quemb.molbe.autofrag.FragmentMap

class quemb.molbe.autofrag.FragmentMap(fsites, fs, edge, center, centerf_idx, ebe_weights, sites, dnames, fragment_atoms, center_atoms, edge_atoms, adjacency_mat, adjacency_graph)

Dataclass for fragment bookkeeping.

Parameters:

  • fsites (list[Sequence[int]]) – List whose entries are sequences (tuple or list) containing all AO indices for a fragment.

  • fs (list[Sequence[Sequence[int]]]) – List whose entries are sequences of sequences, containing AO indices per atom per fragment.

  • edge (list[Sequence[Sequence[int]]]) – List whose entries are sequences of sequences, containing edge AO indices per atom (inner tuple) per fragment (outer tuple).

  • center (list[Sequence[int]]) – List whose entries are sequences of sequences, containing all fragment AO indices per atom (inner tuple) and per fragment (outer tuple).

  • centerf_idx (list[Sequence[int]]) – List whose entries are sequences containing the relative AO index of the origin site within a fragment. Relative is to the own fragment; since the origin site is at the beginning of the motif list for each fragment, this is always a Sequence range(0, n).

  • ebe_weights (list[Sequence]) – Weights determining the energy contributions from each center site (ie, with respect to centerf_idx).

  • sites (list[Sequence]) – List whose entries are sequences containing all AO indices per atom (excluding frozen core indices, if applicable).

  • dnames (list[str]) – List of strings giving fragment data names. Useful for bookkeeping and for constructing fragment scratch directories.

  • fragment_atoms (list[Sequence[int]]) – List whose entries are sequences containing all atom indices for a fragment.

  • center_atoms (list[Sequence[int]]) – List whose entries are sequences giving the center atom indices per fragment.

  • edge_atoms (list[Sequence[int]]) – List whose entries are sequences giving the edge atom indices per fragment.

  • adjacency_mat (ndarray) – The adjacency matrix for all sites (atoms) in the system.

  • adjacency_graph (Graph) – The adjacency graph corresponding to adjacency_mat.

Attributes

fsites: list[Sequence[int]]
fs: list[Sequence[Sequence[int]]]
edge: list[Sequence[Sequence[int]]]
center: list[Sequence[int]]
centerf_idx: list[Sequence[int]]
ebe_weights: list[Sequence]
sites: list[Sequence]
dnames: list[str]
fragment_atoms: list[Sequence[int]]
center_atoms: list[Sequence[int]]
edge_atoms: list[Sequence[int]]
adjacency_mat: ndarray
adjacency_graph: Graph

Methods

__init__(fsites, fs, edge, center, ...)

Method generated by attrs for class FragmentMap.

remove_nonnunique_frags(natm)

Remove all fragments which are strict subsets of another.