Adds an optional pdbfixer directive to the molecules section of the YAML file through PDBFixer, a simple OpenMM-based protein structure processing tool. The following options are accessible through the pdbfixer directive. replace_nonstandard_residues: Replace nonstandard amino acids. remove_heterogens: Remove heterogens (such as ligands and waters). add_missing_residues: Add missing residues from the SEQRES block. add_missing_atoms: Add missing heavy atoms. apply_mutations: Specify protein mutations (e.g., T315I).