Topology
containers.atomistic.topology.Topology(parent)
¶
Bases: AtomeaContainer
Information that specifies the physical atomistic microstates.
cadence = Cadence.MICROSTATE
instance-attribute
¶
ff_atom_type = Data[adt.Str](store_kind=StoreKind.ARRAY, uuid='e34c0e1b-0eaa-4679-b060-3fcfe737aa15', description='Classical force field atom type')
class-attribute
instance-attribute
¶
In the context of force fields used in molecular dynamics simulations, an "atom type" refers to a specific classification assigned to individual atoms within a molecular system based on certain characteristics. Atom types play a crucial role in defining the parameters and potential energy functions used to calculate forces and motions during a simulation.
Each atom in a molecular system is assigned a particular atom type, which is typically associated with a set of parameters defining its behavior. These parameters include values such as atomic mass, partial charges, van der Waals radii, and bond, angle, and dihedral force constants. The specific values for these parameters are determined based on experimental data and quantum mechanical calculations.
id = 'topology'
instance-attribute
¶
ids_component = Data[adt.UInt32](store_kind=StoreKind.ARRAY, uuid='cf39af62-d372-4747-a431-cf2fa0c8e119', description='Unique integer that maps atoms to substructures within a molecule.')
class-attribute
instance-attribute
¶
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).
ids_molecule = Data[adt.UInt32](store_kind=StoreKind.ARRAY, uuid='b490f2db-548e-4c92-a71a-8222c041ca54', description='Uniquely identifying integer mapping atoms to a molecule.')
class-attribute
instance-attribute
¶
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].
labels_component = Data[adt.Str](store_kind=StoreKind.ARRAY, uuid='3466ffde-1ac0-4e07-ad5f-832420c3943f', description='Maps a Component ID to a human-readable label.')
class-attribute
instance-attribute
¶
An array of human-readable component labels on a per-atom basis.