= Caution
-
- This is a test version, specs of these class shall be changed.
-
-= Bio::PDB < Bio::DB
-
- PDB File format class.
-
---- Bio::PDB.new(str)
-
- Creates new object.
-
---- Bio::PDB#entry_id
-
- PDB identifier written in "HEADER". (e.g. 1A00)
-
---- Bio::PDB#accession
-
- Same as Bio::PDB#entry_id
-
---- Bio::PDB#version
-
- Current modification number in "REVDAT".
-
---- Bio::PDB#definition
-
- Title of this entry in "TITLE".
-
---- Bio::PDB#keywords
-
- Keywords in "KEYWDS".
- Returns an array of string.
-
---- Bio::PDB#classification
-
- Classification in "HEADER".
-
---- Bio::PDB#record(name)
-
- Gets all records whose record type is 'name'.
- Returns an array of Bio::PDB::Record.
-
---- Bio::PDB#remark(number = nil)
-
- Gets REMARK records.
- If no arguments, it returns all REMARK records as a hash.
- If remark number is specified, returns only corresponding REMARK records.
- If number == 1 or 2 ("REMARK   1" or "REMARK   2"), returns an array
- of Bio::PDB::Record instances. Otherwise, returns an array of strings.
-
---- Bio::PDB#jrnl(sub_record = nil)
-
- Gets JRNL records.
- If no arguments, it returns all JRNL records as a hash.
- If sub record name is specified, it returns only corresponding records
- as an array of Bio::PDB::Record instances.
-
---- Bio::PDB#seqres(chainID = nil)
-
- Amino acid or nucleic acid sequence of backbone residues in "SEQRES".
- If chainID is given, it returns corresponding sequence as an array of string.
- Otherwise, returns a hash which contains all sequences.
-
---- Bio::PDB#helix(helixID = nil)
-
- Gets HELIX records.
- If no arguments are given, it returns all HELIX records.
- (Returns an array of Bio::PDB::Record instances.)
- If helixID is given, it only returns records corresponding to given helixID.
- (Returns an Bio::PDB::Record instance.)
-
---- Bio::PDB#sheet(sheetID = nil)
-
- Gets SHEET records.
- If no arguments are given, it returns all SHEET records as an array of
- arrays of Bio::PDB::Record instances.
- If sheetID is given, it returns an array of Bio::PDB::Record instances.
-
---- Bio::PDB#turn(turnId = nil)
-
- Gets TURN records.
- If no arguments are given, it returns all TURN records. 
- (Returns an array of Bio::PDB::Record instances.)
- If turnId is given, it only returns a record corresponding to given turnId.
- (Returns an Bio::PDB::Record instance.)
-
---- Bio::PDB.addModel(model)
-
- Adds a model to the current structure
- Returns self
-
---- Bio::PDB.each
-
- Iterates over each of the models in the structure
- Returns Bio::PDB::Models
-
---- Bio::PDB[](key)
-
- Returns the model with the given key as serial number
-
---- Bio::PDB.to_s
-
- Returns a string of Bio::PDB::Models. This propogates down the heirarchy
- till you get to Bio::PDB::Atoms which are outputed in PDB format
-
-
-= Bio::PDB::Record < Hash
-
- A class for single PDB record.
- Basically, each line of a PDB file corresponds to an instance of the class.
- If continuation exists, multiple lines may correspond to single instance.
-
---- Bio::PDB::Record.new(line)
-
- Internal use only.
- Creates a new instance.
-
---- Bio::PDB::Record#add_continuation(line)
-
- Internal use only.
- If continuation is allowed and 'line' is a continuation of this record,
- it adds 'line' and returns self.
- Otherwise, returns false.
-
---- Bio::PDB::Record#original_data
-
- Original text (except that "\n" are truncated) of this record.
- Returns an array of string.
-
---- Bio::PDB::Record#record_type
-
- Record type of this record, e.g. "HEADER", "ATOM".
-
---- Bio::PDB::Record#do_parse
-
- In order to speeding up processing of PDB File format,
- fields have not been parsed before calling this method.
-
- If you want to use this class as a hash (not so recommended),
- you must call this method once.
-
- When accessing via rec.xxxxx style (described below), 
- do_parse is automatically called.
-
- Returns self
-
---- Bio::PDB::Record#"anything"
-
- Same as Bio::PDB::Record#[](:anything) after do_parse.
- For example, r.helixID is same as r.do_parse; r[:helixID] .
-
-
-= Bio::PDB::FieldDef
-
- Internal use only.
- Format definition of each record.
-
-= References
-
-* ((<URL:http://www.rcsb.org/pdb/>))
-* PDB File Format Contents Guide Version 2.2 (20 December 1996)
-  ((<URL:http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html>))
-
-=end