Exclude non-standard residues from ConsecutiveCA filter - #259
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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 filter pulled atom_center for every residue in a chain, including bound metal ions / hetero groups that aren't real backbone residues. Their coordinates aren't near the actual CA trace, so they can produce a spurious long CA-CA jump and wrongly reject an otherwise valid chain. Restrict to is_standard residues first. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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ConsecutiveCA.filter()pulledatom_centerfor every residue in a chain, including bound metal ions / hetero groups that aren't real backbone residues. Since their coordinates aren't near the actual CA trace, they can produce a spurious long CA-CA jump and wrongly reject an otherwise valid chain. Restricts tois_standardresidues before computing consecutive-CA distances.Found and fixed the equivalent bug in fnachon/boltz, which boltzgen's static polymer filters are derived from.