ddaf27dea8
- can pass a single pdffile (or stream(!)) - added options lib.loadOptions() to pass opt string
34 lines
1.0 KiB
Python
34 lines
1.0 KiB
Python
# entry point for propka script
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import propka.lib, propka.molecular_container
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def main():
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"""
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Reads in structure files, calculates pKa values, and prints pKa files
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"""
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# loading options, flaggs and arguments
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options, pdbfiles = propka.lib.loadOptions()
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for pdbfile in pdbfiles:
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my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
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my_molecule.calculate_pka()
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my_molecule.write_pka()
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def single(pdbfile, optargs=None):
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"""Run a single PROPKA calculation using *pdbfile* as input.
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Commandline options can be passed as a **list** in *optargs*.
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.. rubric:: Example
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::
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single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
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"""
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optargs = optargs if optargs is not None else []
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options, ignored_pdbfiles = propka.lib.loadOptions(*optargs)
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my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
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my_molecule.calculate_pka()
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my_molecule.write_pka()
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return my_molecule
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