218 lines
7.1 KiB
Python
218 lines
7.1 KiB
Python
"""Tests for PROPKA"""
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import logging
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import os
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import re
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from pathlib import Path
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import pytest
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from numpy.testing import assert_almost_equal
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from propka.parameters import Parameters
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from propka.molecular_container import MolecularContainer
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from propka.input import read_parameter_file, read_molecule_file
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from propka.lib import loadOptions
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_LOGGER = logging.getLogger(__name__)
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# Number of decimal places for maximum tolerable error. Set by number of
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# decimal places in pKa output as well as need to make unmodified code work
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# on WSL Ubuntu 18.04
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MAX_ERR_DECIMALS = 2
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# This directory
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TEST_DIR = Path("tests")
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# Location for test PDBs
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PDB_DIR = Path("pdb")
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# Location for results for comparing output (allow running from tests/ and
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# ../tests/)
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RESULTS_DIR = Path("tests/results")
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if not RESULTS_DIR.is_dir():
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_LOGGER.warning("Switching to sub-directory")
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RESULTS_DIR = Path("results")
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# Arguments to add to all tests
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DEFAULT_ARGS = []
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def get_test_dirs():
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"""Get locations of test files.
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Returns:
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dictionary with test file locations.
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"""
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path_dict = {}
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for key, path in [("pdbs", PDB_DIR), ("results", RESULTS_DIR)]:
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test_path = TEST_DIR / path
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if test_path.is_dir():
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path_dict[key] = test_path
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else:
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test_path = path
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if test_path.is_dir():
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path_dict[key] = test_path
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else:
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errstr = (
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"Can't find {0:s} test files in {1:s}".format(
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key, [TEST_DIR / path, path]))
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raise FileNotFoundError(errstr)
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return path_dict
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def run_propka(options, pdb_path, tmp_path):
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"""Run PROPKA software.
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Args:
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options: list of PROPKA options
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pdb_path: path to PDB file
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tmp_path: path for working directory
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"""
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options += [str(pdb_path)]
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args = loadOptions(options)
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try:
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_LOGGER.warning(
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"Working in tmpdir {0:s} because of PROPKA file output; "
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"need to fix this.".format(str(tmp_path)))
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cwd = Path.cwd()
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os.chdir(tmp_path)
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parameters = read_parameter_file(args.parameters, Parameters())
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molecule = MolecularContainer(parameters, args)
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molecule = read_molecule_file(str(pdb_path), molecule)
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molecule.calculate_pka()
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molecule.write_pka()
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if args.generate_propka_input:
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molecule.write_propka()
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finally:
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os.chdir(cwd)
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def compare_output(pdb, tmp_path, ref_path):
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"""Compare results of test with reference.
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Args:
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pdb: PDB filename stem
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tmp_path: temporary directory
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ref_path: path with reference results
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Raises:
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ValueError if results disagree.
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"""
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ref_data = []
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with open(ref_path, "rt") as ref_file:
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for line in ref_file:
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ref_data.append(float(line))
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test_data = []
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pka_path = Path(tmp_path) / ("{0:s}.pka".format(pdb))
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with open(pka_path, "rt") as pka_file:
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at_pka = False
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for line in pka_file:
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if not at_pka:
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if "model-pKa" in line:
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at_pka = True
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elif line.startswith("---"):
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at_pka = False
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else:
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match = re.search(r'([0-9]+\.[0-9]+)', line)
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value = float(match.group(0))
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test_data.append(value)
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errstr = (
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"Error exceeds maximum allowed value ({0:d} decimal places)".format(
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MAX_ERR_DECIMALS))
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assert_almost_equal(
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test_data, ref_data, decimal=MAX_ERR_DECIMALS, err_msg=errstr,
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verbose=True)
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@pytest.mark.parametrize("pdb, options", [
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pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"),
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pytest.param('1HPX', [], id="1HPX: no options"),
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pytest.param('4DFR', [], id="4DFR: no options"),
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pytest.param('3SGB', [], id="3SGB: no options"),
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pytest.param('3SGB-subset', [
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"--titrate_only",
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"E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"],
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id="3SGB: --titrate_only"),
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pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")])
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def test_regression(pdb, options, tmp_path):
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"""Basic regression test of PROPKA functionality."""
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path_dict = get_test_dirs()
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ref_path = path_dict["results"] / ("{0:s}.dat".format(pdb))
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if ref_path.is_file():
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ref_path = ref_path.resolve()
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else:
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_LOGGER.warning("Missing results file for comparison: {0:s}".format(
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str(ref_path)))
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ref_path = None
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pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
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if pdb_path.is_file():
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pdb_path = pdb_path.resolve()
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else:
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errstr = "Missing PDB file: {0:s}".format(pdb_path)
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raise FileNotFoundError(errstr)
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tmp_path = Path(tmp_path).resolve()
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run_propka(options, pdb_path, tmp_path)
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if ref_path is not None:
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compare_output(pdb, tmp_path, ref_path)
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def run_propka_stream(options, input_file, tmp_path):
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"""Run PROPKA software.
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Args:
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options: list of PROPKA options
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input_file: file-like PDB object
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tmp_path: path for working directory
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"""
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options += [input_file.name]
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args = loadOptions(options)
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try:
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_LOGGER.warning(
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"Working in tmpdir {0:s} because of PROPKA file output; "
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"need to fix this.".format(str(tmp_path)))
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cwd = Path.cwd()
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os.chdir(tmp_path)
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parameters = read_parameter_file(args.parameters, Parameters())
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molecule = MolecularContainer(parameters, args)
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molecule = read_molecule_file(input_file, molecule,
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filename=input_file.name)
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molecule.calculate_pka()
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molecule.write_pka()
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if args.generate_propka_input:
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molecule.write_propka()
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finally:
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os.chdir(cwd)
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@pytest.mark.parametrize("pdb, options", [
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pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"),
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pytest.param('1HPX', [], id="1HPX: no options"),
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pytest.param('4DFR', [], id="4DFR: no options"),
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pytest.param('3SGB', [], id="3SGB: no options"),
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pytest.param('3SGB-subset', [
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"--titrate_only",
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"E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"],
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id="3SGB: --titrate_only"),
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pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")])
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def test_filestream_regression(pdb, options, tmp_path):
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"""Basic regression but using streams for the input PDB file"""
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path_dict = get_test_dirs()
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ref_path = path_dict["results"] / ("{0:s}.dat".format(pdb))
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if ref_path.is_file():
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ref_path = ref_path.resolve()
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else:
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_LOGGER.warning("Missing results file for comparison: {0:s}".format(
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str(ref_path)))
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ref_path = None
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pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
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if pdb_path.is_file():
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pdb_path = pdb_path.resolve()
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input_file = open(pdb_path)
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else:
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errstr = "Missing PDB file: {0:s}".format(pdb_path)
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raise FileNotFoundError(errstr)
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tmp_path = Path(tmp_path).resolve()
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run_propka_stream(options, input_file, tmp_path)
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if ref_path is not None:
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compare_output(pdb, tmp_path, ref_path)
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