PAINS Small Molecules filter

This protocol uses RDKit to filter a SetOfSmallMolecules by applying the PAINS (Pan-assay interference compounds) filter to each of the small molecules stored. The user can choose whether to use RDKit default PAINS substructures or to provide a custom PAINS file where each line must contain a first column with a SMARTS string and a second column with a short description.

Input

Note

All parameters include a help button that gives further information for each of them.

PAINS Small Molecules filter form

The result of this protocol is a SetOfSmallMolecules containing only those small molecules that pass the filter.

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests pwchem.tests.tests_ligand_filtering.TestPAINSFiltering