Shape Small Molecules filter

This protocol uses RDKit to filter a SetOfSmallMolecules by applying shape filters to each of the small molecules stored. The user can choose whether to use RDKit or Shape-it to calculate the molecules shape and different shape distance options like Tanimoto , Protrude or RMSD distances.

Other parameters include the prealignment of the molecules or to trying atom reordering in order to improve the filter performance.

Note

Currently, Shape-it is not automatically installed with scipion-chem. If the user wants to use it, they must install it manually and define its path in the scipion.conf file as SHAPEIT_HOME.

Input

Note

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

Shape 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.TestShapeFiltering