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Module: enzyme_format Bio/KEGG/Enzyme/

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:

(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.)

Imported modules   
from Martel import *, RecordReader
_define_block_seq (

Define a Martel grouping that can parse a block of groups.

Many of the KEGG entries are formatted as:

TAG blah blah blah blah blah blah blah blah blah blah zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz

Where blah blah... and zzzz... are identically formatted items that can wrap over multiple lines. This function defines a consistent grouping for these blocks.

Arguments: o block_tag - A string of length <= INDENT giving the block tag (i.e. TAG in the example above). o block_group - A callbakc tag for the entire block. o item - A Martel group/expression for a single instance of the data item in this block. (Must NOT include the final newline character).

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This document was automatically generated on Mon Jul 1 12:03:07 2002 by HappyDoc version 2.0.1