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pylipid.api.LipidInteraction.compute_residue_lipidcount

LipidInteraction.compute_residue_lipidcount(residue_id=None)

Calculate the average number of contacting lipids for residues.

This method calculates the number of specified lipid within the lower distance cutoff to a residue. The reported value is averaged from the trajectory frames in which interaction between the specified lipid and the residue is formed. Thus the returned values report the average number of surrounding lipid molecules when the lipids are bound.

The returned lipid count list contains data from each of the protein copies and each of the trajectories.

Parameters

residue_id (int or list of int, default=None) – The residue ID, or residue index, that is used by PyLipID for identifying residues. The ID starts from 0, i.e. the ID of N-th residue is (N-1). If None, all residues are selected.

Returns

lipidcounts – A list of lipid counts, of length of n_trajs x n_proteins, or lists of lipid counts if multiple residue IDs are provided.

Return type

list

See also

pylipid.api.LipidInteraction.collect_residue_contacts

Create the lipid index.

pylipid.api.LipidInteraction.compute_site_lipidcount

Calculate binding site lipid count.

pylipid.func.cal_lipidcount

Calculate the average number of contacting molecules.