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Bio::KEGG::Compound::compound_format Namespace Reference


Detailed Description

Martel based parser to read KEGG Ligand/Compound files.

This is a huge regular regular expression for KEGG Ligand/Compound,
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
 


Functions

def _define_block_seq

Variables

tuple blank_space = Rep1(Str1(" "))
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]+"))
tuple dblinks_line
tuple entry = Group("entry", Re("C.*"))
tuple entry_line
string entry_tag = "ENTRY"
tuple enzyme_block = _define_block_seq("ENZYME", "enzyme_block", enzyme_line)
 enzyme_entry = enzyme_id+\
tuple enzyme_id = Group("enzyme_id", Rep1(Integer() + Opt(Str1("."))))
tuple enzyme_line = Rep1(enzyme_entry + Opt(blank_space))
tuple enzyme_role = Group("enzyme_role", Str("R", "C", "I", "E"))
tuple formula = Group("formula", Re(".+"))
tuple formula_line
string formula_tag = "FORMULA"
int INDENT = 12
tuple name = Group("name", wrapped_name)
tuple name_block = _define_block_seq("NAME", "name_block", name)
string name_tag = "NAME"
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 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 wrapped_name


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