No KR domains should be type (R) for a 2S mmal-CoA same as type C1, but are producing a product in C2 configuration. This seems to be because it is not being processed and stereochemistry is copied from the substrate, but the real world KS domain flips this.
One idea rename AT as KSAT, and add a KSq option for loading, or make the loading option trinary (integer) for loading, not loading, KSq loading. The KSAT reaction operator will be updated to set stereochemistry properly without a KR.
The ER domain already checks the methyl group stereochemistry, so this method can be replicated to implement here.
We are going to first check before implementing a fix if natural PKS substrates always have one stereo configuration that gets set the same way by the KS, or if both configurations are possible and just get flipped opposite.
No KR domains should be type (R) for a 2S mmal-CoA same as type C1, but are producing a product in C2 configuration. This seems to be because it is not being processed and stereochemistry is copied from the substrate, but the real world KS domain flips this.
One idea rename AT as KSAT, and add a KSq option for loading, or make the loading option trinary (integer) for loading, not loading, KSq loading. The KSAT reaction operator will be updated to set stereochemistry properly without a KR.
The ER domain already checks the methyl group stereochemistry, so this method can be replicated to implement here.
We are going to first check before implementing a fix if natural PKS substrates always have one stereo configuration that gets set the same way by the KS, or if both configurations are possible and just get flipped opposite.