Add reproducible structural visualization workflows

[jvogan]

Summary

• add a unified structural-biology workflow interface with coordinate QC, declarative figures, comparisons, residue/interface stories, restraints, assemblies, cryo-EM, ensembles, electrostatics, pockets, and chemical-site triage
• emit replayable PyMOL/ChimeraX scripts and sessions with privacy-safe JSON provenance and execution summaries
• add optional DockQ/Foldseek integration, chain-aware PAE analysis, package-parity enforcement, workflow documentation, and regression coverage

Verification

• 125 unit tests pass
• both canonical and packaged skills pass quick validation
• package parity, release hygiene, diff checks, and Gitleaks pass
• representative workflows were executed successfully in installed PyMOL and ChimeraX, including comparison, residue, assembly, ensemble, cryo-EM, electrostatics, annotation, restraint, interface, and chemical-site paths

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Read contact residues from the correct key

When proteus.py compare ... --ligand is used, this loop never collects any contacts because interaction_report.analyze_interactions() emits each ligand group's residues under contacting_residues, not contact_residues. As a result reference_contacts, mobile_contacts, gained_in_mobile, lost_in_mobile, and preserved are all reported as empty even for structures with ligand contacts.

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[chatgpt-codex-connector]

Respect chain overrides for variant context

For variant-focused residue stories with --chain, the visual selection and mutation triage use the requested chain, but the pocket/interface context gets only variant_arg; downstream selectors therefore have chain: null and include every chain with the same residue number. In multichain structures this can report ligand/interface context for the wrong chain, so pass a chain-qualified residue selector for variants when chain is set.

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