mdciao.contacts.per_traj_ctc¶
-
mdciao.contacts.
per_traj_ctc
(top, itraj, ctc_residxs_pairs, chunksize, stride, traj_idx, **mdcontacts_kwargs)¶ Wrapper for
mdtraj.contacts
for strided, chunked computation of contactsInput can be directly
mdtraj.Trajectory
objects or trajectory files on disk (e.g. xtcs, dcs etc)You can fine-tune the computation itself using mdcontacts_kwargs
Prints out progress report while working
- Parameters
top (~mdtraj.Topology) –
itraj (~mdtraj.Trajectory or filename) –
ctc_residxs_pairs (iterable of pairs of residue indices) – Distances to be computed
chunksize (int) – Size (in frames) of the “chunks” in which the contacts will be computed. Decrease the chunksize if you run into memory errors
stride (int) – Stride with which the contacts will be streamed over
traj_idx (int) – The index of the trajectory being computed. For completeness of the progress report
mdcontacts_kwargs –
Optional keyword arguments to pass to
mdtraj.contacts
If “scheme” is contained in mdcontacts_kwargs and scheme==COM, the center of mass will be computed
- Returns
ictcs, itime, iatps
ictcs (2D np.ndarray (Nframes, Nctcs), where Nctcs= len(ctc_residxs_pairs)) – time traces of the wanted contacts, in
itime (1D np.ndarray of len Nframes) – timestamps of the computed contacts
iatps (2D np.ndarray (Nframes, 2*Nctcs)) – atom-indices yielding distances in ictcs, helps dis-aggregate the residue interaction into backbone-backbone, backbone-sidechain, or sidechain-sidechain