It has to be defined or "defineable" for the users where stereochem should be accounted for and where not. E.g. displaying/preserving stereo-info of imported molecules could be one setting. Whether stereochem is accounted for during fragmentation could be an individual setting of the fragmenters because it is, e.g., less important for functional groups and slightly more important for scaffolds. But when this is introduced, the actual fragmentation routines have to be checked for how well they preserve stereo-info when it is present. This is accounted for in Scaffold Generator but for the other two existing algorithms, it was never tested.
It has to be defined or "defineable" for the users where stereochem should be accounted for and where not. E.g. displaying/preserving stereo-info of imported molecules could be one setting. Whether stereochem is accounted for during fragmentation could be an individual setting of the fragmenters because it is, e.g., less important for functional groups and slightly more important for scaffolds. But when this is introduced, the actual fragmentation routines have to be checked for how well they preserve stereo-info when it is present. This is accounted for in Scaffold Generator but for the other two existing algorithms, it was never tested.