Feature - animated 2Ds showing transition between 2D structures from PDB files

[fryzjergda]

Summary

• Added support for RNAVIEW installation in the Dockerfile.
• Added functionality of generating secondary structure diagrams from PDB files.
• Added functionality of generation animated transictions between structures from PDB files.
• Updated tests to test RNAVIEW, and animated structures from PDB functionalities

Changes Made

• Modified base Dockerfile to include RNAVIEW installation steps.
• Added two scripts rnaview.py and animate3d.py
• Added TestRnaview to validate generation of secondary structure diagram from PDB.
• Added TestAnimateBulk to validate animation from PDBs.

Testing

• Built the Docker image locally and verified RNAVIEW installation, and new scripts functionality.
• Ran the test suite with new tests, ensuring they pass.

Notes

• Requires repository maintainers to tag the new base image after the merge.

[AntonPetrov]

Thank you very much Tomasz! I will check it out and get back to you in the next few days! 🚀

Fix #146

[AntonPetrov]

I left some first comments - I am building the image locally and will test it in more detail. Thank you for working on this Tomasz! Exciting times! ✨

[AntonPetrov]

@fryzjergda Tomasz, this is really good, thank you so much for your great work! I tried it and it mostly works as expected (except for one test).

I left some minor comments - once addressed, this can be merged and ready to go. Many thanks for such a clean PR! Looking forward to seeing this be part of core R2DT. 👏👏👏

[AntonPetrov]

Would it be possible to add a test case for non-bulk animation as well?

Similar to this command from the docs:

python3 utils/animate3d.py \
    examples/PZ1_solution_0.pdb \
    examples/PZ1_Bujnicki_1.pdb \
    examples/PZ1_solution_0_to_PZ1_Bujnicki_1.animated.svg