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protonate_site(mols, site, ph_min, ph_max, precision)

Protonate a specific site in a list of molecules.

PARAMETER	DESCRIPTION
mols	List of molecule objects. TYPE: list[Mol]
site	ProtonationSite object with protonation information. TYPE: ProtonationSite
ph_min	Minimum pH to expose the site to. TYPE: float
ph_max	Maximum pH to expose the site to. TYPE: float
precision	pKa standard deviation prefactor to consider. TYPE: float

RETURNS	DESCRIPTION
list[Mol]	List of appropriately protonated molecule objects. If there is any issue, this will return an empty list.

set_protonation_charge(mols, idx, charges, prot_site_name)

Set atomic charge on a specific site for a set of molecules.

PARAMETER	DESCRIPTION
mols	List of input molecule objects. TYPE: list[Mol]
idx	Index of the atom to modify. TYPE: int
charges	List of charges to assign at this site. TYPE: list[int]
prot_site_name	Name of the protonation site. TYPE: str

RETURNS	DESCRIPTION
list[Mol]	List of processed molecule objects. If anything goes wrong, then we return an empty list.