feat(visualization): add molecular structure viewer

[dsk-dev-ai]

Summary

Implements Phase 6.12 — Molecular Structure Viewer.

Adds a reusable 3D molecular structure viewer to GenomeAI using the existing React/TypeScript visualization architecture.

Features

• Added reusable molecular structure viewer component.
• Added typed molecular structure data models.
• Added structure loading/data-source boundary.
• Added molecular structure parsing and validation.
• Added 3D structure rendering.
• Added camera rotation, zoom, and pan controls.
• Added reset and fit-to-structure controls.
• Added molecular representation controls.
• Added loading, empty, and error states.
• Added responsive viewer layout.
• Added keyboard-accessible viewer controls.
• Added proper renderer/resource cleanup on unmount.
• Added isolated fixture/sample structure data where production structure APIs are not yet available.
• Added dedicated molecular structure viewer route.
• Preserved existing visualization components and architecture.

Testing

Added coverage for:

• Molecular structure data types.
• Structure validation.
• Structure loading.
• Empty structures.
• Invalid structures.
• Loading errors.
• Successful structure loading.
• Representation state.
• Viewer controls.
• Reset/fit behavior.
• Component lifecycle.
• Renderer cleanup.
• Accessibility controls.
• Data-source boundaries.

WebGL/3D rendering is isolated from normal unit tests so the test suite does not require a real GPU.

Documentation

Added documentation covering:

• Molecular Structure Viewer architecture.
• Rendering technology.
• Supported structure format.
• Data-source boundary.
• Loading lifecycle.
• Supported representations.
• Viewer controls.
• Accessibility.
• Performance and resource cleanup.
• Testing strategy.
• Current limitations.
• Future extension points.

Updated:

• docs/visualization/README.md
• docs/visualization/roadmap.md

Constraints

• No C++.
• No CUDA.
• No WebAssembly.
• No WebGPU.
• No unnecessary rendering architecture.
• No molecular docking or molecular dynamics.
• No protein prediction.
• No new scientific-analysis engine.
• No unnecessary backend changes.
• Existing visualization architecture is preserved.

Validation

Completed:

• make setup
• make lint
• make typecheck
• make test
• pnpm turbo build
• Web development server verification
• Visualization route verification
• Molecular Structure Viewer manual verification

Verified:

• Structure rendering.
• Camera controls.
• Representation switching.
• Reset behavior.
• Fit-to-structure behavior.
• Loading state.
• Empty state.
• Error state.
• Keyboard accessibility.
• Renderer/resource cleanup.

Phase

Phase 6.12 — Molecular Structure Viewer

This completes the planned Phase 6 Visualization Platform milestones.

Next

After this PR is merged, Phase 6 should be considered complete and development can move to the next master-roadmap phase.

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⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 691c9759-f14a-46fa-b6e8-e0fa7e21f908

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