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"""Tests for PROPKA's run module"""
import logging
import os
from pathlib import Path
from io import StringIO
import pytest
import propka.run as pkrun
from .test_basic_regression import compare_output
from .test_streamio import get_paths
_LOGGER = logging.getLogger(__name__)
@pytest.mark.parametrize("pdb, options", [
pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: 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_single_file(tmpdir, pdb, options):
"""Basic regression test using propka.run.single and local file for the
input PDB file"""
ref_path, pdb_path = get_paths(pdb)
filename = str(pdb_path)
with tmpdir.as_cwd():
pkrun.single(filename, options)
compare_output(pdb, Path.cwd(), ref_path)
assert os.path.isfile(f'{pdb}.pka')
@pytest.mark.parametrize("pdb, options", [
pytest.param("1FTJ-Chain-A", (), id="1FTJ-Chain-A: 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_single_filestream(tmpdir, pdb, options):
"""Basic regression test using StringIO streams for the input PDB file"""
ref_path, pdb_path = get_paths(pdb)
filename = f"{pdb}.pdb"
with open(pdb_path, 'r') as writer:
filestream = StringIO(writer.read())
with tmpdir.as_cwd():
pkrun.single(filename, options, stream=filestream)
compare_output(pdb, Path.cwd(), ref_path)
assert os.path.isfile(f'{pdb}.pka')
filestream.close()
def test_single_nopka(tmpdir):
"""Basic test to check that the pKa file is not written when write_pka is
`False`"""
pdb = "1FTJ-Chain-A"
ref_path, pdb_path = get_paths(pdb)
filename = f"{pdb}.pdb"
with open(pdb_path, 'r') as writer:
filestream = StringIO(writer.read())
pkrun.single(filename, stream=filestream, write_pka=False)
assert not os.path.isfile(f"{pdb}.pka")
def test_single_extra_files_logwarn(tmpdir, caplog):
"""Tests that a logging warning is thrown if passing files via optargs"""
pdb = "1FTJ-Chain-A"
options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb')
ref_path, pdb_path = get_paths(pdb)
filename = str(pdb_path)
with tmpdir.as_cwd():
pkrun.single(filename, options)
wmsg = ("Ignoring extra filenames passed: [' foo.pdb bar.pdb', "
"' test.pdb test2.pdb']")
assert wmsg in caplog.records[0].message
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