Add file first 3D protein structure rendering#28
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- TmapViz.add_3d_structure_files(paths) auto-copies PDB/CIF files into the output bundle as a relative sidecar directory - TmapViz.add_3d_structures(values, source="url"|"text") for URL or embedded-text transports; default source is url - protein.html.j2 template renders structures with 3Dmol.js, no AlphaFold or UniProt fetches - protein template auto-selected when a 3D structure column is attached - sequence_properties splits Biopython-backed vs dep-free properties; biopython moves to an optional [proteins] extra - new notebook 13_local_protein_structures walks the file-first workflow
Add file-first 3D protein structure rendering
- add reproducibility; if set to True makes HNSW single threaded so its reproducible at the cost of being slower - add tree hops. Counts number of hops (or nodes) to reach one node from another
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