Function matches_def 

pub fn matches_def(
    def: &AtomTypeDef,
    idx: usize,
    atoms: &[AtomGeneric],
    env_all: &[AtomEnvData],
    bonds: &[BondGeneric],
    adj: &[Vec<usize>],
) -> bool

Checks each atom against a FF def to determine if it’s a match. If it is, we assign the FF type from the def.