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Pull request overview
This PR updates docking and pocket-finding flows to align with newer platform tooling and improves local/mock test behavior by standardizing endpoints and fixtures.
Changes:
- Adds/updates SDF fixtures for bulk docking and cleans up an existing ligand fixture.
- Deprecates
Protein.find_pockets()in favor ofPocketFinder, and updates docs/notebooks accordingly. - Introduces
Entitydownload support plus Pocket model changes for remote-path/lazy coordinate loading, and bumps the bulk docking tool version.
Reviewed changes
Copilot reviewed 53 out of 95 changed files in this pull request and generated 10 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/fixtures/files/testing/brd-9.sdf | Adds test ligand fixture (compound 9). |
| tests/fixtures/files/testing/brd-8.sdf | Adds test ligand fixture (compound 8). |
| tests/fixtures/files/testing/brd-7.sdf | Adds test ligand fixture (compound 7). |
| tests/fixtures/files/testing/brd-6.sdf | Adds test ligand fixture (compound 6). |
| tests/fixtures/files/testing/brd-5.sdf | Adds test ligand fixture (compound 5). |
| tests/fixtures/files/testing/brd-4.sdf | Adds test ligand fixture (compound 4). |
| tests/fixtures/files/testing/brd-3.sdf | Adds test ligand fixture (compound 3). |
| tests/fixtures/files/testing/brd-2.sdf | Cleans up fixture to remove multipart/form-data wrapper and extra fields. |
| tests/fixtures/files/docking/brd-2/ef091970-fd5c-47f2-b05c-58be5cc46130.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/cb1b1de5-5400-45be-82f9-424d04c47d18.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/b6378671-dc11-4af5-af61-7ee0c87a9849.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/b5d1c56d-e418-4930-ba54-b3dcbd35ac52.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/b110fa65-4735-4e9e-8dcf-98459348fa67.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/aacd8d02-a938-43d5-9627-abd795a9fa6b.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/9d72d378-ad13-40c9-925d-e00e0f9ce09d.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/8e07bc10-87ff-4854-8ee8-1db51e1f6e86.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/856f45c2-d927-4dfc-ae65-5e95a70102cd.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/732277f7-2981-4bed-94a0-c0629a76f575.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/654baf26-79a1-4f27-96f7-53f42983f791.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/4c2877f5-fab5-4b3b-889f-c98091a0e236.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/41a75564-901a-4685-b0cc-3de6b884f2ff.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/3747fa13-e216-4393-803b-0387e772dc8f.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/30e60b4d-f003-40ed-822b-14572a503378.sdf | Adds docking pose fixture output. |
| tests/fixtures/files/docking/brd-2/15b068ad-2409-456d-9a50-310501f8af93.sdf | Adds docking pose fixture output. |
| tests/conftest.py | Updates remote paths and adds a Pocket fixture; adds a tool-exists helper. |
| src/utils/constants.py | Splits local gateway vs mock endpoints; makes local default to mock server. |
| src/platform/constants.py | Bumps bulk docking tool version to 0.7.7. |
| src/exceptions.py | Adds MethodDeprecatedError and exports it. |
| src/drug_discovery/structures/protein.py | Deprecates Protein.find_pockets() and raises a dedicated error. |
| src/drug_discovery/structures/pocket.py | Makes Pocket an Entity, adds lazy remote loading, path resolution, hashing, and file writing helpers. |
| src/drug_discovery/structures/entity.py | Adds remote_path/local_path and a generic download() helper. |
| src/drug_discovery/pocket_finder.py | Clarifies run() semantics and propagates status. |
| src/drug_discovery/execution_mixins.py | Hardens quotation parsing when field is null. |
| docs/notebooks/clean/pocketfinder.ipynb | Adds a cleaned PocketFinder usage notebook. |
| docs/notebooks/clean/docking-single-ligand.ipynb | Updates notebook to current APIs (Docking, Pocket.from_result, BRD fixtures). |
| docs/notebooks/clean/docking-many-ligands.ipynb | Replaces deprecated find_pockets() usage with PocketFinder. |
| docs/dev/mock-server.md | Documents local mock behavior and gateway override environment variable. |
| docs/dd/tutorial/docking.md | Updates tutorial to use PocketFinder instead of deprecated method. |
| docs/dd/how-to/proteins.md | Updates “find pockets” examples to use PocketFinder. |
| docs/dd/how-to/find-pockets.md | Updates guide to PocketFinder API and quotes/runs semantics. |
| conftest.py | Removes special-casing/overrides now that local endpoint defaults to mock. |
| Dockerfile | Removes container build file. |
| .cursor/skills/fix-failing-test.md | Updates internal guide snippet to use PocketFinder. |
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| _remote_path_base = "entities/pockets/" | ||
| _preferred_ext = ".pdb" |
| else: | ||
| raise ValueError("Could not extract coordinates from structure") | ||
|
|
||
| def _ensure_coordinates(self) -> np.ndarray: |
Contributor
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Pull request overview
Updates the drug-discovery test/fixture setup and documentation to support new Pocket/Protein/Ligand local/remote paths, lazy file loading, and the newer PocketFinder API while expanding docking-related fixtures.
Changes:
- Add/normalize SDF fixtures (testing ligands and docking pose outputs) used by notebook and platform/mock-driven tests.
- Introduce shared
Entityremote/local path + lazydownload()behavior and updatePocketto use it; deprecateProtein.find_pockets()in favor ofPocketFinder. - Update platform/test constants and docs/notebooks to align with the local mock server default and
PocketFinderusage.
