4.2.7. propka.run¶

4.2.7.1. Script functionality¶

The run module provides a high-level interface to PROPKA 3.

The propka3 script consists of the main() function. If similar functionality is desired from a Python script (without having to call the propka script itself) then the single() function can be used instead.

Functions

`main`([optargs])	Read in structure files, calculate pKa values, and print pKa files.
`single`(pdbfile[, optargs])	Run a single PROPKA calculation using pdbfile as input.

propka.run.main(optargs=None)[source]¶: Read in structure files, calculate pKa values, and print pKa files.

propka.run.single(pdbfile, optargs=None)[source]¶

Run a single PROPKA calculation using pdbfile as input.

Commandline options can be passed as a list in optargs.

Example

Given an input file “protein.pdb”, run the equivalent of propka3 --mutation=N25R/N181D -v --pH=7.2 protein.pdb as:

propka.run.single("protein.pdb",
                  optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])