Bio.KEGG.Enzyme package

Module contents

Code to work with the KEGG Enzyme database.

Functions:

  • parse - Returns an iterator giving Record objects.

Classes:

  • Record - Holds the information from a KEGG Enzyme record.

class Bio.KEGG.Enzyme.Record

Bases: object

Holds info from a KEGG Enzyme record.

Attributes:

  • entry The EC number (without the ‘EC ‘).

  • name A list of the enzyme names.

  • classname A list of the classification terms.

  • sysname The systematic name of the enzyme.

  • reaction A list of the reaction description strings.

  • substrate A list of the substrates.

  • product A list of the products.

  • inhibitor A list of the inhibitors.

  • cofactor A list of the cofactors.

  • effector A list of the effectors.

  • comment A list of the comment strings.

  • pathway A list of 3-tuples: (database, id, pathway)

  • genes A list of 2-tuples: (organism, list of gene ids)

  • disease A list of 3-tuples: (database, id, disease)

  • structures A list of 2-tuples: (database, list of struct ids)

  • dblinks A list of 2-tuples: (database, list of db ids)

__init__()

Initialize a new Record.

__str__()

Return a string representation of this Record.

Bio.KEGG.Enzyme.parse(handle)

Parse a KEGG Enzyme file, returning Record objects.

This is an iterator function, typically used in a for loop. For example, using one of the example KEGG files in the Biopython test suite,

>>> with open("KEGG/enzyme.sample") as handle:
...     for record in parse(handle):
...         print("%s %s" % (record.entry, record.name[0]))
...
1.1.1.1 alcohol dehydrogenase
1.1.1.62 17beta-estradiol 17-dehydrogenase
1.1.1.68 Transferred to 1.5.1.20
1.6.5.3 NADH:ubiquinone reductase (H+-translocating)
1.14.13.28 3,9-dihydroxypterocarpan 6a-monooxygenase
2.4.1.68 glycoprotein 6-alpha-L-fucosyltransferase
3.1.1.6 acetylesterase
2.7.2.1 acetate kinase
Bio.KEGG.Enzyme.read(handle)

Parse a KEGG Enzyme file with exactly one entry.

If the handle contains no records, or more than one record, an exception is raised. For example:

>>> with open("KEGG/enzyme.new") as handle:
...     record = read(handle)
...     print("%s %s" % (record.entry, record.name[0]))
...
6.2.1.25 benzoate---CoA ligase