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pylipid.api.LipidInteraction.compute_site_occupancy

LipidInteraction.compute_site_occupancy(binding_site_id=None)

Calculate the percentage of frames in which the specified lipid contacts are formed for binding sites.

Similar to calculation on residues, the lipid occupancy is calculated using the lower cutoff, and calculated as the percentage of frames in which the specified lipid species formed contact with the binding site within the lower distance cutoff. The lipid index for a binding site is generated from merging, with duplicates removed,

The returned list of occupancies contains data from all protein copies and all 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

occupancy_BS – A list of lipid occupancies or lists of lipid occupancies 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_occupancy

Calculate lipid occupancy for residues.

pylipid.func.cal_occupancy

Calculate the percentage of frames in which a contact is formed.