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from propka.input import read_parameter_file, read_molecule_file
from propka.lib import loadOptions
from propka.molecular_container import MolecularContainer
from propka.parameters import Parameters
from pathlib import Path
from pytest import approx
TESTS = Path(__file__).resolve().parent
def load_molecule(code):
pdb_path = TESTS / f"pdb/{code}.pdb"
options = [str(pdb_path)]
args = loadOptions(options)
parameters = read_parameter_file(args.parameters, Parameters())
molecule = MolecularContainer(parameters, args)
molecule = read_molecule_file(str(pdb_path), molecule)
return molecule
def test_MolecularContainer_get_pi():
molecule = load_molecule("1HPX")
molecule.average_of_conformations()
molecule.calculate_pka()
pi_folded, pi_unfolded = molecule.get_pi()
assert pi_folded == approx(9.54, abs=1e-2)
assert pi_unfolded == approx(8.90, abs=1e-2)
def test_MolecularContainer_top_up_conformations():
molecule = load_molecule("conf-alt-AB")
assert len(molecule.conformations) == 2
assert len(molecule.conformations["1A"]) == 16
assert len(molecule.conformations["1B"]) == 16
molecule = load_molecule("conf-alt-BC")
assert len(molecule.conformations) == 3
assert len(molecule.conformations["1A"]) == 16
assert len(molecule.conformations["1B"]) == 16
assert len(molecule.conformations["1C"]) == 16
molecule = load_molecule("conf-alt-AB-mutant")
assert len(molecule.conformations) == 2
assert len(molecule.conformations["1A"]) == 16
assert len(molecule.conformations["1B"]) == 17
molecule = load_molecule("conf-model-mutant")
assert len(molecule.conformations) == 2
assert len(molecule.conformations["1A"]) == 16
assert len(molecule.conformations["2A"]) == 17
molecule = load_molecule("conf-model-missing-atoms")
assert len(molecule.conformations) == 3
assert len(molecule.conformations["1A"]) == 17
assert len(molecule.conformations["2A"]) == 17
assert len(molecule.conformations["3A"]) == 17
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