quemb.molbe.autofrag.GraphGenArgs

class quemb.molbe.autofrag.GraphGenArgs(*, connectivity='euclidean', cutoff=20.0, remove_nonnunique_frags=True)

Graphgen specific arguments.

Parameters:

  • connectivity (Final[Literal['euclidean']]) – Keyword string specifying the distance metric to be used for edge weights in the fragment adjacency graph. Currently supports “euclidean” (which uses the square of the distance between atoms in real space to determine connectivity within a fragment.)

  • cutoff (Final[float]) – Atoms with an edge weight beyond cutoff will be excluded from the shortest_path calculation. This is crucial when handling very large systems, where computing the shortest paths from all to all becomes non-trivial. Defaults to 20.0.

  • remove_nonunique_frags – Whether to remove fragments which are strict subsets of another fragment in the system. True by default.

Attributes

connectivity: Final[Literal['euclidean']]
cutoff: Final[float]
remove_nonnunique_frags: Final[bool]

Methods

__init__(*[, connectivity, cutoff, ...])

Method generated by attrs for class GraphGenArgs.