mdciao.contacts.trajs2ctcs¶
-
mdciao.contacts.
trajs2ctcs
(trajs, top, ctc_residxs_pairs, stride=1, consolidate=True, chunksize=1000, return_times_and_atoms=False, n_jobs=1, progressbar=False, **mdcontacts_kwargs)¶ Time-traces of residue-residue distances from a list of trajectories
- Parameters
trajs (list) – list of trajectories. Each item can be a str with the path to a file or an
Trajectory
object.top (str or
mdtraj.Topology
) – Topology that matches :obj:xtcsctc_residxs_pairs (iterable) – List of (zero-indexed) residue pairs
stride (int, default is 1) – Stride the trajectory data down by this value
consolidate (boolean, default is True) – Return the time-traces consolidated into one array by using np.vstack
chunksize (integer, default is 1000) – How many frames will be read into memory for computation of the contact time-traces. The higher the number, the higher the memory requirements
return_times_and_atoms (boolean, default is False) – Return also the time array in ps and the indices of the atoms behind the distanes in
ctcs
. Seeper_traj_ctcs
for more infon_jobs (int, default is 1) – To how many processors to parallellize. The algorithm parallelizes over the trajectories themeselves, having 3 trajs and n_jobs=4 is equal t n_jobs=3
progressbar (bool, default is False) – Use a fancy
tqdm.tqdm
progressbar
- Returns
ctcs
ctcs, time_trajs, atom_idxs if return_time=True