Guard get_delta_sasa against empty atom selections - #254
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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>
biotite's sasa() raises ValueError on an empty atom array, which happens whenever the target and/or design chain(s) have no resolved atoms in the structure being scored. This crashed the whole analysis step; return NaN for the SASA metrics instead so the pipeline can continue. Fixes HannesStark#166 Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Fixes #166.
biotite's
sasa()raisesValueError: Coordinates are emptywhen passed an empty atom array, which happens whenever the target and/or design chain(s) have no resolved atoms in the structure being scored (e.g. thesmall_molecule_from_file_and_smilesexample underv0.2.0). This crashed the whole analysis step. Returns(nan, nan, nan)for the SASA metrics in that case instead, so the pipeline can continue rather than aborting on step 5/6.