quemb.molbe.autofrag.FragmentMap

class quemb.molbe.autofrag.FragmentMap(AO_per_frag, fs, AO_per_edge, ref_frag_idx_per_edge, relAO_per_origin, weight_and_relAO_per_center, sites, dnames, motifs_per_frag, origin_per_frag, edge_atoms, adjacency_mat, adjacency_graph)

Dataclass for fragment bookkeeping.

Parameters:

  • AO_per_frag (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.

  • AO_per_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 whose entries are sequences of sequences, containing all fragment AO indices per atom (inner tuple) and per fragment (outer tuple).

  • centerf_idx – 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).

  • weight_and_relAO_per_center (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.

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

  • origin_per_frag (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

AO_per_frag: list[Sequence[int]]
fs: list[Sequence[Sequence[int]]]
AO_per_edge: list[Sequence[Sequence[int]]]
ref_frag_idx_per_edge: list[Sequence[int]]
relAO_per_origin: list[Sequence[int]]
weight_and_relAO_per_center: list[Sequence]
sites: list[Sequence]
dnames: list[str]
motifs_per_frag: list[Sequence[int]]
origin_per_frag: list[Sequence[int]]
edge_atoms: list[Sequence[int]]
adjacency_mat: ndarray
adjacency_graph: Graph

Methods

__init__(AO_per_frag, fs, AO_per_edge, ...)

Method generated by attrs for class FragmentMap.

remove_nonnunique_frags(natm)

Remove all fragments which are strict subsets of another.

to_FragPart(mol, n_BE, frozen_core)