Add chain gap detection to prevent artificial gap closure during mini…#10
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Add chain gap detection to prevent artificial gap closure during mini…#10
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…mization Detects missing residues in protein chains by checking residue numbering discontinuities and C-N bond distances. Chains are split at gaps before OpenMM minimization to prevent the creation of unrealistic peptide bonds across gaps. Original chain IDs are restored after minimization. - Add chain_gaps.py module with detect_chain_gaps, split_chains_at_gaps, and restore_chain_ids functions - Integrate gap detection into relaxer.py relax() method - Add split_chains_at_gaps config option (enabled by default) - Add --no-split-gaps CLI flag to disable the feature - Add comprehensive tests for chain gap detection
…atom The bug was assigning a new chain ID for every atom at a gap start residue instead of just once when entering a new segment. Added tracking of processed gap starts to prevent duplicate chain assignments.
- Free up disk space by removing unused .NET, GHC, and Boost packages - Install CPU-only PyTorch to avoid large CUDA dependencies - Use --no-cache-dir to minimize pip cache usage The GitHub Actions runner was running out of disk space when installing PyTorch with CUDA dependencies (~5-7GB) alongside conda packages. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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…mization
Detects missing residues in protein chains by checking residue numbering discontinuities and C-N bond distances. Chains are split at gaps before OpenMM minimization to prevent the creation of unrealistic peptide bonds across gaps. Original chain IDs are restored after minimization.