Fix deprecated from pmg

[minhsueh]

Fix deprecated pymatgen methods in this PR

Replaces deprecated pymatgen graph construction methods with their current equivalents:

MoleculeGraph.with_empty_graph() -> MoleculeGraph.from_empty_graph()
StructureGraph.with_empty_graph() -> StructureGraph.from_empty_graph()
MoleculeGraph.with_local_env_strategy() -> MoleculeGraph.from_local_env_strategy()
StructureGraph.with_local_env_strategy() -> StructureGraph.from_local_env_strategy()