99 lines
3.0 KiB
Python
99 lines
3.0 KiB
Python
"""Reproduce tests from original PROPKA."""
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import os
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import re
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from subprocess import call
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import sys
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import unittest
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import logging
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import propka.lib
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import propka.molecular_container
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# This error tolerance was chosen to make Ubuntu 18.04 pass under Windows
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# Subsystem Linux.
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ACCEPTABLE_ERROR = 0.001
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def run_propka(args):
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"""Run PROPKA.
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Args:
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args: command-line arguments for PROPKA
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"""
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options = propka.lib.loadOptions()
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raise NotImplementedError("Need to incorporated command-line arguments")
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pdbfiles = options.filenames
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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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# Setting this up as a direct translation of the original runtest.py script
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# that will be run as part of 'python setup.py test'. This takes on the
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# order of 10s to run.
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class SystemTest(unittest.TestCase):
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"""
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Run the program and compare against reference results.
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"""
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def test_pka_calc(self):
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pdbs = ['1FTJ-Chain-A',
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'1HPX',
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'4DFR']
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test_dir = os.path.dirname(__file__)
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base_dir = os.path.dirname(test_dir)
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executable = os.path.join(base_dir, "scripts", "propka31.py")
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env = { "PYTHONPATH" : base_dir }
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for pdb in pdbs:
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input_filename = os.path.join(test_dir, "pdb", pdb + ".pdb")
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output_filename = os.path.join(test_dir, pdb + ".out")
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output_file = open(output_filename, "w")
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call([sys.executable, executable, input_filename],
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stdout=output_file, env=env)
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output_file.close()
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# Check pka predictions.
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ref = open(os.path.join(test_dir, "results", pdb + ".dat"))
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output = open(output_filename)
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atpka = False
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errors = []
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for line in output:
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if not atpka:
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# Start testing pka values.
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if "model-pKa" in line:
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atpka = True
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continue
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m = re.search('([0-9]+\.[0-9]+)', line)
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if not m:
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break
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expected_value = float(ref.readline())
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value = float(m.group(0))
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value_error = (value-expected_value)/expected_value
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if abs(value_error) > ACCEPTABLE_ERROR:
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logging.error(value_error)
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identity = line[:m.start()].strip()
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errors.append("%12s %8.2f %8.2f" %
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(identity, expected_value, value))
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os.remove("%s.pka" % pdb)
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os.remove("%s.propka_input" % pdb)
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ref.close()
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output.close()
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if errors:
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error_header = " Group Expected Calculated\n"
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self.fail("Unexpected pKa values:\n" + error_header +
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"\n".join(errors))
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