libmdt

Functions that wrap around MDTraj library.

Functions contained in this module operate with MDTraj functionalities, wither by using MDTraj to access Molecular Dynamics data or by receiving MDTraj data structures and parsing them in some way.

Simtk OpenMM is also used in some functions.

Read our citing documentation to understand how to cite multiple libraries.

taurenmd.libs.libmdt.imagemol_protocol1(traj)[source]

Attempt to image molecules acting on the whole traj.

taurenmd.libs.libmdt.imagemol_protocol2(traj)[source]

Attempt to image molecules frame by frame.

taurenmd.libs.libmdt.load_traj(topology, trajectories, insort=False)[source]

Load trajectory with MDTraj.

Uses mdtraj.load.

Example

>>> libmdt.load_traj('bigtopology.cif', 'trajectory.dcd')
Parameters

  • topology (str or Path or list) – Path to the topology file. Accepts MDTraj compatible topology files. mmCIF format is loaded using OpenMM.

  • trajectory (str or Path) – Path to the trajectory file. Accepts MDTraj compatible files

Returns

MDTraj trajectory – Trajectory object.