[BioRuby-cvs] bioruby/lib/bio/shell demo.rb,1.1,1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell
In directory dev.open-bio.org:/tmp/cvs-serv28438/lib/bio/shell

Modified Files:
	demo.rb 
Log Message:
* 1st commit test on dev.open-bio.org after the server migration
* fixed some typos in BioRuby shell demo


Index: demo.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/demo.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** demo.rb	27 Feb 2006 09:33:22 -0000	1.1
--- demo.rb	26 Mar 2006 00:38:10 -0000	1.2
***************
*** 90,94 ****
        run(%q[head ent_1bl8], "Head part of the entry ...", false) &&
        run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) &&
!       run(%q[less "data/1bl8.pdb"], "Look through the entire entry ...", false) &&
        run(%q[pdb_1bl8 = flatparse(ent_1bl8)], "Parsing the entry ...", false) &&
        run(%q[pdb_1bl8.entry_id], "Showing the entry ID ...", true) &&
--- 90,94 ----
        run(%q[head ent_1bl8], "Head part of the entry ...", false) &&
        run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) &&
!       run(%q[disp "data/1bl8.pdb"], "Look through the entire entry ...", false) &&
        run(%q[pdb_1bl8 = flatparse(ent_1bl8)], "Parsing the entry ...", false) &&
        run(%q[pdb_1bl8.entry_id], "Showing the entry ID ...", true) &&
***************
*** 98,112 ****
  
      def pdb_hetdic
!       run(%q[het_dic = open("http://deposit.pdb.org/het_dictionary.txt").read],
!           "Retrieving the het_dic database ...", false) &&
!       run(%q[savefile("data/het_dictionary.txt", het_dic)],
!           "Saving the file ... ", false) &&
        run(%q[het_dic.size], "Bytes of the file ...", true) &&
!       run(%q[less "data/het_dictionary.txt"], "Take a look on the contents ...", true) &&
        run(%q[flatindex("het_dic", "data/het_dictionary.txt")],
            "Creating index to make the seaarchable database ...", false) &&
        run(%q[ethanol = flatsearch("het_dic", "EOH")], "Search an ethanol entry ...", true) &&
        run(%q[osake = flatparse(ethanol)], "Parse the entry ...", true) &&
!       run(%q[sake.conect], "Showing connect table (conect) of the molecule ...", true) &&
        true
      end
--- 98,112 ----
  
      def pdb_hetdic
! #      run(%q[het_dic = open("http://deposit.pdb.org/het_dictionary.txt").read],
! #          "Retrieving the het_dic database ...", false) &&
! #      run(%q[savefile("data/het_dictionary.txt", het_dic)],
! #          "Saving the file ... ", false) &&
        run(%q[het_dic.size], "Bytes of the file ...", true) &&
!       run(%q[disp "data/het_dictionary.txt"], "Take a look on the contents ...", true) &&
        run(%q[flatindex("het_dic", "data/het_dictionary.txt")],
            "Creating index to make the seaarchable database ...", false) &&
        run(%q[ethanol = flatsearch("het_dic", "EOH")], "Search an ethanol entry ...", true) &&
        run(%q[osake = flatparse(ethanol)], "Parse the entry ...", true) &&
!       run(%q[osake.conect], "Showing connect table (conect) of the molecule ...", true) &&
        true
      end