Compute delta SASA against designed chain(s), not designed residues - #250
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fnachon wants to merge 9 commits into
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Compute delta SASA against designed chain(s), not designed residues#250fnachon 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>
The design-side atom mask used for delta SASA was built from the residue-level design_mask, which excludes fixed/scaffold residues that belong to a designed chain. This understates buried surface area for partial-chain redesigns. Use the chain-level design mask (already computed as atom_chain_mask for other metrics) instead. Fixes HannesStark#150 Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Fixes #150.
The design-side atom mask used for delta SASA was built from the residue-level
design_mask, which excludes fixed/scaffold residues that belong to a designed chain (e.g. partial-chain redesigns). This understates buried surface area. Uses the chain-level design mask (already computed elsewhere in the same function asatom_chain_mask) instead, consistently for both the original and refolded delta SASA calls.