autofragment.core.types

Core data types for autofragment.

This module defines the fundamental data structures used throughout the package: - ChemicalSystem: Canonical representation of a full system (all atoms + metadata) - Fragment/FragmentTree: Canonical outputs from partitioning - Molecule: Lightweight helper for isolated fragments/geometry utilities

Functions

molecule_centroid(molecule)	Compute the centroid of an isolated molecule.
molecule_to_coords(molecule)	Convert an isolated molecule to a (N, 3) array of coordinates.
molecules_to_system(molecules, *[, bonds, ...])	Create a ChemicalSystem from isolated molecules.
system_to_molecules(system, *[, ...])	Convert a ChemicalSystem to isolated molecules.

Classes

Atom(symbol, coords[, charge])	A single atom with element symbol and 3D coordinates.
ChemicalSystem([atoms, bonds, metadata, lattice])	Canonical representation of a complete chemical system.
Fragment(id[, symbols, geometry, ...])	A fragment containing atoms and/or sub-fragments.
FragmentTree(fragments[, ...])	A container for fragments with metadata.
FragmentationScheme(algorithm[, parameters, ...])	Configuration for a fragmentation algorithm.