How to Ensure Complete Reproducibility in REINVENT4? #272
-
|
Hello, I am currently working with REINVENT4 for a project that I plan to submit for publication (targeting Q1). My workflow involves:
My questions are:
I would greatly appreciate guidance, preferably with basic examples of how to correctly implement random seed settings in REINVENT4. Thank you, |
Beta Was this translation helpful? Give feedback.
Replies: 4 comments 5 replies
-
|
I use
Where are further place where I should fix the random seeds to make complete reproducible? |
Beta Was this translation helpful? Give feedback.
-
|
REINVENT is highly sttochastic at multiple levels and the seed only controls some aspected of this. This also means that reproducibility of a stochastic process does and can not mean faithful repeatability. It doesn't make scientifical sense to attempt to do so. Rather you would do multiple runs and provide some statistics as to the the spread of the data. As for your protocol, point 3 (sampling after RL) is a common misconception. You already produce compounds in 2 and use 4 for postprocessing. Why would you throw away good compounds? Besides, sampling does not guarantee you compounds in line with your filtering criteria. I suggest to carry out multiple RL runs, combine the data and assess statitics. As for the scoring componds, QED is a compound score including MW (with a certain weight) so is rather redundant. Its more typical to directly control parameters, in essence Lipinski and Veber rules plus pattern match regarding wanted and unwanted substructural features. Jaccard distance assumes that you want structural closeness. It would probably be better if you had a 3D alignment method like ROCS. The SA score is mostly a measure of complexity and typically correlates not that well with more sophisticated methods. We offer an interface to our retrosynthesis tool AiZynthFinder which may be too expensive to use with RL but post-processing is doable after filtering. |
Beta Was this translation helpful? Give feedback.
-
|
Consult the OpenEye documentation on ROCS. I can't help here. |
Beta Was this translation helpful? Give feedback.
-
|
Hi, if RL already generated compounds and provided scoring for designated components. Out of curiosity, why do I need to run scoring.toml for generated compound again in post-processing? |
Beta Was this translation helpful? Give feedback.
Consult the OpenEye documentation on ROCS. I can't help here.