Potential duplicate functions

[Strandgaard96]

@tlinjordet

There are two versions of the "compare_dataframes" function in the files linked. Can we potentially remove one of them? I am not sure which one to keep as it seems that both are used currently.

Since the first file only has this function it would be nice to just have the ligand_generation/utils.py file to avoid files with same name.

https://github.com/uiocompcat/tmcinvdes/blob/7673bcf86dc1406f36041875ecb779e11c92e1f4/tmcinvdes/utils.py
https://github.com/uiocompcat/tmcinvdes/blob/7673bcf86dc1406f36041875ecb779e11c92e1f4/tmcinvdes/ligand_generation/utils.py

[tlinjordet]

@Strandgaard96
I will solve this on my #45 branch before merging to main.
Will move the shared utility functions to tmcinvdes/utils.py since, e.g., processing substitution atoms functions are also used outside of the ligand_generation part of the workflow. The relationship between the two versions of the "compare_dataframes" function is already flagged in the docstring of the more general version, in tmcinvdes/utils.py, which is the one that should be used under the --xtent test.

I will @ you when it's addressed.

[Strandgaard96]

@tlinjordet Sound good!