Module: Bio::URLGenerators

Included in:
URL
Defined in:
lib/bio/db/url.rb

Overview

A module dedicated to providing URLs to common bioinformatic databases.

Instance Method Summary collapse

Instance Method Details

#cath_url(pdbId) ⇒ Object 



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# File 'lib/bio/db/url.rb', line 24

def cath_url(pdbId)
  "http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB"
end

#hhmi_pfam_family_url(pfam_family_id) ⇒ Object 



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# File 'lib/bio/db/url.rb', line 8

def hhmi_pfam_family_url(pfam_family_id)
  "http://pfam.janelia.org/family?entry=#{pfam_family_id}&type=Family"
end

#pantherdb_panther_family_url(panther_id) ⇒ Object 



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# File 'lib/bio/db/url.rb', line 4

def pantherdb_panther_family_url(panther_id)
  "http://www.pantherdb.org/panther/family.do?clsAccession=#{panther_id}"
end

#pdb_url(pdbId) ⇒ Object 



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# File 'lib/bio/db/url.rb', line 16

def pdb_url(pdbId)
  "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}"
end

#pdbsum_url(pdbId) ⇒ Object 



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# File 'lib/bio/db/url.rb', line 20

def pdbsum_url(pdbId)
  "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}"
end

#plasmodb_gene_url(plasmodb_id) ⇒ Object 



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# File 'lib/bio/db/url.rb', line 12

def plasmodb_gene_url(plasmodb_id)
  "http://plasmodb.org/gene/#{plasmodb_id}"
end

#scop_url(pdbId) ⇒ Object 



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# File 'lib/bio/db/url.rb', line 28

def scop_url(pdbId)
  "http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}"
end