2021-10-19 Pulido/Wagner Check in

IP – Do we really need to know aromaticity of atoms and bonds?

JW – I don’t think so – We should be able to DERIVE the aromaticity of atoms and bonds if we know the bond orders and formal charges.

IP – I’ve cleaned up the from_pdb method to mostly use offmols and not rdmols.

• JW – This looks great.

JW – I added a peptide bond smarts to the _patch_known_problems method.

JW – I fixed a bug that was causing the substructure libraries to get really large (the recursive leaving-atom function was never resetting its list of return values between amino acids, so it just kept getting bigger - This is fixed now)

IP – I’ve consolidated the loading-from-pdb tests into a new test class

JW – I will add additional loading-from-PDB tests, and figure out what’s wrong with our t4 test.

IP – I will wire up metadata loading from PDB