I'm a user without much experience and I'm trying to use Docker in the same way that I use GOLD (Wizard) and I have some doubts. Could someone help me?
1 - In the Wizard I use the box: "Generate a cavity atoms file from the selection". How to use in API?
2 - I am using it to add the "Reference ligand" in the "Select Ligands" step:
native_ligand = 'native.mol2'
settings.reference_ligand_file = native_ligand
But I have seen the use of MoleculeReader is it necessary to use it?
By the way in the CSD Python API documentation - Setting up a docking run - Essential steps
There is a step:
>>> MLL1_ligand_file = 'SAH.mol2'
>>> MLL1_ligand = MoleculeReader(MLL1_ligand_file)
>>> settings.add_ligand_file(MLL1_ligand_file, 10)
Why is MoleculeReader being used if MLL1_ligand is not called?
3 - In my studies I leave unchecked the "Save lone pairs" box in the output options. How would I do it through the API?
4 - Is it possible to calculate the RMSD between the results obtained for each input molecule, between m1 to m10?