7563a706cf
* Fixes #82 * Changes: * input arguments now reflects the changes made to read_molecule_file in #84 * Writing of pKa file is now optional (default behaviour has been kept). This will be particularly useful downstream where we would just want to have access to the MoleculeContainer object. * new test_run file specific for testing run. * add tests * add docs
102 lines
3.2 KiB
Python
102 lines
3.2 KiB
Python
"""Tests for PROPKA's run module"""
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import logging
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import os
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from pathlib import Path
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from io import StringIO
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import pytest
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import propka.run as pkrun
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from .test_basic_regression import compare_output
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from .test_streamio import get_paths
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_LOGGER = logging.getLogger(__name__)
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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('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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])
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def test_single_file(tmpdir, pdb, options):
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"""Basic regression test using propka.run.single and local file for the
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input PDB file"""
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ref_path, pdb_path = get_paths(pdb)
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filename = str(pdb_path)
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with tmpdir.as_cwd():
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pkrun.single(filename, options)
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compare_output(pdb, Path.cwd(), ref_path)
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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('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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])
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def test_single_filestream(tmpdir, pdb, options):
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"""Basic regression test using StringIO streams for the input PDB file"""
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ref_path, pdb_path = get_paths(pdb)
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filename = f"{pdb}.pdb"
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with open(pdb_path, 'r') as writer:
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filestream = StringIO(writer.read())
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with tmpdir.as_cwd():
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pkrun.single(filename, options, stream=filestream)
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compare_output(pdb, Path.cwd(), ref_path)
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filestream.close()
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def test_single_nopka(tmpdir):
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"""Basic test to check that the pKa file is not written when write_pka is
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`False`"""
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pdb = "1FTJ-Chain-A"
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ref_path, pdb_path = get_paths(pdb)
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filename = f"{pdb}.pdb"
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with open(pdb_path, 'r') as writer:
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filestream = StringIO(writer.read())
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pkrun.single(filename, stream=filestream, write_pka=False)
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assert not os.path.isfile(f"{pdb}.pka")
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def test_single_propka_input(tmpdir):
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"""Basic test to check that the propka_input file is written when
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`--generate-propka-input` is passed"""
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pdb = "1FTJ-Chain-A"
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options = ('--generate-propka-input',)
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ref_path, pdb_path = get_paths(pdb)
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filename = f"{pdb}.pdb"
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with open(pdb_path, 'r') as writer:
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filestream = StringIO(writer.read())
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with tmpdir.as_cwd():
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pkrun.single(filename, options, stream=filestream)
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assert os.path.isfile(f"{pdb}.propka_input")
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def test_single_extra_files_logwarn(tmpdir, caplog):
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"""Tests that a logging warning is thrown if passing files via optargs"""
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pdb = "1FTJ-Chain-A"
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options = ('-f foo.pdb bar.pdb', '-f test.pdb test2.pdb',
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'--generate-propka-input')
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ref_path, pdb_path = get_paths(pdb)
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filename = str(pdb_path)
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with tmpdir.as_cwd():
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pkrun.single(filename, options)
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wmsg = ("Ignoring extra filenames passed: [' foo.pdb bar.pdb', "
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"' test.pdb test2.pdb']")
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assert wmsg in caplog.records[0].message
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