Add merged structure IO and mmCIF parity#74
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heathcliff233 wants to merge 2 commits intosteineggerlab:masterfrom
Open
Add merged structure IO and mmCIF parity#74heathcliff233 wants to merge 2 commits intosteineggerlab:masterfrom
heathcliff233 wants to merge 2 commits intosteineggerlab:masterfrom
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- add Python split compression and merged fragment database reads - expose source fragment indices for merged entries - support format-selectable decompression in Python and CLI (pdb|mmcif|cif) - add shared mmCIF atom writer in C++ output path - harden tar/db output path handling with parent-directory checks - expand tests and docs using existing multichain fixture
Author
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Hi authors, thanks for the great tool and the efforts on maintaining it. I have checked the error log and followed the black formatting requirements. Other errors seem to be on the github server side that failed on apt install. This PR aims to add protein multimer support based on the current storage format. It seems that there is already support for segment storage, so I reuse it for multi-chain support and add an additional layer to allow sample-level iteration (with additional mmcif write option by gemmi). Hope it can help. Best, |
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Summary
This PR adds practical multi-chain support while keeping FCZ chunk storage unchanged (single-chain per chunk).
Highlights
compress(..., split=True)andopen(..., merge_fragments=True)pdb | mmcif | ciffoldcomp decompress --output-format ...Compatibility
Validation
conda run -n foldcomp pytest test -q→12 passedconda run -n foldcomp ./build.sh test→ pass