Class: Bio::KEGG::REACTION [BioRuby API documentation]

Creates a new Bio::KEGG::REACTION object.

Arguments:

(required) entry: (String) single entry as a string

Returns:

    # File lib/bio/db/kegg/reaction.rb, line 38
38:   def initialize(entry)
39:     super(entry, TAGSIZE)
40:   end

definition()

Definition of the reaction, described in the DEFINITION line.

Returns:

String

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 59
59:   def definition
60:     field_fetch('DEFINITION')
61:   end

entry_id()

ID of the entry, described in the ENTRY line.

Returns:

String

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 45
45:   def entry_id
46:     field_fetch('ENTRY')[/\S+/]
47:   end

enzymes()

Enzymes described in the ENZYME line.

Returns:

Array containing String

[Source]

     # File lib/bio/db/kegg/reaction.rb, line 117
117:   def enzymes
118:     unless @data['ENZYME']
119:       @data['ENZYME'] = fetch('ENZYME').scan(/\S+/)
120:     end
121:     @data['ENZYME']
122:   end

equation()

Chemical equation, described in the EQUATION line.

Returns:

String

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 66
66:   def equation
67:     field_fetch('EQUATION')
68:   end

name()

Name of the reaction, described in the NAME line.

Returns:

String

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 52
52:   def name
53:     field_fetch('NAME')
54:   end

orthologs()

Alias for orthologs_as_hash

orthologs_as_hash()

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

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 30
30:   def orthologs_as_hash; super; end

orthologs_as_strings()

Orthologs described in the ORTHOLOGY lines.

Returns:

Array containing String

[Source]

     # File lib/bio/db/kegg/reaction.rb, line 127
127:   def orthologs_as_strings
128:     lines_fetch('ORTHOLOGY')
129:   end

pathways()

Alias for pathways_as_hash

pathways_as_hash()

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

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 25
25:   def pathways_as_hash; super; end

pathways_as_strings()

Pathway information, described in the PATHWAY lines.

Returns:

Array containing String

[Source]

     # File lib/bio/db/kegg/reaction.rb, line 110
110:   def pathways_as_strings
111:     lines_fetch('PATHWAY')
112:   end

rpairs()

Alias for rpairs_as_hash

rpairs_as_hash()

KEGG RPAIR (ReactantPair) information, described in the RPAIR lines. Returns a hash of RPair IDs and [ name, type ] informations, for example,

  { "RP12733" => [ "C00022_C00900", "trans" ],
    "RP05698" => [ "C00011_C00022", "leave" ],
    "RP00440" => [ "C00022_C00900", "main" ]
  }

Returns:

Hash

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 85
85:   def rpairs_as_hash
86:     unless defined? @rpairs_as_hash
87:       rps = {}
88:       rpairs_as_strings.each do |line|
89:         namespace, entry_id, name, rptype = line.split(/\s+/)
90:         rps[entry_id] = [ name, rptype ]
91:       end
92:       @rpairs_as_hash = rps
93:     end
94:     @rpairs_as_hash
95:   end

rpairs_as_strings()

KEGG RPAIR (ReactantPair) information, described in the RPAIR lines.

Returns:

Array containing String

[Source]

    # File lib/bio/db/kegg/reaction.rb, line 73
73:   def rpairs_as_strings
74:     lines_fetch('RPAIR')
75:   end

rpairs_as_tokens()

Returns the content of the RPAIR entry as tokens (RPair signature, RPair ID, , RPair type).

Returns:

Array containing String

[Source]

     # File lib/bio/db/kegg/reaction.rb, line 103
103:   def rpairs_as_tokens
104:     fetch('RPAIR').split(/\s+/)
105:   end

Methods

Included Modules

Constants

Public Class methods

Public Instance methods

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