[BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb, 1.1, 1.2 pdb.rb, 1.1, 1.2 utils.rb, 1.1, 1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv9021/lib/bio/db/pdb

Modified Files:
	atom.rb pdb.rb utils.rb 
Log Message:
* expanded tab at the line head


Index: atom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/atom.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** atom.rb	8 Mar 2004 07:30:40 -0000	1.1
--- atom.rb	8 Sep 2005 01:22:11 -0000	1.2
***************
*** 63,67 ****
  
        attr_accessor :serial, :element, :alt_loc, :x, :y, :z,
! 	:occ, :bfac, :residue
  
        def initialize(serial, element, alt_loc, x, y, z,
--- 63,67 ----
  
        attr_accessor :serial, :element, :alt_loc, :x, :y, :z,
!         :occ, :bfac, :residue
  
        def initialize(serial, element, alt_loc, x, y, z,
***************
*** 71,77 ****
          @element = element
          @alt_loc = alt_loc
! 	@x       = x
! 	@y       = y
! 	@z       = z
          @occ     = occ
          @bfac    = bfac
--- 71,77 ----
          @element = element
          @alt_loc = alt_loc
!         @x       = x
!         @y       = y
!         @z       = z
          @occ     = occ
          @bfac    = bfac
***************
*** 88,92 ****
        #Returns an array of the xyz positions
        def to_a
! 	[@x, at y, at z]
        end
        
--- 88,92 ----
        #Returns an array of the xyz positions
        def to_a
!         [@x, at y, at z]
        end
        

Index: utils.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/utils.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** utils.rb	8 Mar 2004 07:30:40 -0000	1.1
--- utils.rb	8 Sep 2005 01:22:11 -0000	1.2
***************
*** 36,43 ****
        
        self.each_atom{ |atom|
! 	x += atom.x
! 	y += atom.y
! 	z += atom.z
! 	count += 1
        }
        
--- 36,43 ----
        
        self.each_atom{ |atom|
!         x += atom.x
!         y += atom.y
!         z += atom.z
!         count += 1
        }
        
***************
*** 69,78 ****
        
        self.each_atom{ |atom|
! 	element = atom.element[0,1]
! 	mass    = ElementMass[element]
! 	total += mass
! 	x += atom.x * mass
! 	y += atom.y * mass
! 	z += atom.z * mass
        }
        
--- 69,78 ----
        
        self.each_atom{ |atom|
!         element = atom.element[0,1]
!         mass    = ElementMass[element]
!         total += mass
!         x += atom.x * mass
!         y += atom.y * mass
!         z += atom.z * mass
        }
        
***************
*** 196,200 ****
      def each_chain()
        self.each_model{ |model|
! 	model.each{ |chain| yield chain }
        }
      end
--- 196,200 ----
      def each_chain()
        self.each_model{ |model|
!         model.each{ |chain| yield chain }
        }
      end
***************
*** 211,215 ****
      def each_residue()
        self.each_chain{ |chain|
! 	chain.each{ |residue| yield residue }
        }
      end
--- 211,215 ----
      def each_residue()
        self.each_chain{ |chain|
!         chain.each{ |residue| yield residue }
        }
      end
***************
*** 226,230 ****
      def each_atom()
        self.each_residue{ |residue|
! 	residue.each{ |atom| yield atom }
        }
      end
--- 226,230 ----
      def each_atom()
        self.each_residue{ |residue|
!         residue.each{ |atom| yield atom }
        }
      end

Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** pdb.rb	8 Mar 2004 07:30:40 -0000	1.1
--- pdb.rb	8 Sep 2005 01:22:11 -0000	1.2
***************
*** 49,53 ****
      module Pdb_Integer
        def self.new(str)
! 	str.strip.to_i
        end
      end
--- 49,53 ----
      module Pdb_Integer
        def self.new(str)
!         str.strip.to_i
        end
[...2082 lines suppressed...]
!         @seqres
        end
      end
***************
*** 1356,1362 ****
      def dbref(chainID = nil)
        if chainID then
! 	self.record('DBREF').find_all { |f| f.chainID == chainID }
        else
! 	self.record('DBREF')
        end
      end
--- 1356,1362 ----
      def dbref(chainID = nil)
        if chainID then
!         self.record('DBREF').find_all { |f| f.chainID == chainID }
        else
!         self.record('DBREF')
        end
      end