v0.0.8.8 Beta (01/02/2025)

New features

• Refactor IO_Tools module to improve the code quality and readability.
• Add unit tests with pytest for the modules:
  • IO_Tools
  • Tools
  • CJSON
  • Framework
  • BuildingBlock
• Add the LON and LON-A nets as a result of Implementing LON topology #61.
• Add the FXT and FXT-A nets.
• Add the geometry module to handle the geometry identification of molecular structures.
• Now the building blocks are not save by default.
  • The user can activate the save of the building blocks by setting the save_bb variable to True on the Framework class.
  • Adds the PRZN2 as a result of Addition of a bb #71

Bugfixes

• Fix bond types not following the CCDC conventions.
• Fix a bug where the folder for building blocks was created even if the user did not want to save the building blocks.
• Fix a bug where the save_dir was not created if it did not exist.
• Fix the out_path variable on the Framework class to save the structure on the correct folder.

Known bugs

• The geometry module is not fully implemented yet.
• The calculation of bonds is taking too long for large structures.
• The bonds calculation does not identify the bond types.
• The bond assignment is done after the structure is created, which can lead to errors in the structure creation. The bond assignment should be done before the structure creation, and the bonds betweeen building blocks should be assigned manually on the creation of the structure.
• The positioning of the building blocks on FXT and FXT-A nets is still not perfect.
• On FXT and FXT-A nets the cell parameters for R4 building blocks are not being calculated correctly.
• The BOR network is not working properly.
• Some S4 and R4 building blocks are not being positioned correctly on the structure.

Closes #61, Closes #71