109 lines
3.5 KiB
Python
109 lines
3.5 KiB
Python
"""Tests for PROPKA stream io"""
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import logging
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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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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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from .test_basic_regression import get_test_dirs, compare_output
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_LOGGER = logging.getLogger(__name__)
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def get_paths(pdb):
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"""Helper function to get the path to the input and reference files"""
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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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pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
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return ref_path.resolve(), pdb_path.resolve()
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def run_propka_stream(options, input_file, filename):
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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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filename: filename for the file-like PDB object
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tmp_path: path for working directory
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"""
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options += [filename]
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args = loadOptions(options)
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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, filename)
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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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@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_textio_filestream(tmpdir, pdb, options):
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"""Basic regression test using TextIO streams for the input PDB file"""
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# Get the relevant paths
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ref_path, pdb_path = get_paths(pdb)
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filename = f"{pdb}.pdb"
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filestream = open(pdb_path, 'r')
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with tmpdir.as_cwd():
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run_propka_stream(options, filestream, filename)
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compare_output(pdb, Path.cwd(), ref_path)
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filestream.close()
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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_stringio_filestream(tmpdir, pdb, options):
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"""Basic regression test using StringIO streams for the input PDB file"""
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# Get the relevant paths
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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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run_propka_stream(options, filestream, filename)
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compare_output(pdb, Path.cwd(), ref_path)
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filestream.close()
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def test_typerror_nofilename(tmpdir):
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"""Tests for raised TypeError when not passing a filename to
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read_molecule_file and using a file-like object without a name"""
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pdb = "1FTJ-Chain-A"
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options = []
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ref_path, pdb_path = get_paths(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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errmsg = "Path of provided input_file could not be determined"
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with pytest.raises(TypeError, match=errmsg):
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# default value of filename is None
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run_propka_stream(options, filestream, filename=None)
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