Atom at the origin cause incorrect res_atom_elements results

[wanggaa]

Hello lucidrain, firstly thank you very much for the pytorch reproduction of alphafold3.

In file inputs.py function extract_canonical_molecules_from_biomolecule_chains

in some cif_file, certain key ion coordinates are set to the origin, which causes this line of code res_atom_positions = atom_positions[res_ligand_atom_mask] can not get the corresponding result correctly, its return res_atom_elements is null.

when use in later function create_mol_from_atom_positions_and_types, it raise an exception ValueError: The length of atom_elements and xyz_coordinates must be the same.

You can reproduce this problem using the 1qyl_assembly1.cif file as input, which has two vanadium ions that are each at the origin with 25% probability.