Change

charge_log_probabilities(state, pka, ph)

Scores each charge a pKa site is enumerated with, so that truncation can keep the likeliest states rather than the first ones generated.

Uses the Henderson-Hasselbalch fraction at the site's mean pKa. A state with only one charge shifts every variant's score equally, so it scores 0 rather than a large constant that would cost precision.

PARAMETER	DESCRIPTION
state	The site's target state at the pH range. TYPE: ProtonationState
pka	The site's mean pKa. TYPE: float
ph	The pH to score at. TYPE: float

RETURNS	DESCRIPTION
list[float]	log10 of the fraction in each charge state, in the order of
list[float]	state.get_charges().

log10_one_plus_pow10(x)

Computes log10(1 + 10x) without evaluating 10x, which overflows for the extreme pKa values in the SMARTS file (e.g., Nitro's -1000).

PARAMETER	DESCRIPTION
x	The exponent. TYPE: float

RETURNS	DESCRIPTION
float	log10(1 + 10**x).

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.

site_log_probabilities(site, ph_min, ph_max, precision, ph)

Scores every variant protonate_site makes from one parent molecule, in the same order, so callers can rank the variants it returns.

PARAMETER	DESCRIPTION
site	The protonation site. TYPE: ProtonationSite
ph_min	Minimum pH of the range, which sets each pKa's state. TYPE: float
ph_max	Maximum pH of the range. TYPE: float
precision	pKa standard deviation prefactor. TYPE: float
ph	The pH to score at. TYPE: float

RETURNS	DESCRIPTION
list[float]	log10 probability of each variant, relative to its parent.