This changes the RelativeFEPSetup to accept a list of smiles as input.
It does it by trying to read the input parameter as smiles using the openff.toolkit.Molecule object and if it fails with a specific exception it assumes it is then a list of path to sdf/mol2 files.
Motivation and context
Resolves #1155
How has this been tested?
Test is failing with the following error
E AssertionError: the difference between the atoms_with_positions_reduced_potential and the sum of atoms_with_positions_reduced_potential_components is nan
../rjmc/geometry.py:493: AssertionError
I think there is some information getting mixed up or lost when we do the trip from openff.toolkit.Molecule to OEMol using the .to_openeye() method from openff.
Description
This changes the
RelativeFEPSetupto accept a list of smiles as input.It does it by trying to read the input parameter as smiles using the
openff.toolkit.Moleculeobject and if it fails with a specific exception it assumes it is then a list of path to sdf/mol2 files.Motivation and context
Resolves #1155
How has this been tested?
Test is failing with the following error
I think there is some information getting mixed up or lost when we do the trip from
openff.toolkit.MoleculetoOEMolusing the.to_openeye()method from openff.Change log