Repository navigation
Conversation
Contributor
There was a problem hiding this comment.
Copilot review overview
🟡 Changes recommended
Unresolved critical and moderate findings remain in minimization, pose selection, rescoring, and complex rebuilding.
Get a fresh assessment by requesting another Copilot review.
Review effort: Lite
Findings: 1
Open (2)
What changed in this PR
Adds pocket-aware DiffDock pose selection, prepared-receptor rescoring, analysis utilities, tests, documentation, and a version bump.
Changes:
- Adds
auto,box, andblindpocket modes. - Aligns selection, rescoring, complexes, and PoseBusters.
- Adds minimization, hydrogen handling, benchmark scripts, and tests.
| File | Summary |
|---|---|
uv.lock |
Updates the locked package version. |
tests/bulk_run/test_diffdock_pocket.py |
Tests DiffDock selection and rescoring. |
scripts/run_guild.py |
Adds the pocket-mode CLI option. |
run_posebusters.py |
Adds a PoseBusters runner. |
run_native_rmsd.py |
Adds native-ligand RMSD analysis. |
README.md |
Documents DiffDock pocket behavior. |
pyproject.toml |
Bumps the project version. |
Makefile |
Forwards pocket configuration. |
guild/transformers/converters.py |
Supports optional ligand hydrogens. |
guild/tools/bulk.py |
Builds complexes from selected poses. |
guild/support/diffdock_model_args.yaml |
Updates DiffDock sampling settings. |
guild/docking/vina.py |
Adds optional pose minimization. |
guild/docking/gnina.py |
Adds local minimization support. |
guild/docking/diffdock.py |
Implements pose selection, receptor handling, and rescoring. |
guild/constants/diffdock.py |
Defines pocket and selection constants. |
guild/bulk.py |
Propagates pocket configuration. |
guild/analysis/posebusters.py |
Uses recorded DiffDock selections. |
build_sweep_table.py |
Adds sweep-table generation. |
💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.
Comment on lines
+148
to
+151
| siblings = sorted( | ||
| glob.glob(os.path.join(glob.escape(boxes_dir), f"{glob.escape(protein_conf_id)}_*.txt")) | ||
| ) | ||
| return siblings[0] if siblings else None |
Add error handling for energy return value. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
AJPreto
commented
Sep 25, 2026
AJPreto
left a comment
AJPreto
left a comment
Collaborator
Author
There was a problem hiding this comment.
Diffdock now supports zooming in on specific chains rather than global raw pdb only input
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.