Error with creating generators with initial geometries

[rdguha1995]

@orionarcher . As discussed 1-on-1, there are some issues with creating the generators when initial geometries are provided. This is the stacktrace for a simple benzene molecule.

File /global/u2/r/rdguha/.conda/envs/op_mm/code/pymatgen-io-openmm/pymatgen/io/openmm/utils.py:517, in add_conformers(openff_mol, geometries, max_conformers)
    515 is_isomorphic, atom_map = get_atom_map(inferred_mol, openff_mol)
    516 if not is_isomorphic:
--> 517     raise ValueError(
    518         f"An isomorphism cannot be found between smile {openff_mol.to_smiles()} "
    519         f"and the provided geometry {geometry.xyz}."
    520     )
    521 new_mol = pymatgen.core.Molecule.from_sites(
    522     [geometry.xyz.sites[i] for i in atom_map.values()]
    523 )
    524 openff_mol.add_conformer(new_mol.cart_coords * angstrom)

ValueError: An isomorphism cannot be found between smile [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] and the provided geometry Full Formula (H6 C6)
Reduced Formula: HC
Charge = 0, Spin Mult = 1
Sites (12)
0 C    -3.115850     0.207740     1.067370
1 C    -2.005660     1.051040     1.067370
2 C    -0.720240     0.511230     1.067370
3 C    -0.545020    -0.871880     1.067370
4 C    -1.655210    -1.715180     1.067370
5 C    -2.940630    -1.175370     1.067370
6 H    -2.142310     2.129710     1.067370
7 H     0.145590     1.168910     1.067370
8 H    -3.806460    -1.833050     1.067370
9 H    -4.118340     0.628730     1.067370
10 H     0.457470    -1.292870     1.067370
11 H    -1.518560    -2.793850     1.067370

If the generator is called without the geometry like so:-

dry_benzene = [
    {
        "smile": 'c1ccccc1',
        "count": 1,
        "name": "benzene",
    },
]
i=0
input_set = openmm_generator.get_input_set(dry_benzene, density = 0.00001)
input_set.write_input(f"input_benzene_{i+1}")

It works