kinetics

Map kinetics from gibbs data to md trajectory.

This module provides the MapKinetics class, which creates trajectories and weighted densities based on the clustered gibbs data and original trajectory.

class kinetics.MapKinetics(gibbs, contacts)

The MapKinetics class takes processed Gibbs sampler data (an instance of the Gibbs class) and the contact file to create costomized trajectories, containing all of sel1 from the initial contact analysis and a single sel2 residue.

Parameters:

• gibbs (str) – Processed instance of Gibbs class

• contacts (str) – Contact pickle file (contacts-{cutoff}.pkl)

create_traj(top_n=None)

Create the customized trajectories for the individual mixture components of the model. If top_n is None, a single trajectory is created with all of sel1 and a single sel2 residue, with every contact accounted for (ie. a single frame in the original trajectory may be used multiple times due to multiple contacts formed with the sel1 residue of interest at that frame).

Parameters:

top_n (int) – Number of frames desired for the individual trajectories (sorted in order of decreasing classification probability).

weighted_densities(step=1, top_n=None, filterP=0)

Create weighted densities based on the marginal posterior probabilities of the model component classification.

Parameters:

• step (int) – Use every Nth frame

• top_n (int) – Use the N most likely frames for each component to compute the weighted densities from.

• filterP (float) – Probabilities less than filterP are not used in the weighted density calculation

kinetics.get_parser()

kinetics.main()