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pylipid.api.LipidInteraction.compute_site_lipidcount

LipidInteraction.compute_site_lipidcount(binding_site_id=None)

Calculate the average number of contacting lipids for binding site.

This method calculates the number of specified lipid within the lower distance cutoff to a binding site. The reported value is averaged from the trajectory frames in which interaction between the specified lipid and the binding site 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

binding_site_id (int or list of int, default=None) – The binding site ID used in PyLipID. This ID is the index in the binding site node list that is calculated by the method compute_binding_nodes. The ID of the N-th binding site is (N-1). If None, the contact duration of all binding sites are calculated.

Returns

lipidcount_BS – A list of lipid counts or lists of lipid counts if multiple binding site IDs are provided.

Return type

list

See also

pylipid.api.LipidInteraction.collect_residue_contacts

Create the lipid index.

pylipid.api.LipidInteraction.compute_residue_lipidcount

Calculate lipid count for residues.

pylipid.func.cal_lipidcount

Calculate the average number of contacting molecules.