Main Methods

getTitrableSites(pdb)

Gets the all titrable sites from the pdb

Parameters:

pdb (string) – The filename a PDB file

Returns:

All titrable sites residue numbers found in the pdb file

Return type:

list

class Titration

Main pypka class

getAverageProt(self, site, pH)

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

Parameters:

• site (string) – 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:

Average protonation of the site at the selected pH value

Return type:

float

getProtStategetProtState(self, site, pH)

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

Parameters:

• 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

Return type:

tuple

getParameters()

Get the parameters used in the calculations

Returns:

Current state of DelPhi parameters

Return type:

string