When mmpdb transform is called, the algorithm currently fragments the input molecule and searches for replacements for all fragments in the DB. This can then be filtered by the substructure filter and others, but fundamentally all fragments are searched. A huge speedup can potentially be gained if the user could specify the fragment she wants to exchange in the query.
This requires a check whether the fragment as specified exists at all, potentially some fragment cleanup (e.g. specification of the attachment atoms), and the a filter to the specific fragment after fragmentation of the input compound
When mmpdb transform is called, the algorithm currently fragments the input molecule and searches for replacements for all fragments in the DB. This can then be filtered by the substructure filter and others, but fundamentally all fragments are searched. A huge speedup can potentially be gained if the user could specify the fragment she wants to exchange in the query.
This requires a check whether the fragment as specified exists at all, potentially some fragment cleanup (e.g. specification of the attachment atoms), and the a filter to the specific fragment after fragmentation of the input compound