"""
Script functionality
====================
The :mod:`run` module provides a high-level interface to PROPKA 3.
The :program:`propka3` script consists of the :func:`main`
function. If similar functionality is desired from a Python script
(without having to call the :program:`propka` script itself) then the
:func:`single` function can be used instead.
"""
import logging
import sys
from typing import IO, Iterable, Optional
from propka.lib import loadOptions
from propka.input import read_parameter_file, read_molecule_file
from propka.parameters import Parameters
from propka.molecular_container import MolecularContainer
from propka.output import _PathArg
_LOGGER = logging.getLogger(__name__)
[docs]
def main(optargs=None):
"""Read in structure files, calculate pKa values, and print pKa files.
.. versionchanged:: 3.4.0
Removed ability to write out PROPKA input files.
"""
# loading options, flags and arguments
logger = logging.getLogger("")
stdout_handler = logging.StreamHandler(sys.stdout)
stdout_handler.setFormatter(logging.Formatter("%(message)s"))
logger.addHandler(stdout_handler)
optargs = optargs if optargs is not None else []
options = loadOptions(*optargs)
pdbfiles = options.filenames
parameters = read_parameter_file(options.parameters, Parameters())
for pdbfile in pdbfiles:
my_molecule = MolecularContainer(parameters, options)
my_molecule = read_molecule_file(pdbfile, my_molecule)
my_molecule.calculate_pka()
my_molecule.write_pka()
[docs]
def single(filename: _PathArg,
optargs: Iterable[str] = (),
stream: Optional[IO[str]] = None,
write_pka: bool = True):
"""Run a single PROPKA calculation using ``filename`` as input.
Args:
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:
:class:`~propka.molecular_container.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
:class:`~propka.molecular_container.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.
:class:`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
:class:`~propka.molecular_container.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.
.. seealso::
:func:`propka.input.read_molecule_file`
.. versionchanged:: 3.4.0
Removed ability to write out PROPKA input files.
"""
filename = str(filename)
# Deal with input optarg options
optargs = tuple(optargs)
optargs += (filename,)
options = loadOptions(optargs)
parameters = read_parameter_file(options.parameters, Parameters())
# Only filename present should be the one passed via the arguments
# Anything else will probably have been passed using optargs' `-f` flag.
ignored_list = [i for i in options.filenames if i != filename]
if ignored_list:
_LOGGER.warning(f"Ignoring extra filenames passed: {ignored_list}")
options.filenames = [filename]
my_molecule = MolecularContainer(parameters, options)
my_molecule = read_molecule_file(filename, my_molecule, stream=stream)
my_molecule.calculate_pka()
# write outputs
if write_pka:
my_molecule.write_pka()
return my_molecule