Get poses

[sg-s]

No description provided.

[Copilot]

Pull Request Overview

This PR introduces a new method to aggregate docked poses into a LigandSet and updates the tutorial to demonstrate its usage.

• Adds get_poses to collect all SDF docked poses into a LigandSet
• Updates imports in docking.py to include LigandSet
• Revises tutorial docs to show how to retrieve and save poses

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/drug_discovery/docking.py	Added get_poses method and adjusted imports
docs/dd/tutorial/docking.md	Updated tutorial section to use get_poses example

Comments suppressed due to low confidence (3)

src/drug_discovery/docking.py:96

• [nitpick] The loop variable name file shadows the built-in. Consider renaming it to file_path for clarity and to avoid masking built-ins.

        for file in file_paths:

src/drug_discovery/docking.py:87

• Add unit tests for get_poses, covering both the case where SDF results exist and where get_results returns None, to ensure correct behavior.

    def get_poses(self) -> LigandSet | None:

docs/dd/tutorial/docking.md:162

• The example does not indicate that get_poses can return None if no results are available. Either update the doc to mention handling of the None case or change the method to always return an empty LigandSet.

poses = sim.docking.get_poses()

[Copilot]

[nitpick] For consistency with other public methods in this class, consider adding a @beartype decorator to enforce the declared signature at runtime.

Suggested change

	@beartype

[checkmarx-do]

Checkmarx One – Scan Summary & Details – 51340c1d-1d62-45a6-9769-417f9c37f47f

Great job, no security vulnerabilities found in this Pull Request