Class | Bio::KEGG::ENZYME
In: | lib/bio/db/kegg/enzyme.rb
Parent: | KEGGDB

### Methods

all_reac classes cofactors comment dblinks dblinks_as_hash dblinks_as_strings diseases entry entry_id genes genes_as_hash genes_as_strings inhibitors iubmb_reactions kegg_reactions motifs name names new obsolete? orthologs orthologs_as_hash orthologs_as_strings pathways pathways_as_hash pathways_as_strings products reaction structures substrates sysname

### Included Modules

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

### Constants

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

### Public Class methods

new(entry)

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 41
    41:   def initialize(entry)
    42:     super(entry, TAGSIZE)
    43:   end

### Public Instance methods

all_reac()

ALL_REAC ’;’

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 83
    83:   def all_reac
    84:     field_fetch('ALL_REAC')
    85:   end

classes()

CLASS

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 68
    68:   def classes
    69:     lines_fetch('CLASS')
    70:   end

cofactors()

COFACTOR

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 116
    116:   def cofactors
    117:     field_fetch('COFACTOR').split(/\s*;\s*/)
    118:   end

comment()

COMMENT

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 121
    121:   def comment
    122:     field_fetch('COMMENT')
    123:   end

dblinks()

Alias for dblinks_as_hash

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/enzyme.rb, line 23
    23:   def dblinks_as_hash; super; end

dblinks_as_strings()

DBLINKS

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 161
    161:   def dblinks_as_strings
    162:     lines_fetch('DBLINKS')
    163:   end

diseases()

DISEASE

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 141
    141:   def diseases
    142:     lines_fetch('DISEASE')
    143:   end

entry()

ENTRY

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 46
    46:   def entry
    47:     field_fetch('ENTRY')
    48:   end

entry_id()

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 50
    50:   def entry_id
    51:     entry[/EC (\S+)/, 1]
    52:   end

genes()

Alias for genes_as_hash

genes_as_hash()

Returns a Hash of the organism ID and an Array of entry IDs in GENES field.

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 38
    38:   def genes_as_hash; super; end

genes_as_strings()

GENES

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 136
    136:   def genes_as_strings
    137:     lines_fetch('GENES')
    138:   end

inhibitors()

INHIBITOR

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 111
    111:   def inhibitors
    112:     field_fetch('INHIBITOR').split(/\s*;\s*/)
    113:   end

iubmb_reactions()

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 87
    87:   def iubmb_reactions
    88:     all_reac.sub(/;\s*\(other\).*/, '').split(/\s*;\s*/)
    89:   end

kegg_reactions()

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 91
    91:   def kegg_reactions
    92:     reac = all_reac
    93:     if reac[/\(other\)/]
    94:       reac.sub(/.*\(other\)\s*/, '').split(/\s*;\s*/)
    95:     else
    96:       []
    97:     end
    98:   end

motifs()

MOTIF

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 146
    146:   def motifs
    147:     lines_fetch('MOTIF')
    148:   end

name()

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 63
    63:   def name
    64:     names.first
    65:   end

names()

NAME

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 59
    59:   def names
    60:     field_fetch('NAME').split(/\s*;\s*/)
    61:   end

obsolete?()

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 54
    54:   def obsolete?
    55:     entry[/Obsolete/] ? true : false
    56:   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/enzyme.rb, line 33
    33:   def orthologs_as_hash; super; end

orthologs_as_strings()

ORTHOLOGY

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 131
    131:   def orthologs_as_strings
    132:     lines_fetch('ORTHOLOGY')
    133:   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/enzyme.rb, line 28
    28:   def pathways_as_hash; super; end

pathways_as_strings()

PATHWAY

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 126
    126:   def pathways_as_strings
    127:     lines_fetch('PATHWAY')
    128:   end

products()

PRODUCT

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 106
    106:   def products
    107:     field_fetch('PRODUCT').split(/\s*;\s*/)
    108:   end

reaction()

REACTION

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 78
    78:   def reaction
    79:     field_fetch('REACTION')
    80:   end

structures()

STRUCTURES

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 151
    151:   def structures
    152:     unless @data['STRUCTURES']
    153:       @data['STRUCTURES'] = fetch('STRUCTURES').sub(/(PDB: )*/,'').split(/\s+/)
    154:     end
    155:     @data['STRUCTURES']
    156:   end

substrates()

SUBSTRATE

[Source]

         # File lib/bio/db/kegg/enzyme.rb, line 101
    101:   def substrates
    102:     field_fetch('SUBSTRATE').split(/\s*;\s*/)
    103:   end

sysname()

SYSNAME

[Source]

        # File lib/bio/db/kegg/enzyme.rb, line 73
    73:   def sysname
    74:     field_fetch('SYSNAME')
    75:   end

[Validate]