Site

class titsite.Titsite(res_number, molecule)

Titrable Site with more than one Tautomer

addAtom(aname, anumb)

Args:

aname (str): atom name anumb (int): atom id number

addChargeSets()

Stores the charge set of each existing tautomer for the present Site

addReferenceTautomer()

Gets last tautomer from .sites file adds one and saves it as the reference tautomer

calc_interaction_between(site2)

Calculates the pairwise interaction energies related to the two sites

Args:

site1 (Titsite) site2 (Titsite)

Ensures:

to_write (str): site interaction energies formatted to be written in .dat file

getAverageProt(pH)

Calculates the average protonation of a site at a given pH value

Args:

site (str): Residue number of the site with the suffix ‘N’ or ‘C’ to indicate a N-ter or C-ter, respectively.

pH (float): pH value

Returns:

A float of the average protonation of the site at the selected pH value

getProtState(pH)

Indicates the most probable protonation state of a site at a given pH value

Args:

site (str): Residue number of the site with the suffix ‘N’ or ‘C’ to indicate a N-ter or C-ter, respectively.

pH (float): pH value

Returns:

A tuple with two elements. Example: (‘protonated’, 0.9)

The first element is a string indicating the most probable state of the site. It can be either ‘protonated’, ‘deprotonated’ or ‘undefined’. The ‘undefined’ state is prompted if the average protonation state is between 0.1 and 0.9.

The second element is a float of the average protonation of the site

getTautomers()

Returns list of all tautomers instances except the tautomers of reference

setTautomers(ntauts, resname)

Adds Tautomers from res_tauts to self.tautomers

Args:

res_tauts (list): tautomers from sites file