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Bio::KEGG::Enzyme::enzyme_format Namespace Reference


Detailed Description

Martel based parser to read KEGG Ligand/Enzyme files.

This is a huge regular expression for KEGG Ligand/Enzyme,
built using the 'regular expressions on steroids' capabilities of
Martel.

A description of the format can be found in the 'ligand.doc' file
from the Ligand distribution, available from:

 http://www.genome.ad.jp/kegg

(Note that as of KEGG release 19.0, the 'enzyme' file that comes
as part of the Ligand distribution does not conform 100% to this
description. In particular, some entries contain data items that
are not ordered as they should be according the description. This
Biopython format description has been weakened to accomodate parsing
of these irregular entries.)
 


Functions

def _define_block_seq

Variables

tuple blank_space = Rep1(Str1(" "))
tuple class_block = _define_block_seq("CLASS", "class_block", class_name)
tuple class_name = Group("classname", composite_name)
tuple cofactor = Group("cofactor", wrapped_name)
tuple cofactor_block
tuple comment_block
tuple composite_name = Rep1(Opt(Str1(" ")) + partial_name + Opt(Str1(" ")))
tuple dblinks_block = _define_block_seq("DBLINKS", "dblinks_line", dblinks_line)
tuple dblinks_db = Group("dblinks_db", Rep1(AnyBut(":")))
tuple dblinks_id = Group("dblinks_id", Re("[\S]+"))
 dblinks_line = dblinks_db+\
tuple disease_block = _define_block_seq("DISEASE", "disease_block", disease_line)
tuple disease_db = Group("disease_db", Re("[\w]+"))
 disease_desc = partial_desc+\
tuple disease_id = Group("disease_id", Re("[\w]+"))
tuple disease_line = disease_db+Str1(":")
tuple effector = Group("effector", wrapped_name)
tuple effector_block
tuple entry
tuple entry_line
string entry_tag = "ENTRY"
tuple gene_id = Group("gene_id", Re("[\S]+"))
 genes = organism+\
tuple genes_block = _define_block_seq("GENES", "genes_block", genes)
int INDENT = 12
tuple inhibitor = Group("inhibitor", wrapped_name)
tuple inhibitor_block
tuple motif = Group("motif", wrapped_motif)
tuple motif_block = _define_block_seq("MOTIF", "motif_block", motif_line)
tuple motif_db = Group("motif_db", Re("[\w]+"))
tuple motif_id = Group("motif_id", Re("[\w]+"))
tuple motif_line = motif_db+Str1(":")
tuple name = Group("name", wrapped_name)
tuple name_block = _define_block_seq("NAME", "name_block", name)
string name_tag = "NAME"
tuple organism = Group("organism", Re("[\w]{3}"))
tuple partial_desc = Group("disease_desc", Re(".*"))
tuple partial_motif = Re("\S.*")
tuple partial_name = Re("[\S]+")
tuple pathway_block = _define_block_seq("PATHWAY", "pathway_block", pathway_line)
tuple pathway_db = Group("pathway_db", Re("[\w]+"))
tuple pathway_desc = Group("pathway_desc", Re(".*"))
tuple pathway_id = Group("pathway_id", Re("[\w]+"))
tuple pathway_line = pathway_db+Str1(":")
tuple point = Str1(".")
tuple product = Group("product", wrapped_name)
tuple product_block
tuple reaction_block
tuple record
tuple record_end
tuple record_format
tuple structure_db = Group("structure_db", Re("[\w]+"))
tuple structure_id = Group("structure_id", Re("[\w]+"))
tuple structures_block
 structures_line = structure_db+\
tuple substrate = Group("substrate", wrapped_name)
tuple substrate_block
tuple sysname = Group("sysname", wrapped_name)
tuple sysname_block = _define_block_seq("SYSNAME", "sysname_block", sysname)
 wrapped_motif = partial_motif+\
tuple wrapped_name


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