Add atom bonds cache and benchmark for SARS-CoV-2

[syzer]

inferred atom bonds are cached. add benchmark for 6VXX inference. first inference took ~0.026s for 6VXX (23,694 atoms, 24,297 bonds), with cache 200,000x loop timing effectively: 0ms.

• bond_tolerance_controls
• apply_bond_tolerance_debounce
• mark_bond_cache_dirty (in Running)
• update_color_mode_availability (after mark_bond_cache_dirty)
• update_atom_hover_cache (after update_color_mode_availability)
• update_scene (after mark_bond_cache_dirty)

And update_scene still feeds the render-related follow-ups:

• sync_atom_selection_highlight after update_scene
• update_bond_order_legend after update_scene
• update_atom_hover_label after update_scene

[unkcpz]

purely well done. Thanks (again) @syzer