simulation.readdy.data_structures

Data structures for ReaDDy simulations.

Classes

FrameData	Data class representing one ReaDDy timestep.
ParticleData	Data class representing a ReaDDy particle.
TopologyData	Data class representing a ReaDDy topology of connected particles.

class TopologyData

Data class representing a ReaDDy topology of connected particles.

__init__(uid: int, type_name: str, particle_ids: list[int])

uid: int

Unique ID of the topology from ReaDDy.

type_name: str

ReaDDy type name of the topology.

particle_ids: list[int]

List of unique IDs of each particle in the topology.

class ParticleData

Data class representing a ReaDDy particle.

__init__(uid: int, type_name: str, position: ndarray, neighbor_ids: list[int])

uid: int

Unique ID of the particle from ReaDDy.

type_name: str

ReaDDy type name of the particle.

position: ndarray

The x,y,z position of the particle.

neighbor_ids: list[int]

List of unique IDs of each neighbor particle connected by an edge.

class FrameData

Data class representing one ReaDDy timestep.

__init__(time: float, topologies: dict[int, TopologyData] | None = None, particles: dict[int, ParticleData] | None = None, edge_ids: list[list[int]] | None = None)

time: float

Current time of the simulation for this frame.

topologies: dict[int, TopologyData]

Mapping of topology ID to a TopologyData for each topology.

particles: dict[int, ParticleData]

Mapping of particle ID to a ParticleData for each particle.

edge_ids: list[list[int]]

List of edges, each is a list of IDs of the two connected particles.