Protein files from an input path - regex name parsing#13

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youngdashu merged 2 commits intomainfrom

feat/input_path_file_names_regex_parsing

May 4, 2026

Commits on May 3, 2026

Enhance archive extraction by implementing stem-to-path mapping and resolving protein IDs. Introduce functions to prefer .cif files and handle versioning, improving file management and retrieval ef…
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Use ids_file tokens (e.g. plain UniProt) plus chain as the canonical dataset index keys
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