packing_defect.core.analyzers.packing

Classes

PackingDefectAnalyzer(universe, atomgroups, ...)

Analyze packing defects using atom radii and classification codes.

class packing_defect.core.analyzers.packing.PackingDefectAnalyzer(universe, atomgroups, radii, output_dir: str = './', leaflet: str = 'both', defect_types=None, defect_thresholds=None, start=None, stop=None, stride=1)

Bases: BaseDefectAnalyzer

Analyze packing defects using atom radii and classification codes.

Parameters:

• universe (MDAnalysis.Universe) – System with topology and trajectory.

• atomgroups (list[MDAnalysis.core.groups.AtomGroup]) – Atom groups that define the membrane region to analyze.

• radii (dict[str, dict[str, tuple[float, int]]]) – Mapping radii[resname][atomname] -> (radius, code) used to stamp atoms into the defect grid and label them by integer code.

• output_dir (str, optional) – Destination for outputs.

• leaflet ({"both", "up", "dw"}, optional) – Which leaflet(s) to analyze.

• defect_types (list[str], optional) – Labels for defect classes; used when writing outputs.

• defect_thresholds (dict[str, int], optional) – Map from defect type to grid code; defaults to 1..N.

• start (int, optional) – Frame slicing parameters for the trajectory.

• stop (int, optional) – Frame slicing parameters for the trajectory.

• stride (int, optional) – Frame slicing parameters for the trajectory.

plot(*args, **kwargs)

Placeholder plotting method (extend later).

run()

Run analysis over trajectory frames.

save_results(filename: str, data)

Save results to a file inside output_dir.