Raise a clear error on invalid ligand SMILES instead of crashing - #257
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fnachon wants to merge 9 commits into
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Raise a clear error on invalid ligand SMILES instead of crashing#257fnachon wants to merge 9 commits into
fnachon wants to merge 9 commits into
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Changes made to run without errors on the Mac MPS device: torch.autocast, number of devices and workers to use on M1-5 chips, workaround for CUDA-specific code, handling of float64 incompatibilities for MPS.
Replace hardcoded torch.autocast("cuda") with device-agnostic
device_type=tensor.device.type in confidence_utils, inverse_fold,
and writer modules introduced in the upstream merge.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Python pickle does not preserve RDKit atom-level SetProp values. When PyTorch DataLoader spawns worker processes (default num_workers=1 on macOS), self.canonicals is pickled and all atom 'name' properties are lost, causing KeyError in process_atom_features. Fix: load all required molecules directly from the moldir zip inside each get_sample() / get_feat() call instead of using the pickled self.canonicals. The moldir zip handle is cached per-process by _get_zipfile(), so there is no repeated I/O overhead. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ders - Disable pin_memory on MPS (unsupported, causes UserWarning) - Enable persistent_workers when num_workers > 0 (avoids repeated worker init overhead and the PL suggestion warning) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
AllChem.MolFromSmiles() returns None for unparseable SMILES, and the code immediately called AllChem.AddHs(mol) on it, producing a cryptic/unhandled error instead of identifying the bad input. Also calls UpdatePropertyCache(strict=True) before AddHs so malformed valence issues surface as a clean error there rather than somewhere downstream. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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AllChem.MolFromSmiles()returnsNonefor an unparseable SMILES string, and both call sites immediately passed that intoAllChem.AddHs(mol), producing a cryptic/unhandled error instead of identifying which input was bad. Added amol is Nonecheck that raises a clearValueErrornaming the offending SMILES, plusmol.UpdatePropertyCache(strict=True)beforeAddHsso valence issues surface as a clean error at the same point rather than somewhere downstream.Found by comparing against an equivalent crash fix in fnachon/boltz.