quemb.molbe.chemfrag

This module implements the fragmentation of a molecule based on chemical connectivity that uses the overlap of tabulated van der Waals radii.

There are three main classes:

• BondConnectivity contains the connectivity data of a molecule

  and is fully independent of the BE fragmentation level or used basis sets. After construction the knowledge about motifs in the molecule are available, if hydrogen atoms are treated differently then the motifs are all non-hydrogen atoms, while if hydrogen atoms are treated equal then all atoms are motifs.

• PurelyStructureFragmented is depending on the BondConnectivity

  and performs the fragmentation depending on the BE fragmentation level, but is still independent of the used basis set. After construction this class knows about the assignment of origins, centers, and edges.

• Fragmented is depending on the PurelyStructureFragmented

  and assigns the AO indices to each fragment and is responsible for the book keeping of which AO index belongs to which center and edge.

Functions

chemgen(mol, n_BE, args, frozen_core, ...)	Fragment a molecule based on chemical connectivity.
restrict_keys(D, keys)	Restrict the keys of a dictionary to a subset.
union_of_seqs(*seqs)	Merge multiple sequences into a single OrderedSet.

Classes

BondConnectivity(bonds_atoms, motifs, ...[, ...])	Data structure to store the connectivity data of a molecule.
ChemGenArgs(*[, treat_H_different, ...])	Additional arguments for ChemGen fragmentation.
Fragmented(*, mol, conn_data, ...)	Contains the whole BE fragmentation information, including AO indices.
PurelyStructureFragmented(*, mol, ...)	Data structure to store the fragments of a molecule.