psamm.datasource.modelseed – ModelSEED data parser

Module related to loading ModelSEED database files.

exception psamm.datasource.modelseed.ParseError

Exception used to signal errors while parsing

psamm.datasource.modelseed.decode_name(s)

Decode names in ModelSEED files

class psamm.datasource.modelseed.CompoundEntry(id, names, formula, filemark=None)

Representation of entry in a ModelSEED compound table

id

Identifier of entry.

name

Name of entry (or None).

formula

Chemical formula of compound.

properties

Properties of entry as a Mapping subclass (e.g. dict).

Note that the properties are not generally mutable but may be mutable for specific subclasses. If the id exists in this dictionary, it must never change the actual entry ID as obtained from the id property, even if other properties are mutable.

filemark

Position of entry in the source file (or None).

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

Iterate over the compound entries in the given file