schrodinger.trajectory.utils module¶
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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.
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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
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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
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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
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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
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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
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
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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
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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
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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
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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.
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schrodinger.trajectory.utils.
wrap_trajectory
(cms_model, frames)¶ 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.
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))
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schrodinger.trajectory.utils.
unroll_pos
(ct, rep_vec, xyz0)¶ Set coordinates for all copies of the replicated CT.