def run_propka(options, pdb_path, tmp_path):
"""Run PROPKA software.
Args:
options: list of PROPKA options
pdb_path: path to PDB file
tmp_path: path for working directory
"""
options += [str(pdb_path)]
args = loadOptions(options)
try:
_LOGGER.warning(
"Working in tmpdir {0:s} because of PROPKA file output; "
"need to fix this.".format(str(tmp_path)))
cwd = Path.cwd()
os.chdir(tmp_path)
parameters = read_parameter_file(args.parameters, Parameters())
molecule = MolecularContainer(parameters, args)
molecule = read_molecule_file(str(pdb_path), molecule)
molecule.calculate_pka()
molecule.write_pka()
if args.generate_propka_input:
molecule.write_propka()
finally:
os.chdir(cwd)
def single(pdbfile, optargs=None):
"""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"])
.. todo::
Test :func:`single`, not sure if it is correctly processing ``pdbfile``.
"""
optargs = optargs if optargs is not None else []
options = loadOptions(*optargs)
pdbfile = options.filenames.pop(0)
parameters = read_parameter_file(options.parameters, Parameters())
if len(options.filenames) > 0:
_LOGGER.warning("Ignoring filenames: {0:s}".format(options.filenames))
my_molecule = MolecularContainer(parameters, options)
my_molecule = read_molecule_file(pdbfile, my_molecule)
my_molecule.calculate_pka()
my_molecule.write_pka()
if options.generate_propka_input:
my_molecule.write_propka()
return my_molecule
def main(optargs=None):
"""Read in structure files, calculate pKa values, and print pKa files."""
# loading options, flags and arguments
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()
if options.generate_propka_input:
my_molecule.write_propka()
def run_propka_stream(options, input_file, filename):
"""Run PROPKA software.
Args:
options: list of PROPKA options
input_file: file-like PDB object
filename: filename for the file-like PDB object
"""
options += [filename]
args = loadOptions(options)
parameters = read_parameter_file(args.parameters, Parameters())
molecule = MolecularContainer(parameters, args)
molecule = read_molecule_file(filename, molecule, stream=input_file)
molecule.calculate_pka()
molecule.write_pka()
if args.generate_propka_input:
molecule.write_propka()
def single(pdbfile, optargs=None):
"""Run a single PROPKA calculation using *pdbfile* as input.
Commandline options can be passed as a **list** in *optargs*.
.. rubric:: Example
::
single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v",
"--pH=7.2"])
"""
optargs = optargs if optargs is not None else []
options = loadOptions(*optargs)
pdbfile = options.filenames.pop(0)
parameters = read_parameter_file(options.parameters, Parameters())
if len(options.filenames) > 0:
_LOGGER.warning("Ignoring filenames: {0:s}".format(options.filenames))
my_molecule = MolecularContainer(parameters, options)
my_molecule = read_molecule_file(pdbfile, my_molecule)
my_molecule.calculate_pka()
my_molecule.write_pka()
if options.generate_propka_input:
my_molecule.write_propka()
return my_molecule
def single(file, optargs: tuple = (), 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`
"""
# 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(file, my_molecule)
my_molecule.calculate_pka()
# write outputs
if options.generate_propka_input:
my_molecule.write_propka()
if write_pka:
my_molecule.write_pka()
return my_molecule