Paul Pillot
Paul Pillot
@arose yes, sure. It's on my TODO list! I was very much interested into displaying the ionic interactions at the time of this question, but false positives are quite frequent,...
> This look good, thank you! I would like to do some more tests or see some more examples (if feasible) before merging it. Thanks! Agreed, that would be preferable.
Example: 1GAH, around MAN 473 Molstar current version: Molstar this PR  The interactions from the current version encircled in gold, look wrong: between H atoms, or between 2 acceptors....
Example: 1st frame of trajectory from GPCR md db: https://www.gpcrmd.org/dynadb/dynamics/id/85/ Focus on ASN64 Chain B Current Mol* version This PR: 
This PDB file breaks several assumptions about the PDB file format: - residue number must be unique for a given residue (resnum `1` is used at 2 places, first for...
> Additionally, in our case, we would satisfy the `donHAngle` check -- given that the Hs exist, why should we check the `X -- N` angle at all? Maybe we...
I think I've found where the issue is. The `isConjugated` function, l:44 states ```ts if (hetero && bondCount(structure, unit, index) === 4) return false; ``` This addresses the special case...
So... before making any changes, I've checked with the 4.8.0 release. The geometry is correctly inferred as trigonal on the arginine guanidine Nitrogens and Carbon. I've merged the sdf and...
> Thanks for the debugging! Is there a branch pushed with the atom information in the labels, like in your screenshots? Sure, it's there but you need to set the...