Conversation
- Vendor LigandMPNN files into graphrelax/LigandMPNN/ instead of submodule - Fix np.int -> np.int64 in residue_constants.py for NumPy 1.24 compat - Add download script for LigandMPNN model weights - Update GitHub Actions to download weights and run integration tests - Add ubiquitin (1UBQ) as realistic integration test case - Update imports in designer.py and relaxer.py Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update simtk.openmm imports to fallback to openmm namespace - Use conda for openmm/pdbfixer in GitHub Actions integration tests Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Move math import to top of utils.py - Move openmm imports to top of relaxer.py - Keep cli.py imports lazy (required for fast CLI startup and test isolation) - Remove HAS_PDBFIXER fallback logic - pdbfixer is now required Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add openfold/data/data_transforms.py for sc_utils dependency
- Add openfold/utils/{feats,loss,rigid_utils,tensor_utils}.py for loss.py dependency
- Add openfold/config.py for ml_collections replacement
- Fix unit conversion in _add_restraints() to use OpenMM internal units
(kJ/mol/nm^2 instead of kcal/mol/A^2) for CustomExternalForce
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Move graphrelax/ to src/graphrelax/ - Update pyproject.toml to use src layout - Update pre-commit exclude paths for new layout Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Fix tolerance units in relaxer.py and amber_minimize.py: OpenMM minimizeEnergy expects kJ/mol/nm, not kcal/mol - Fix from_pdb_string to use io.StringIO for PDB parsing: PDBParser.get_structure expects file handle, not raw string - Update .gitignore (linter modification) These fixes resolve: - TypeError: Unit "kilocalorie/mole" is not compatible - OSError: File name too long (PDB string used as filename) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Vendor LigandMPNN files into graphrelax/LigandMPNN/ instead of submodule - Fix np.int -> np.int64 in residue_constants.py for NumPy 1.24 compat - Add download script for LigandMPNN model weights - Update GitHub Actions to download weights and run integration tests - Add ubiquitin (1UBQ) as realistic integration test case - Update imports in designer.py and relaxer.py Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Move math import to top of utils.py - Move openmm imports to top of relaxer.py - Keep cli.py imports lazy (required for fast CLI startup and test isolation) - Remove HAS_PDBFIXER fallback logic - pdbfixer is now required Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
….com/delalamo/GraphRelax into clarifying_installation_instructions
Keep HETATM separation fix for proper terminal detection in pdbfixer. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
…x-design-ligand-error
…/GraphRelax into fix-design-ligand-error
- Trigger on v* tags instead of GitHub release events - Use PYPI_API_TOKEN secret instead of trusted publishing - Add workflow_dispatch for manual triggering - Matches working SAbR publish workflow Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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
1 participant
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.