REOS

KCH Workflows
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This is a companion discussion topic for the original entry at https://kni.me/w/PCWLCqtfswMflA0G
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Hi authors,

The REOS filter is a great implementation. But we can’t use that as a standalone module since we don’t have access to “REOS.txt” file. Would you mind sharing the REOS.txt file somewhere so we can take a better use of this tool?

Thanks,
Cheng

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Hi @chf42

I believe the list of REOS alerts can be found inside the -REOS Tagger- component available here:

The REOS list is hard coded in a -Table Creator- node inside the -REOS Tagger- component:

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Maybe the component author @Alice_Krebs from KNIME can comment or add some extra information on this.

Hope it helps.

Best
Ael

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Hi @chf42

It is like aworker said, I hardcoded the rule sets and alerts in the Table Creator node. The list of structural alerts I used here has been assembled in that form by Pat Walters (all credits to him) and is available on his Github: raw.githubusercontent.com/PatWalters/rd_filters/master/rd_filters/data/alert_collection.csv

Hope that helps!
Best,
Alice

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Thanks Alice! Appreciate your efforts of making rdfilter available in KNIME. I was aware of rdfilters, but I was looking for the original implementation of REOS based on the paper that contains 100-200 SMARTS structural alerts. “https://www.sciencedirect.com/science/article/abs/pii/S1367593199800581”. I was thinking of implementing it by myself but then I found this node that does exactly what I want to do. I think I can implement it easily by myself and will compare it with rdfilters.

Thank you all for your insightful comments!

Cheng