Small Molecule Conformer Error

[thomas-tugwell]

Hi RoseTTAFold-All-Atom team!
I am having an issue with a small molecule I want to dock into my protein. Given the molecule is a bit complex (contains Fe and Si), I want to opt out of openbabel generating conformers using the default (or any) forcefield. I thought I disabled this feature by making the relevant changes in small_molecule.py and parsers.py:

def parse_mol(filename, filetype="mol2", string=False, remove_H=False, find_automorphs=False, generate_conformer: bool = False):

in parsers.py

and

def load_small_molecule(input_file, input_type, model_runner):
    if input_type == "smiles":
        is_string = True
    else:
        is_string = False

    obmol, msa, ins, xyz, mask = parse_mol(
        input_file, filetype=input_type, string=is_string, generate_conformer=False
    )
    return compute_features_from_obmol(obmol, msa, xyz, model_runner)

in small_molecules.py

I am however still seeing a different structure that I submitted with my sdf file. Is there some other relaxation of the small_molecule that I'm missing?If this is part of the docking algorithm, can you point me in the right direction for troubleshooting?