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
-