Diversity filter options specific for libinvent

[natarajbalakrishnan]

Hi ,
What is the equivalent parameter value for "NoFilter" and "NoFilterWithPenalty" in REINVENT4 . In REINVENT4 we can see three options under diversity filter # IdenticalTopologicalScaffold, # ScaffoldSimilarity, PenalizeSameSmiles. So which of these options is equivalent to NoFilterWithPenalty when libinvent.prior is used for workflow.
Regards,
Nataraj

[halx]

Hi,

many thanks for your interest in REINVENT and welcome to the community!

PenalizeSameSmiles = NoFilterWithPenalty
If you don't need a filter at all, leave out the [diversity_filter] section.

Many thanks,
Hannes.

[natarajbalakrishnan]

Thank you very much, Hannes, for your immediate response. Now I see REINVENT4 runs with the prior libinvent.prior also take other diversity filters like "IdenticalTopologicalScaffold" and "ScaffoldSimilarity" as types and generate output. However, how are these filters useful when the scaffold is provided as input for libinvent for scaffold decoration purposes?

[halx]

When you use a scaffold filter with Libinvent you need to understand how a Murcko scaffold is defined. Basically it means that to satisfy the filter you would have to add at least one ring to your predefined scaffold. The nature of that ring (size, composition) can still change of course.

Overall, this may make your RL run struggle to find new molecules and increase the duplicate rate. The scaffold DF filters also keep track of duplicates and zero-score every additional occurence so making the whole process even more difficult. Doing so can be effective but only in a limited fashion and probably only over short runs.

[natarajbalakrishnan]

Thank you very much Halx for your response and it really helps to understand the diversity filter purpose