def test_forcefields(args, input_pdb, output_pqr, expected_pqr, tmp_path):
"""Basic code to run 1AFS with --whitespace for different forcefields."""
common.run_pdb2pqr(
args=args,
input_pdb=input_pdb,
output_pqr=output_pqr,
expected_pqr=expected_pqr,
tmp_path=tmp_path,
)
def test_other_options(args, input_pdb, output_pqr, expected_pqr, tmp_path):
"""Basic code to run 1AFS with --whitespace."""
common.run_pdb2pqr(
args=args,
input_pdb=input_pdb,
output_pqr=output_pqr,
expected_pqr=expected_pqr,
tmp_path=tmp_path,
)
def test_basic(args, input_pdb, output_pqr, expected_pqr, tmp_path):
"""Basic code to run 1AFS."""
common.run_pdb2pqr(
args=args,
input_pdb=input_pdb,
output_pqr=output_pqr,
expected_pqr=expected_pqr,
tmp_path=tmp_path,
)
def test_broken_backbone(input_pdb, tmp_path):
"""Test graceful failure of optimization with missing backbone atoms."""
args = "--log-level=INFO --ff=AMBER --drop-water"
output_pqr = Path(input_pdb).stem + ".pqr"
common.run_pdb2pqr(
args=args,
input_pdb=input_pdb,
output_pqr=output_pqr,
tmp_path=tmp_path,
)
def test_basic_cif(input_pdb, tmp_path):
"""Non-regression tests on CIF-format biomolecules without ligands."""
args = "--log-level=INFO --ff=AMBER --drop-water --apbs-input=apbs.in"
output_pqr = Path(input_pdb).stem + ".cif"
common.run_pdb2pqr(
args=args,
input_pdb=input_pdb,
output_pqr=output_pqr,
tmp_path=tmp_path,
)
def test_propka_apo(input_pdb, tmp_path):
"""PROPKA non-regression tests on biomolecules without ligands."""
args = ("--log-level=INFO --ff=AMBER --drop-water "
"--titration-state-method=propka")
output_pqr = Path(input_pdb).stem + ".pqr"
common.run_pdb2pqr(
args=args,
input_pdb=input_pdb,
output_pqr=output_pqr,
tmp_path=tmp_path,
)
def test_ligand_biomolecule(input_pdb, tmp_path):
"""PROPKA non-regression tests on biomolecules without ligands."""
input_pdb = Path(input_pdb)
ligand = Path("tests/data") / f"{input_pdb.stem}-ligand.mol2"
args = f"--log-level=INFO --ff=AMBER --drop-water --ligand={ligand}"
output_pqr = Path(input_pdb).stem + ".pqr"
_LOGGER.debug(f"Running test in {tmp_path}")
common.run_pdb2pqr(
args=args,
input_pdb=input_pdb,
output_pqr=output_pqr,
tmp_path=tmp_path,
)
def test_log_output_in_pqr_location(
capture, input_file, output_file, tmp_path
):
"""Test that a log file is generated when calling the __init__.py"""
args = "--log-level=INFO --ff=AMBER"
input_path = common.DATA_DIR / input_file
output_pqr = output_file
common.run_pdb2pqr(
args=args,
input_pdb=input_path,
output_pqr=output_pqr,
tmp_path=tmp_path,
)
# This match tests that the log file is output to the same location
# as the output pqr
capture.check_present(
(
"pdb2pqr.io",
"INFO",
f'Logs stored: {tmp_path / output_file.split(".")[0]}.log',
)
)