schrodinger.application.desmond.packages.traj_util module

Advanced utilities for trajectory handling

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.application.desmond.packages.traj_util.TrajectoryUnreadableError

Bases: exceptions.Exception

schrodinger.application.desmond.packages.traj_util.extract_atoms(cms_model, selector, tr, format='maestro', is_subsystem=False)

A generator to extract the specified atoms from the trajectory.

Parameters:
  • cms_model (schrodinger.structure.Structure) – This must be consistent with the trajectory tr.
  • selector (str or a callable) – If the value is a str, it must a valid ASL expression consistent with cms_model. The expression will be repeatedly applied to each frame, which means that the selected atoms may differ from frame to frame. If the value is an callable, which should take a CMS model as the argument and return a list of selected atom indices.
  • tr (list of traj.Frame objects) – Trajectory
  • format (str) – Currently, we support only “maestro” (or “mae” in short) and None. If it’s “maestro”, this function will return a schrodinger.structure.Structure object for the subsystem, or it will return a traj.Frame object for the subsystem.
  • is_subsystem (bool) –
    • If true, this function will extract the specified subsystem from the trajectory. It’s important to understand what we mean by “subsystem”, for this, refer to the docstring of the topo.extract_subsystem function.
    • If false, this function will extract an arbitrary set of atoms as specified by selector.
Return type:

A tuple. The first element is a schrodinger.structure.Structure object if format="maestro", or a traj.Frame object if format=None The second element is the corresponding aids
schrodinger.application.desmond.packages.traj_util.read_cms_and_traj(cms_file)

Read the .cms file and the associated trajectory, and return the msys model, the cms model, and the trajectory. The associated trajectory is assumed to be in the same directory as the given .cms file.

Parameters:cms_file (str) – CMS file path.
Returns:msys System, CMS, and list of frames.
Return type:(msys.System, cms.Cms, list of traj.Frame)
Raises:TrajectoryUnreadableError – If there is an error reading the files.