molfoundry.Trajectory#

class molfoundry.Trajectory(artifact)#

Bases: object

A loaded trajectory artifact, ready for downstream analysis.

Parameters:: artifact (Dict[str, Any])

version: int#

kind: str#: "stochsim" or "multiphase".

title: str#

columnKeys: List[str]#: All column keys, in simulator node order.

species: Dict[str, Species]#: One Species per DG vertex, keyed by column key.

reactions: List[Dict[str, Any]]#: Reaction / flow / channel topology (dicts with reaction, kind, inputKeys, outputKeys, label, discovery).

times: List[float]#: Time stamp of each recorded step.

stepReactions: List[str | None]#: Name of the reaction that fired at each step (None for the start step and no-reaction markers).

static load(path)#

Parameters:: path (str | Path)
Return type:: Trajectory

series(key)#

Per-step count of the species with column key, aligned with times.

Parameters:: key (str)
Return type:: List[int]

seriesByCanon(canonIdentity)#

Per-step count of a chemical species followed by its canonical identity — summed across every vertex id it ever held (so a removed-then-re-added species reads as one continuous series).

Parameters:: canonIdentity (str)
Return type:: List[int]

counts()#

The full dense count series of every column key, keyed by column key.

Return type:: Dict[str, List[int]]