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 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 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 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