A simple example of how to use Pypka as an API is provided below. In this snippet we are estimating the pKa values for all titrable sites in the 4lzt.pdb structure downloaded from the Protein Data Bank.
from pypka.pypka import Titration
params = {
'structure' : '4lzt.pdb',
'ncpus' : -1,
'epsin' : 15,
'ionicstr' : 0.1,
'pbc_dimensions': 0
#Set the ffinput when using PDB files from simulations
#'ffinput': 'GROMOS' # options: GROMOS, AMBER, CHARMM
}
tit = Titration(params)
pH = 7.0
for site in tit:
state = site.getProtState(pH)[0]
print(site.res_name, site.res_number, site.pK, state) You may also try it out on a online notebook.
The same calculation can be done via CLI by resorting to a input parameter file.
structure = 4lzt.pdb
epsin = 15
ionicstr = 0.1
pbc_dimensions = 0
ncpus = -1
sites = all
#Set the ffinput when using PDB files from simulations
#Options: GROMOS, AMBER, CHARMMTo execute pypka simply type one of the two:
pypka parameters.dat
python3 -m pypka parameters.datstructure
- type
str
the PDB filename
epsin
- type
float
internal dielectric to be used in the PB calculations.
ionicstr
- type
float
ionic strength of the medium
pbc_dimensions
- type
int
number of dimensions with periodic boundaries. 0 for solvated proteins and 2 for lipidic systems
ncpus
- type
int
number of CPUs to use in the calculations (-1 to use all available)