Addition of protein ribbon + ligand rendering

[JamesOBrien2]

Summary

Addition of protein ribbon + ligand rendering, additional highlight style (halo), ligand highlighting, protein-ligand NCI visualisation, and mmCIF rendering/handling (This would however, require a specific fork of ASE, potentially better to stash this for the time being).

What’s Included

• Added/updated protein ribbon rendering pipeline and semantics integration.

• Protein styles simplified to:

  • gloss (default for --protein)
  • illustration

• Added/standardized ligand UX:

  • --highlight-ligand for ligand highlighting
  • --halo ligand for ligand highlighting (halo)
  • --ligand-color for ligand highlight styling
  • --nci-ligand for ligand-protein NCIs

• Renderer behavior:

  • NCI dotted edges remain visible in protein mode
  • Protein mode defaults ghosts off unless explicitly requested (--ghosts) for better performance

• CIF/mmCIF protein semantics path improved in parser/reader flow to preserve metadata for SS handling.

• Added/updated tests across CLI/API/protein/highlight/semantics paths.

• Added README and example assets for:

  • protein styles
  • ligand highlight
  • ligand-focused NCI
  • caffeine halo

Why

This consolidates the recent protein/ligand work into one coherent user-facing experience with consistent CLI semantics, better defaults, and more reliable protein+NCI output quality.

Dependency

Part of this PR depends on the xyzgraph protein semantics PR (feature/protein-semantics-foundation):

• Required to render protein substructures without explicit substructure information in the .pdb file.
  Part of this PR depends on the ase mmCIF file-format reader PR (feature/mmcif-reader).
• Required to render/read macromulecular CIF (.cif) files (default file format for protein databank etc.)

[JamesOBrien2]

I swear a lot of the code line additions are just the .pdb files 🫣