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"""Tests for PROPKA"""
import logging
import os
import re
import json
from pathlib import Path
import pytest
from pytest import approx
from propka.parameters import Parameters
from propka.molecular_container import MolecularContainer
from propka.input import read_parameter_file, read_molecule_file
from propka.lib import loadOptions
from typing import List
_LOGGER = logging.getLogger(__name__)
# Number of decimal places for maximum tolerable error. Set by number of
# decimal places in pKa output as well as need to make unmodified code work
# on WSL Ubuntu 18.04
MAX_ERR_DECIMALS = 2
MAX_ERR_ABS = 10**-MAX_ERR_DECIMALS
# This directory
TEST_DIR = Path("tests")
# Location for test PDBs
PDB_DIR = Path("pdb")
# Location for results for comparing output (allow running from tests/ and
# ../tests/)
RESULTS_DIR = Path("tests/results")
if not RESULTS_DIR.is_dir():
_LOGGER.warning("Switching to sub-directory")
RESULTS_DIR = Path("results")
def get_test_dirs():
"""Get locations of test files.
Returns:
dictionary with test file locations.
"""
path_dict = {}
for key, path in [("pdbs", PDB_DIR), ("results", RESULTS_DIR)]:
test_path = TEST_DIR / path
if test_path.is_dir():
path_dict[key] = test_path
else:
test_path = path
if test_path.is_dir():
path_dict[key] = test_path
else:
errstr = (
"Can't find {0:s} test files in {1:s}".format(
key, [TEST_DIR / path, path]))
raise FileNotFoundError(errstr)
return path_dict
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)
cwd = Path.cwd()
try:
_LOGGER.warning(
"Working in tmpdir {0:s} because of PROPKA file output; "
"need to fix this.".format(str(tmp_path)))
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()
finally:
os.chdir(cwd)
def parse_pka(pka_path: Path) -> dict:
"""Parse testable data from a .pka file into a dictionary.
"""
pka_list: List[float] = []
data: dict = {"pKa": pka_list}
with open(pka_path, "rt") as pka_file:
at_pka = False
for line in pka_file:
if at_pka:
if line.startswith("---"):
at_pka = False
else:
m = re.search(r'\d+\.\d+', line[13:])
assert m is not None
pka_list.append(float(m.group()))
elif "model-pKa" in line:
at_pka = True
else:
m = re.match(
r"The pI is *(\d+\.\d+) .folded. and *(\d+\.\d+) .unfolded.",
line)
if m is not None:
data["pI_folded"] = float(m.group(1))
data["pI_unfolded"] = float(m.group(2))
return data
def compare_output(pdb, tmp_path, ref_path):
"""Compare results of test with reference.
Args:
pdb: PDB filename stem
tmp_path: temporary directory
ref_path: path with reference results
Raises:
ValueError if results disagree.
"""
with open(ref_path, "rt") as ref_file:
if ref_path.name.endswith(".json"):
ref_data = json.load(ref_file)
else:
ref_data = {"pKa": [float(line) for line in ref_file]}
test_data = parse_pka(tmp_path / f"{pdb}.pka")
for key in ref_data:
assert test_data[key] == approx(ref_data[key], abs=MAX_ERR_ABS), key
@pytest.mark.parametrize("pdb, options", [
pytest.param('sample-issue-140', [], id="sample-issue-140: no options"),
pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"),
pytest.param('1HPX', [], id="1HPX: no options"),
pytest.param('4DFR', [], id="4DFR: no options"),
pytest.param('3SGB', [], id="3SGB: no options"),
pytest.param('3SGB-subset', [
"--titrate_only",
"E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"],
id="3SGB: --titrate_only"),
pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet")])
def test_regression(pdb, options, tmp_path):
"""Basic regression test of PROPKA functionality."""
path_dict = get_test_dirs()
ref_path = None
for ext in ["json", "dat"]:
ref_path = path_dict["results"] / f"{pdb}.{ext}"
if ref_path.is_file():
ref_path = ref_path.resolve()
break
else:
_LOGGER.warning("Missing results file for comparison: {0:s}".format(
str(ref_path)))
ref_path = None
pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
if pdb_path.is_file():
pdb_path = pdb_path.resolve()
else:
errstr = "Missing PDB file: {0:s}".format(pdb_path)
raise FileNotFoundError(errstr)
tmp_path = Path(tmp_path).resolve()
run_propka(options, pdb_path, tmp_path)
if ref_path is not None:
compare_output(pdb, tmp_path, ref_path)
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