Substructure Conditioner - Supplementary Appendix O about chroma HOT 4 CLOSED

Hi! Thanks for the question.

That conditioner is a research concept for completeness, and we didn't include an implementation or benchmarking it. It is essentially just solve for the distribution between two residues given a noise level.

If you want to impose inter residue distance, you can probably get some luck by including a harmonic restraint in a custom Conditioner.

from chroma.

Thanks so much for your quick response. Yeah, my naive approach has been to impose multiple harmonic restraints with a custom conditioner, but I stumbled upon that SI appendix O and figured I'd ask if this approach [multiple harmonics] was the right direction or if there was something more involved [SI?] that may be advantageous over harmonic restraints. It sounds like that is not known to be the case?

from chroma.

you are right. For the task for restraining pair distances, we don't know what works better in practice.

Appendix O attempted to address the research question of getting sampler to approximately sample $p(x_0 | d^{ij} = d_{target})$ using the classifier guidance formulation, and provides a non-paramteric solution for the conditional scorer (with some assumptions). And as you see the implementation might be a little involved.

For the [multiple harmonics], it certainly will bias the sampling, but we are not sure what distribution it will sample, and it certainly does not sample $p(x_0 | d^{ij} = d_{target})$.

from chroma.

close this due to inactivity, feel free to reopen.

from chroma.