schrodinger.trajectory.utils module

schrodinger.trajectory.utils.is_desmond_product_installed()

Check if desmond product is installed or not. We can not view trajectory features if there is no Desmond product.

schrodinger.trajectory.utils.get_trajectory_path(proj, eid)

Return trajectory file path if any, or None Old trajectory was not storing trajectory directory path in the property, but stores .idx file path. So, we need to do idx trajectory path treatment to know the trajectory directory name.

Parameters

  • proj (Project) – Project on which to operate.

  • eid (int or str) – Entry id associated with the given project.

schrodinger.trajectory.utils.get_cms_file_path(proj, eid)

Return trajectory file path if there is any, or None It attemtps to find cms file path in the same directory where trajectory exists, otherwise retrieves from the project.

Parameters

  • proj (Project) – Project on which to operate.

  • eid (int or str) – Entry id associated with the given project.

schrodinger.trajectory.utils.get_hidden_cms_file_path(proj, eid)

Return trajectory hidden cms file path, or None

Parameters

  • proj (Project) – Project on which to operate.

  • eid (int or str) – Entry id associated with the given project.

schrodinger.trajectory.utils.get_unique_cms_file_name(directory_path, base_name)

Gets unique cms file name in the given directory for the given base name. It will prefix an increasing number in case the file already exists.

Parameters

  • directory_path (str) – Directory path in which unique cms file name is requested.

  • base_name (str) – Base name for the unique cms file name.

schrodinger.trajectory.utils.generate_cms_file_from_entry(proj, eid)

Generates cms file from entry and sets the generated cms file path to entry’s s_m_hidden_generated_cms_file property.

Parameters

  • proj (Project) – Project on which to operate.

  • eid (int or str) – Entry id associated with the given project.

schrodinger.trajectory.utils.set_trajectory_path(eid: Union[str, int], path: str)

Update the s_chorus_trajectory_file property.

Parameters

  • eid – The entry id being checked.

  • path – The new s_chorus_trajectory_file value to set

schrodinger.trajectory.utils.clone_workspace_selection(st: schrodinger.structure._structure.Structure)

Clones the selection from workspace structure to given structure.

Parameters

st – Structure for which selection needs to be applied.

schrodinger.trajectory.utils.wrap_trajectory(cms_model, frames, fract_offset=0.0001)

Wraps the trajectory within a unit cell box.

Parameters

  • cms_model (schrodinger.application.desmond.cms.Cms) – The trajectory’s cms model.

  • frames (list(schrodinger.application.desmond.packages.traj.Frame)) – The list of trajectory frames.

  • fract_offset (float) – The threshold used to compare floating point fractional coordinate values and in particular those that are on the cell boundary

Returns

Returns a tuple of modified cms_model and the list of trajectory frames.

Return type

tuple(schrodinger.application.desmond.cms.Cms, list(schrodinger.application.desmond.packages.traj.Frame))

schrodinger.trajectory.utils.unroll_pos(ct, rep_vec, xyz0)

Set coordinates for all copies of the replicated CT.