Using SWAG to search smaller vendors

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In addition to the included databases that SWAG can search by default (see here), it is possible to search any other database with a SmallWorld mapping. Recent interest has been expressed by multiple lab members in searching the vendor OnePot's CORE database for potential compounds to purchase. The below instructions describe how to search OnePot specifically, but can be adapted for any other vendor whose catalog has been mapped with SmallWorld.

Instructions

Connect to either epyc or epyc2 on the lab cluster. Make a working directory in the location of your choice, open that directory, and copy query.smi (your SMILES of interest) into the directory. Copy and paste the following code: 

 source /nfs/home/zdingman/environments/SWAG/bin/activate
 cp /nfs/home/zdingman/scripts/SWAG_v1-3-1/SWAG.py .
 ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map local.anon.map
 ln -s /nfs/db5/newdb/Purchasable/maps/onDemandPlus/onepot-tst.smi.anon.map.blm local.anon.map.blm
 python SWAG.py -f query.smi -o lookup -d local -p [0]

SWAG will begin to lookup your SMILES. The file lookup_responses.csv contains the compounds that were successfully found in the vendor's catalog. Don't be surprised if the coverage is subpar for larger compounds; at larger HAC tranches, the overlap between ZINC22 and OnePot is fairly minimal.

Notes

- If you're willing to explore single-atom changes, you can instead specify -p [1] when running SWAG.

- The above instructions here make use of SWAG's local map feature. More detail and uses for local maps can be found here.

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