propka.run

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`(filename[, optargs, stream, write_pka])	Run a single PROPKA calculation using `filename` as input.

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

Changed in version 3.4.0: Removed ability to write out PROPKA input files.

propka.run.single(filename: PathLike | str, optargs: Iterable[str] = (), stream: IO[str] | None = None, write_pka: bool = True)[source]

Run a single PROPKA calculation using filename as input.

Parameters:

filename (str) – name of input file. If filestream is not passed via stream, should be a path to the file to be read.
optargs (tuple) – Optional, commandline options for propka. Extra files passed via optargs will be ignored, see Notes.
stream – optional filestream handle. If None, then filename will be used as path to input file for reading.
write_pka (bool) – Controls if the pKa file should be writen to disk.

Returns:

MolecularContainer object.

Examples

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"])

By default, a pKa file will be written. However in some cases one may wish to not output this file and just have access to the MolecularContainer object. If so, then pass False to write_pka:

mol = propka.run.single("protein.pdb", write_pka=False)

In some cases, one may also want to pass a file-like (e.g. io.StringIO) object instead of a file path as a string. In these cases the file-like object should be passed to the stream argument and a string indicating the file type in the filename argument; this string only has to look like a valid file name, it does not need to exist because the data are actually read from stream. This approach is necessary because file-like objects do not usually have names, and propka uses the filename argument to determine the input file type, and assigns the file name for the MolecularContainer object:

mol = propka.run.single('input.pdb', stream=string_io_file)

In this case, a PDB file-like object was passed as string_io_file. The resultant pKa file will be written out as input.pka.

Notes

Only a single input structure file will be processed, defined by filename (and stream if passing a file-like object). Any additional files passed via the -f or –file flag to optargs will be ignored.