Bio.KEGG.Compound package

Module contents

Code to work with the KEGG Ligand/Compound database.

Functions:

  • parse - Returns an iterator giving Record objects.

Classes:

  • Record - A representation of a KEGG Ligand/Compound.

class Bio.KEGG.Compound.Record

Bases: object

Holds info from a KEGG Ligand/Compound record.

Attributes:

  • entry The entry identifier.

  • name A list of the compound names.

  • formula The chemical formula for the compound

  • mass The molecular weight for the compound

  • pathway A list of 3-tuples: (‘PATH’, pathway id, pathway)

  • enzyme A list of the EC numbers.

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

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

__init__()

Initialize as new record.

__str__()

Return a string representation of this Record.

Bio.KEGG.Compound.parse(handle)

Parse a KEGG Ligan/Compound 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/compound.sample") as handle:
...     for record in parse(handle):
...         print("%s %s" % (record.entry, record.name[0]))
...
C00023 Iron
C00017 Protein
C00099 beta-Alanine
C00294 Inosine
C00298 Trypsin
C00348 all-trans-Undecaprenyl phosphate
C00349 2-Methyl-3-oxopropanoate
C01386 NH2Mec