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refactor: seperated logic in the visualization

Adam Faraidon Wahab requested to merge refactor/clean_opengl_visualization into main

Cleaned up the OPENGL 3D protein visualization. Before everything was connected and written in one file, this was to ensure everything worked as intended.

Relevant logic, shaders, and 3D vector math has been seperated, to ensure low coupling, but also to make further additions to the UI more comprehensible.

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