schrodinger.application.desmond.packages.traj_util module

Advanced utilities for trajectory handling

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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