Merge pull request #5759 from RosettaCommons/roccomoretti/interactive_improve_ligand_validation
[Foldit] Attempt to address a number of the soft crashes.
We're getting a large number of "soft" crashes reported for the ligand puzzles. (Molecules which are being rejected for internal issues.) This PR should address the bulk of them, or at least set us up for handling them later.
* A large number of the reports are for "texas" carbons, nitrogens, oxygens, etc. We have valence checking code, but it wasn't being run in at least one location before passing to RDKit - fix that.
* RDKit can handle some odd valences of iodine, which we're not considering (and which lead to issues later). Add iodine to the list of things we explicitly check for.
* We're getting some issues related to the reprotonation of aromatic nitrogen and phosphorus. I'm not sure where these are coming from, and I haven't been able to reproduce this locally. Add annotations of the starting molecule to the soft crash, which will allow me to better debug the issues later.
No Release Notes. (These changes are only internally relevant.)