Feature/af-opacity

[t03i]

Add Transparency Support for AlphaFold Confidence Visualization

Status: 🚧 DRAFT - Not Ready for Review

This PR attempts to add transparency visualization support for AlphaFold confidence scores. It is currently blocked by an implementation issue with the transparency transform in PDBe-MolStar.

Changes

• Added MolstarWrapper class to encapsulate viewer functionality
• Moved structure viewer logic from component to wrapper class
• Added transparency visualization methods based on the PDBe Molstart AlphaFold Transparency implementation
• Updated dependencies to include direct molstar package for transparency construction

Current Blocker

The transparency transform implementation is failing with: Error: No suitable parent found for 'transparency-{parentRef}'

This issue is reported in molstar/pdbe-molstar#127 as well as we can't reasonably debug.

Next Steps

We need either:

1. A resolution/workaround for the transparency transform issue in PDBe-MolStar
2. A Svelte-compatible reimplementation of the transparency functionality

Testing Notes

• Basic structure viewer functionality remains working
• Transparency features are currently non-functional
• No breaking changes to existing visualization features

Related Issues

• No suitable parent found when applying transparency transform "hack" molstar/pdbe-molstar#127

This PR will remain in draft status until we have a working solution for the transparency implementation.