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()
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()
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 run_propka(args, biomolecule):
"""Run a PROPKA calculation.
:param args: command-line arguments
:type args: argparse.Namespace
:param biomolecule: biomolecule object
:type biomolecule: Biomolecule
:return: (DataFrame-convertible table of assigned pKa values, pKa information from PROPKA)
:rtype: (list, str)
"""
# TODO - eliminate need to write temporary file
lines = io.print_biomolecule_atoms(atomlist=biomolecule.atoms,
chainflag=args.keep_chain,
pdbfile=True)
with NamedTemporaryFile("wt", suffix=".pdb", delete=False) as pdb_file:
for line in lines:
pdb_file.write(line)
pdb_path = pdb_file.name
parameters = pk_in.read_parameter_file(args.parameters, Parameters())
molecule = MolecularContainer(parameters, args)
molecule = pk_in.read_molecule_file(pdb_path, molecule)
molecule.calculate_pka()
# Extract pKa information from PROPKA
# write_pka( self, self.version.parameters, filename=filename, conformation='AVR', reference=reference)
lines = []
# lines.append(f"{pk_out.get_propka_header()}")
# lines.append(f"{pk_out.get_references_header()}")
# lines.append(
# pk_out.get_determinant_section(
# molecule, 'AVR', molecule.version.parameters
# )
# )
# lines.append(
# pk_out.get_summary_section(
# molecule, "AVR", molecule.version.parameters
# )
# )
# lines.append(pk_out.get_the_line())
lines.append(
pk_out.get_folding_profile_section(
molecule,
conformation="AVR",
reference="neutral",
window=[0.0, 14.0, 1.0],
))
lines.append(
pk_out.get_charge_profile_section(molecule, conformation="AVR"))
lines.append(pk_out.get_the_line())
pka_str = "\n".join(lines)
# Summarize in pKas in DataFrame for later use
conformation = molecule.conformations["AVR"]
rows = []
for group in conformation.groups:
row_dict = OrderedDict()
atom = group.atom
row_dict["res_num"] = atom.res_num
row_dict["res_name"] = atom.res_name
row_dict["chain_id"] = atom.chain_id
row_dict["group_label"] = group.label
row_dict["group_type"] = getattr(group, "type", None)
row_dict["pKa"] = group.pka_value
row_dict["model_pKa"] = group.model_pka
if group.coupled_titrating_group:
row_dict["coupled_group"] = group.coupled_titrating_group.label
else:
row_dict["coupled_group"] = None
rows.append(row_dict)
return rows, pka_str
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