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pylipid.func.vectorize_poses

pylipid.func.vectorize_poses(bound_poses, binding_nodes, protein_atom_indices, lipid_atom_indices)

Convert the bound poses to distance vectors.

This function takes the protein-lipid complex structure, and translate the bound lipid poses to distance vectors, which contains the minimum distances of each of the lipid molecule atom to the binding site residues. It uses the function mdtraj.compute_distances to calculate atom-wise distances.

Parameters

• bound_poses (mdtraj.Trajectory) – mdtraj.Trajectory object that contain protein-lipid complex coordinates.

• binding_nodes (list) – Binding site residue indices.

• protein_atom_indices (list) – A list of residue atom indices in the protein-lipid complex structure, i.e. [[0,1,2],[3,4,5],[6,7]] means the first residue contains atom 0,1,2, and the second residue contains atom 3,4,5.

• lipid_atom_indcies (list) – The atom indices of the lipid molecule in the protein-lipid complex structure.

Returns

dist_matrix – The distance matrix of the bound poses, in the shape of [n_lipid_atoms, n_poses, n_binding_site_residues]

Return type

numpy.ndarray