Iván Pulido

@hannahbaumann , this is amazing work! Thanks for this contribution. I checked the connectivity of the networks and I found out that some of them are disconnected (maybe that's expected?)....

I think Lomap has been modified to be able to generate connected networks when net charge transformations are present. We should probable regenerate these networks here with the latest version...

> Not had time to look at this sorry - Just a quick 2 mins input, I think some of the ligands.yaml entries for the formal charges need changing. @IAlibay...

From running a single iteration with perses using these edges I'm facing the following problems with eight (8) of the edges: ``` cdk8/out_18617587_22.stderr:ValueError: could not convert string to float: '...

Oh, I just realized that the edges information has `atom mapping` as key, while I'm not sure this is problematic, we probably want to avoid using spaces here, so we...

@hannahbaumann thank you for this input and analysis! This is great. * Tnks2: According to independent discussions with @jchodera , we concluded that we should add the hydrogen as it...

@hannahbaumann Yes, that sounds great. Happy to collaborate to include the improvements in this dataset, thanks for all this work! I think we probably want to shift to use the...

From current set we have the following types in the corresponding `ligands.yml` data files ```bash ❯ grep " type:" **/*.yml | awk '{print $NF}' | sort -u dg dh ic50...

This should be ready for review. I just need to double check that they run and it should be good to go.

This is the link to the alternate structure with [PDB 3ELJ](https://www.rcsb.org/structure/3ELJ) mentioned in the paper.