Prepares a Molecule object for atom typing.
mol (Molecule object) – The protein to prepare
guessBonds (bool) – Drops the bonds in the molecule and guesses them from scratch
protonate (bool) – Protonates the protein for the given pH and optimizes hydrogen networks
pH (float) – The pH for protonation
segment (bool) – Automatically guesses the segments of a protein by using the guessed bonds
verbose (bool) – Set to False to turn of the printing
mol – The prepared Molecule