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"""Tests for PROPKA stream io"""
import logging
from pathlib import Path
from io import StringIO
import pytest
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 .test_basic_regression import get_test_dirs, compare_output
_LOGGER = logging.getLogger(__name__)
def get_paths(pdb):
"""Helper function to get the path to the input and reference files"""
path_dict = get_test_dirs()
ref_path = path_dict["results"] / ("{0:s}.dat".format(pdb))
pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
return ref_path.resolve(), pdb_path.resolve()
def run_propka_stream(options, input_file, filename):
"""Run PROPKA software.
Args:
options: list of PROPKA options
input_file: file-like PDB object
filename: filename for the file-like PDB object
"""
options += [filename]
args = loadOptions(options)
parameters = read_parameter_file(args.parameters, Parameters())
molecule = MolecularContainer(parameters, args)
molecule = read_molecule_file(filename, molecule, stream=input_file)
molecule.calculate_pka()
molecule.write_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_textio_filestream(tmpdir, pdb, options):
"""Basic regression test using TextIO streams for the input PDB file"""
# Get the relevant paths
ref_path, pdb_path = get_paths(pdb)
filename = f"{pdb}.pdb"
filestream = open(pdb_path, 'r')
with tmpdir.as_cwd():
run_propka_stream(options, filestream, filename)
compare_output(pdb, Path.cwd(), ref_path)
filestream.close()
@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_stringio_filestream(tmpdir, pdb, options):
"""Basic regression test using StringIO streams for the input PDB file"""
# Get the relevant paths
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():
run_propka_stream(options, filestream, filename)
compare_output(pdb, Path.cwd(), ref_path)
filestream.close()
def test_valuerror_nofiletype():
"""Tests for raised ValueError when an unknown filename is passed to
read_molecule_file"""
pdb = "1FTJ-Chain-A"
options = []
ref_path, pdb_path = get_paths(pdb)
with open(pdb_path, 'r') as writer:
filestream = StringIO(writer.read())
errmsg = "Unknown input file type"
with pytest.raises(ValueError, match=errmsg):
run_propka_stream(options, filestream, filename="test.dat")
def test_valuerror_notpdb():
"""Tests for raised ValueError when a stream object that isn't a PDB
is passed to read_molecule_file"""
pdb = "1FTJ-Chain-A"
options = []
ref_path, pdb_path = get_paths(pdb)
filestream = StringIO()
errmsg = "The pdb file does not seem to contain any "
with pytest.raises(ValueError, match=errmsg):
run_propka_stream(options, filestream, filename="test.pdb")
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