Ids

IDs(parent)

Bases: Container

Information that specifies the physical atomistic ensemble.

Note that this topology is assumed constant; a reactive topology needs to be implemented.

cadence = Cadence.ENSEMBLE

components = Data[adt.UInt32](store_kind=(StoreKind.ARRAY), uuid='cf39af62-d372-4747-a431-cf2fa0c8e119', description='Unique integer that maps atoms to substructures within a molecule.')

Assigns atoms from a single id_molecule into various substructures. Substructures and represent functional groups in organic compounds, amino acids in proteins, nucleotides in DNA, etc.

The number of unique components is constant between microstates. Atoms can change components; for example, a proton transfer would result in one hydrogen changing from one component to another (e.g., 32 -> 59).

label = 'ids'

molecules = Data[adt.UInt32](store_kind=(StoreKind.ARRAY), uuid='b490f2db-548e-4c92-a71a-8222c041ca54', description='Uniquely identifying integer mapping atoms to a molecule.')

A uniquely identifying integer specifying which atoms belong to a single, physical, covalently bonded molecule. A molecule can be an organic compound, ion, protein, single-stranded DNA, etc. For example, a water and methanol molecule could be [0, 0, 0, 1, 1, 1, 1, 1, 1].