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.

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

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

Whether the entry with given entry id has a trajectory associated with it

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

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

Whether the entry with given entry id has desmond trajectory

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

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

Whether the entry with given entry id has materials trajectory

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

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

Return trajectory file path if there is any, or None

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

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

Return trajectory hidden cms file path, or None

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

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.

Param

directory_path: Directory path in which unique cms file name is

requested. :type: directory_path: str

Param

base_name: Base name for the unique cms file name.

Type

base_name: str

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.

Param

proj: Project on which to operate.

Type

proj: Project

Param

eid: Entry id associated with the given project.

Type

eid: int or str

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)

Wraps the trajectory within a unit cell box.

Parameters
Returns

Returns a tuple of modified cms_model and the list of trajectory

frames. :rtype: 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.