schrodinger.application.desmond.packages.traj_util module

Advanced utilities for trajectory handling

Copyright Schrodinger, LLC. All rights reserved.

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 (cms.Cms) – This must be consistent with the trajectory tr and created from topo.read_cms.

  • 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, thus the selected atoms may differ from frame to frame. If the value is a callable, it should take a full system CT 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. If no atoms are selected for a frame, the first element is None and the second element is an empty list.

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

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.desmond.packages.traj_util.read_traj(cms_model, cms_file)

Read the trajectory associated with cms_model, and return it.

Parameters

  • cms_model (cms.Cms) – cms.Cms object.

  • cms_file (str) – CMS file path.

Returns

list of frames.

Return type

list of traj.Frame

Raises

TrajectoryUnreadableError – If there is an error reading the files.

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.

schrodinger.application.desmond.packages.traj_util.find_trajectories(fname_pattern='*', *, recursive=False) → List[str]

Finds all trajectory files that match the specified file name pattern (fname_pattern), and returns a list of names of the found trajectory files.

fname_pattern follows the glob syntax. If the pattern doesn’t contain a supported trajectory extension name, it will be treated as the pattern of the base name.

recursive will lead to searching into all subdirectories if fname_pattern contains the **/ pattern.

To find all trajectories that have a specified base name in only the current directory, simply call this function: find_trajectories(<basename>).

This function returns an empty list if no matches found.

schrodinger.application.desmond.packages.traj_util.pretty_filesize(size_in_byte)