[BioRuby] URL Generation in Bioruby

[Adam Kraut]

I typically put these in Rails/Merb helpers.  I extracted a few from one of
my apps.  I'm still not sure if these belong in bioruby due to the huge
number of resources and urls.  I also think they're somewhat
project-specific.  You're welcome to include or modify these:

    def pdb_url_for(pdbId)
      "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}<http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#%7BpdbId%7D>
"
    end

    def pdbsum_url_for(pdbId)
      "
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}<http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#%7BpdbId%7D>
"
    end

    def cath_url_for(pdbId)
      "
http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB<http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#%7BpdbId%7D&type=PDB>
"
    end

    def scop_url_for(pdbId)
      "http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}<http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#%7BpdbId%7D>
"
    end

-Adam