psamm.datasource.modelseed
– ModelSEED data parser¶
Module related to loading ModelSEED database files.
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exception
psamm.datasource.modelseed.
ParseError
¶ Exception used to signal errors while parsing
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psamm.datasource.modelseed.
decode_name
(s)¶ Decode names in ModelSEED files
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class
psamm.datasource.modelseed.
CompoundEntry
(id, names, formula, filemark=None)¶ Representation of entry in a ModelSEED compound table
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id
¶ Identifier of entry.
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name
¶ Name of entry (or None).
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formula
¶ Chemical formula of compound.
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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 theid
property, even if other properties are mutable.
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filemark
¶ Position of entry in the source file (or None).
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psamm.datasource.modelseed.
parse_compound_file
(f, context=None)¶ Iterate over the compound entries in the given file