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:xtcs

  • ctc_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. See per_traj_ctcs for more info

  • n_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