lipid_clustering | MDFactory

Lipid clustering and coordination analysis.

func_lipid_clustering_frame(atomgroup, cutoff, residues, atom_to_lipid) → list[dict[str, float | int | str]]

paramatomgroup

paramcutoff

paramresidues

paramatom_to_lipid

Returns

list[dict[str, float | int | str]]

funclipid_clustering(simulation, *, cutoff=4.0, stride=1, backend='multiprocessing', n_workers=4) → pd.DataFrame

Cluster lipids based on atom-level contacts and compute coordination numbers.

paramsimulationSimulation

Simulation instance with universe and build input.

paramcutofffloat

= 4.0

Distance cutoff in Angstrom.

paramstrideint

= 1

Frame stride.

parambackendstr

= 'multiprocessing'

MDAnalysis backend for parallel execution.

paramn_workersint

= 4

Number of workers for parallel execution.

Returns

pandas.DataFrame

Columns: time_ns, frame, resid, resname, cluster_id, cluster_size, coordination_number.