psamm.datasource.kegg – KEGG data parser

Module related to loading KEGG database files.

class psamm.datasource.kegg.CompoundEntry(entry)

KEGG entry with mapped compound properties.

class psamm.datasource.kegg.CompoundMapper

Mapper for raw KEGG compound properties to standard properties.

Public methods are automatically translated into cached properties by the metaclass.

class psamm.datasource.kegg.KEGGEntry(properties, filemark=None)

Base class for KEGG entry with raw values from KEGG.

exception psamm.datasource.kegg.ParseError

Exception used to signal errors while parsing

class psamm.datasource.kegg.ReactionEntry(entry)

KEGG entry with mapped reaction properties.

class psamm.datasource.kegg.ReactionMapper

Mapper for raw KEGG reaction properties to standard properties.

Methods are automatically translated into cached properties by the metaclass.

psamm.datasource.kegg.parse_compound_file(f, context=None)

Iterate over the compound entries in the given file.

psamm.datasource.kegg.parse_kegg_entries(f, context=None)

Iterate over entries in KEGG file.


Parse a KEGG reaction string

psamm.datasource.kegg.parse_reaction_file(f, context=None)

Iterate over the reaction entries in the given file.