class Bio::KEGG::COMPOUND
Description¶ ↑
Bio::KEGG::COMPOUND is a parser class for the KEGG COMPOUND database entry. KEGG COMPOUND is a chemical structure database.
References¶ ↑
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
new(entry)
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Creates a new Bio::KEGG::COMPOUND object.
Arguments:
-
(required) entry: (String) single entry as a string
- Returns
-
Bio::KEGG::COMPOUND object
Calls superclass method
Bio::NCBIDB.new
# File lib/bio/db/kegg/compound.rb, line 45 def initialize(entry) super(entry, TAGSIZE) end
Public Instance Methods
comment()
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COMMENT
# File lib/bio/db/kegg/compound.rb, line 132 def comment field_fetch('COMMENT') end
dblinks_as_hash()
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Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.
Calls superclass method
Bio::KEGG::Common::DblinksAsHash#dblinks_as_hash
# File lib/bio/db/kegg/compound.rb, line 32 def dblinks_as_hash; super; end
Also aliased as: dblinks
dblinks_as_strings()
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DBLINKS
# File lib/bio/db/kegg/compound.rb, line 122 def dblinks_as_strings lines_fetch('DBLINKS') end
entry_id()
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ENTRY
# File lib/bio/db/kegg/compound.rb, line 50 def entry_id field_fetch('ENTRY')[/\S+/] end
enzymes()
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# File lib/bio/db/kegg/compound.rb, line 109 def enzymes unless @data['ENZYME'] field = fetch('ENZYME') if /\(/.match(field) # old version @data['ENZYME'] = field.scan(/\S+ \(\S+\)/) else @data['ENZYME'] = field.scan(/\S+/) end end @data['ENZYME'] end
formula()
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FORMULA
# File lib/bio/db/kegg/compound.rb, line 65 def formula field_fetch('FORMULA') end
glycans()
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# File lib/bio/db/kegg/compound.rb, line 80 def glycans unless @data['GLYCAN'] @data['GLYCAN'] = fetch('GLYCAN').split(/\s+/) end @data['GLYCAN'] end
kcf()
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ATOM, BOND
# File lib/bio/db/kegg/compound.rb, line 127 def kcf return "#{get('ATOM')}#{get('BOND')}" end
mass()
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MASS
# File lib/bio/db/kegg/compound.rb, line 70 def mass field_fetch('MASS').to_f end
name()
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The first name recorded in the NAME field.
# File lib/bio/db/kegg/compound.rb, line 60 def name names.first end
names()
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NAME
# File lib/bio/db/kegg/compound.rb, line 55 def names field_fetch('NAME').split(/\s*;\s*/) end
pathways_as_hash()
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Returns a Hash of the pathway ID and name in PATHWAY field.
Calls superclass method
Bio::KEGG::Common::PathwaysAsHash#pathways_as_hash
# File lib/bio/db/kegg/compound.rb, line 37 def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings()
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# File lib/bio/db/kegg/compound.rb, line 104 def pathways_as_strings lines_fetch('PATHWAY') end
reactions()
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# File lib/bio/db/kegg/compound.rb, line 88 def reactions unless @data['REACTION'] @data['REACTION'] = fetch('REACTION').split(/\s+/) end @data['REACTION'] end
remark()
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REMARK
# File lib/bio/db/kegg/compound.rb, line 75 def remark field_fetch('REMARK') end
rpairs()
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RPAIR
# File lib/bio/db/kegg/compound.rb, line 96 def rpairs unless @data['RPAIR'] @data['RPAIR'] = fetch('RPAIR').split(/\s+/) end @data['RPAIR'] end