pylipid.func

The func package provides tools to collect lipid interactions, calculate koff/residence time, and calculate binding sites in PyLipID

binding_site

get_node_list(corrcoef[, threshold])

Calculate community structures from interaction network.

collect_bound_poses(binding_site_map, …[, …])

Collected the bound poses from trajectories.

vectorize_poses(bound_poses, binding_nodes, …)

Convert the bound poses to distance vectors.

calculate_scores(dist_matrix[, kde_bw, …])

Calculate scores based on probability density.

write_bound_poses(pose_traj, pose_indices, …)

Write selected bound poses to disc.

analyze_pose_wrapper(bs_id, bound_poses, …)

A wrapper function that ranks poses, clusters poses and calculates pose RMSD.

calculate_surface_area_wrapper(trajfile, …)

A wrapper function for calculating surface area.

clusterer

cluster_DBSCAN(data[, eps, min_samples, metric])

Cluster data using DBSCAN.

cluster_KMeans(data, n_clusters)

Cluster data using KMeans.

interactions

cal_contact_residues(dist_matrix, cutoff)

Obtain contact residues as a function of time.

cal_occupancy(contact_list)

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

cal_lipidcount(contact_list)

Calculate the average number of contacting molecules.

Duration(contact_low, contact_high, dt)

Dual cutoff scheme for calculating the interaction durations.

kinetics

cal_koff(durations, t_total, timestep[, …])

Calculate residence time and koff.

cal_survival_func(durations, t_total, …)

Compute the normalised survival function.

calculate_koff_wrapper(durations, title, fn)

Wrapper function that calculates koff and plot koff.