f4enix.output.fispact_legacy_out.PathwayCollection

class f4enix.output.fispact_legacy_out.PathwayCollection(pathways: list[Pathway])

Bases: object

Collection of pathways. This can be created from a list of Pathway objects or directly from a FISPACT legacy output file.

Parameters:

pathways (list[Pathway]) – list of Pathway objects.

Variables:

pathways (list[Pathway]) – list of Pathway objects.

Examples

>>> from f4enix.output.fispact_legacy_out import PathwayCollection
... collection = PathwayCollection.from_file("path/to/fispact/output")
... pathway = collection.pathways[0]
... print(pathway)
... print(pathway.parent, pathway.daughter, pathway.reactions,
...       patway.intermediates, pathway.perc)
Mn55 -(n,g)-> Mn56
Mn55 Mn56 ['n,g'] None 100.0

Methods

__init__(pathways)	Collection of pathways.
from_file(file)	Retrieve pathways from a FISPACT legacy output file and return a list of Pathway objects.
to_dataframe()	Return the pathways as a pandas DataFrame.

classmethod from_file(file: PathLike) → PathwayCollection

Retrieve pathways from a FISPACT legacy output file and return a list of Pathway objects.

Parameters:

file (os.PathLike) – The path to the legacy FISPACT output file.

Returns:

A list of Pathway objects representing the pathways found in the file.

Return type:

list[Pathway]

to_dataframe() → DataFrame

Return the pathways as a pandas DataFrame. columns are “Parent”, “% contribution”, “Intermediates”, “Reactions”, “Daughter”.

Returns:

The pathways as a pandas DataFrame.

Return type:

pd.DataFrame