Ligand preparation Meeko

This protocol uses the new Meeko functionality as a Python module to prepare a SetOfSmallMolecules.

These are prepared by adding hydrogens, fixing bonds and calculating partial charges.

The option for conformer generation is also available, however, in the case of AutoDock docking programs, this step can be skipped since the ligands are treated as flexible on their rotable bonds.

Input

Note

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

The result of this protocol is a SetOfSmallMolecules, containing the prepared ligands.

Test

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

scipion3 tests autodock.tests.test_autodock.TestADMeekoLigands