Support for homocysteine and D-homocysteine disulfides.
Earlier, I implemented params files for a disulfide bonded homocystine and D-homocystine, and I further made it so that Conformation could conceive of these residue connections. That didn't mean that they would be scored, though, or that a variety of protocols that might
have been primed to think of disulfides strictly in terms of SG atoms and comparisons to aa::cys and such were any more prepared.
Now they are: every protocol I could find that had a special disulfide behavior that was specifically about cysteine disulfides (and shouldn't be) no longer makes that assumption.
Now, some caveats. There still aren't centroid files for NCAAs, which include homocysteine and D-homocysteine. I didn't implement them. That said, whenever they're implemented, disulfides formed from them will work, so that's nice. Essentially, I didn't bend over backwards to implement new protocols or new functionality, but my aim was that--for protocols that ought to be agnostic to cysteine type but that for some reason were married to tepid ol' cysteine, now they aren't. Importantly, since there really isn't a wealth of e.g. D-homocy
stine disulfide structural data, it's not easy to empirically validate these structures, but we're expanding our capabilities.