Reviewed changes
Copilot reviewed 53 out of 96 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/fixtures/files/testing/brd-9.sdf | Adds ligand fixture for testing. |
| tests/fixtures/files/testing/brd-8.sdf | Adds ligand fixture for testing. |
| tests/fixtures/files/testing/brd-7.sdf | Adds ligand fixture for testing. |
| tests/fixtures/files/testing/brd-6.sdf | Adds ligand fixture for testing. |
| tests/fixtures/files/testing/brd-5.sdf | Adds ligand fixture for testing. |
| tests/fixtures/files/testing/brd-4.sdf | Adds ligand fixture for testing. |
| tests/fixtures/files/testing/brd-3.sdf | Adds ligand fixture for testing. |
| tests/fixtures/files/testing/brd-2.sdf | Cleans up ligand fixture formatting/metadata for tests. |
| tests/fixtures/files/docking/brd-2/ef091970-fd5c-47f2-b05c-58be5cc46130.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/cb1b1de5-5400-45be-82f9-424d04c47d18.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/b6378671-dc11-4af5-af61-7ee0c87a9849.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/b5d1c56d-e418-4930-ba54-b3dcbd35ac52.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/b110fa65-4735-4e9e-8dcf-98459348fa67.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/aacd8d02-a938-43d5-9627-abd795a9fa6b.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/9d72d378-ad13-40c9-925d-e00e0f9ce09d.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/8e07bc10-87ff-4854-8ee8-1db51e1f6e86.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/856f45c2-d927-4dfc-ae65-5e95a70102cd.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/732277f7-2981-4bed-94a0-c0629a76f575.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/654baf26-79a1-4f27-96f7-53f42983f791.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/4c2877f5-fab5-4b3b-889f-c98091a0e236.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/41a75564-901a-4685-b0cc-3de6b884f2ff.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/3747fa13-e216-4393-803b-0387e772dc8f.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/30e60b4d-f003-40ed-822b-14572a503378.sdf | Adds docking pose output fixture. |
| tests/fixtures/files/docking/brd-2/15b068ad-2409-456d-9a50-310501f8af93.sdf | Adds docking pose output fixture. |
| tests/conftest.py | Adds Pocket fixture and tool-existence helper; updates remote paths. |
| src/utils/constants.py | Splits local endpoints (gateway vs mock) and updates local default mapping. |
| src/platform/results.py | Adds compute_job_id filter parameter to results search. |
| src/platform/constants.py | Bumps docking tool version constant. |
| src/exceptions.py | Exposes new MethodDeprecatedError for deprecated API calls. |
| src/drug_discovery/structures/protein.py | Deprecates find_pockets; updates pocket rendering to use lazy local paths. |
| src/drug_discovery/structures/pocket.py | Refactors Pocket to inherit Entity and support lazy local/remote paths. |
| src/drug_discovery/structures/entity.py | Adds remote_path/local_path and a shared download() helper. |
| src/drug_discovery/pocket_finder.py | Clarifies run() semantics and records status. |
| src/drug_discovery/execution_mixins.py | Hardens quotation parsing when missing/None. |
| docs/notebooks/clean/pocketfinder.ipynb | Adds/updates notebook demonstrating PocketFinder. |
| docs/notebooks/clean/docking-single-ligand.ipynb | Updates notebook to new docking workflow + platform sync steps. |
| docs/notebooks/clean/docking-many-ligands.ipynb | Replaces Protein.find_pockets() with PocketFinder. |
| docs/dev/mock-server.md | Documents local mock/gateway behavior for DO_ENV=local. |
| docs/dd/tutorial/docking.md | Updates tutorial to use PocketFinder. |
| docs/dd/how-to/proteins.md | Updates how-to examples to use PocketFinder. |
| docs/dd/how-to/find-pockets.md | Updates pocket finding guide to PocketFinder and new quote/run semantics. |
| conftest.py | Simplifies local env setup now that local endpoint defaults to mock. |
| Dockerfile | Removes Dockerfile from repository. |
| .cursor/skills/fix-failing-test.md | Updates internal dev notes to use PocketFinder. |
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| self, | ||
| *, | ||
| filter_dict: dict[str, Any] | None = None, | ||
| compute_job_id: str | None = None, | ||
| limit: int | None = 1000, | ||
| select: list[str] | None = None, |
src/platform/results.py
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| # note -- job_compute_id is the same as executionId in the rest of the system | ||
| # IMPORTANT! execution_id is not the same as executionId in the rest of the system |
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| @staticmethod | ||
| def _resolve_paths( | ||
| entry: dict[str, Any], | ||
| idx: int, | ||
| ) -> tuple[str | None, str | None]: |
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| raw_local = entry.get("file_path") or entry.get("local_path") | ||
| raw_remote = entry.get("remote_path") | ||
|
|
||
| has_local = isinstance(raw_local, str) and raw_local.strip() | ||
| has_remote = isinstance(raw_remote, str) and raw_remote.strip() |
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| # make sure we | ||
| for pocket in pockets: | ||
| pocket.download() |
| "id": "ab60e2eb-af8e-4852-a653-0c929e2415e5", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "You don't have to explictitly initialize a client, but you can if you want:" |
| "protein = Protein.from_file(DATA_DIR / \"brd\" / \"brd.pdb\")\n", | ||
| "sim = Complex(protein=protein)\n", | ||
| "sim" | ||
| "You don't have to explictitly initialize a client, but you can if you want:" |
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