Assign label_seq to every subchain of a multi-chain PDB entity - #255
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fnachon wants to merge 9 commits into
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Assign label_seq to every subchain of a multi-chain PDB entity#255fnachon 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>
Previously only entity.subchains[0] was processed, so when a COMPND record declared an entity spanning multiple chains (e.g. "CHAIN: A, B"), residues in every subchain after the first were left with an empty label_seq. That marks them is_present=False, so they get dropped during CIF serialization while feature.pkl still has them, causing a residue-count mismatch that crashes downstream steps (inverse fold, etc.) that load both and expect consistent dimensions. Fixes HannesStark#236 Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Fixes #236.
When a PDB
COMPNDrecord declares an entity spanning multiple chains (e.g.CHAIN: A, B), the parser only processedentity.subchains[0], so residues in every subchain after the first were left with an emptylabel_seq. That marks themis_present=False, so they're dropped during CIF serialization whilefeature.pklstill has them, producing a residue-count mismatch that crashes downstream steps (inverse fold, etc.) that load both and expect consistent dimensions. Now assignslabel_seqto every subchain of the entity, not just the first.