Class Bio::KEGG::GLYCAN
In: lib/bio/db/kegg/glycan.rb
Parent: KEGGDB

Methods

Included Modules

Common::DblinksAsHash Common::PathwaysAsHash Common::OrthologsAsHash

Constants

DELIMITER = RS = "\n///\n"
TAGSIZE = 12

Public Class methods

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 36
36:   def initialize(entry)
37:     super(entry, TAGSIZE)
38:   end

Public Instance methods

COMMENT

[Source]

     # File lib/bio/db/kegg/glycan.rb, line 118
118:   def comment
119:     field_fetch('COMMENT')
120:   end

COMPOSITION

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 51
51:   def composition
52:     unless @data['COMPOSITION']
53:       hash = Hash.new(0)
54:       fetch('COMPOSITION').scan(/\((\S+)\)(\d+)/).each do |key, val|
55:         hash[key] = val.to_i
56:       end
57:       @data['COMPOSITION'] = hash
58:     end
59:     @data['COMPOSITION']
60:   end

COMPOUND

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 76
76:   def compounds
77:     unless @data['COMPOUND']
78:       @data['COMPOUND'] = fetch('COMPOUND').split(/\s+/)
79:     end
80:     @data['COMPOUND']
81:   end
dblinks()

Alias for dblinks_as_hash

Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 23
23:   def dblinks_as_hash; super; end

DBLINKS

[Source]

     # File lib/bio/db/kegg/glycan.rb, line 145
145:   def dblinks_as_strings
146:     unless @data['DBLINKS']
147:       @data['DBLINKS'] = lines_fetch('DBLINKS')
148:     end
149:     @data['DBLINKS']
150:   end

ENTRY

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 41
41:   def entry_id
42:     field_fetch('ENTRY')[/\S+/]
43:   end

ENZYME

[Source]

     # File lib/bio/db/kegg/glycan.rb, line 97
 97:   def enzymes
 98:     unless @data['ENZYME']
 99:       field = fetch('ENZYME')
100:       if /\(/.match(field)      # old version
101:         @data['ENZYME'] = field.scan(/\S+ \(\S+\)/)
102:       else
103:         @data['ENZYME'] = field.scan(/\S+/)
104:       end
105:     end
106:     @data['ENZYME']
107:   end

ATOM, BOND

[Source]

     # File lib/bio/db/kegg/glycan.rb, line 153
153:   def kcf
154:     return "#{get('NODE')}#{get('EDGE')}"
155:   end

CLASS

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 71
71:   def keggclass
72:     field_fetch('CLASS') 
73:   end

MASS

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 63
63:   def mass
64:     unless @data['MASS']
65:       @data['MASS'] = field_fetch('MASS')[/[\d\.]+/].to_f
66:     end
67:     @data['MASS']
68:   end

NAME

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 46
46:   def name
47:     field_fetch('NAME') 
48:   end
orthologs()

Alias for orthologs_as_hash

Returns a Hash of the orthology ID and definition in ORTHOLOGY field.

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 33
33:   def orthologs_as_hash; super; end

ORTHOLOGY

[Source]

     # File lib/bio/db/kegg/glycan.rb, line 110
110:   def orthologs_as_strings
111:     unless @data['ORTHOLOGY']
112:       @data['ORTHOLOGY'] = lines_fetch('ORTHOLOGY')
113:     end
114:     @data['ORTHOLOGY']
115:   end
pathways()

Alias for pathways_as_hash

Returns a Hash of the pathway ID and name in PATHWAY field.

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 28
28:   def pathways_as_hash; super; end

PATHWAY

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 92
92:   def pathways_as_strings
93:     lines_fetch('PATHWAY') 
94:   end

REACTION

[Source]

    # File lib/bio/db/kegg/glycan.rb, line 84
84:   def reactions
85:     unless @data['REACTION']
86:       @data['REACTION'] = fetch('REACTION').split(/\s+/)
87:     end
88:     @data['REACTION']
89:   end

REFERENCE

[Source]

     # File lib/bio/db/kegg/glycan.rb, line 128
128:   def references
129:     unless @data['REFERENCE']
130:       ary = Array.new
131:       lines = lines_fetch('REFERENCE')
132:       lines.each do |line|
133:         if /^\d+\s+\[PMID/.match(line)
134:           ary << line
135:         else
136:           ary.last << " #{line.strip}"
137:         end
138:       end
139:       @data['REFERENCE'] = ary
140:     end
141:     @data['REFERENCE']
142:   end

REMARK

[Source]

     # File lib/bio/db/kegg/glycan.rb, line 123
123:   def remark
124:     field_fetch('REMARK')
125:   end

[Validate]