7d78acac6e
Top up from all conformations, not just first. Fixes https://github.com/jensengroup/propka/issues/147
57 lines
2.0 KiB
Python
57 lines
2.0 KiB
Python
from propka.input import read_parameter_file, read_molecule_file
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from propka.lib import loadOptions
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from propka.molecular_container import MolecularContainer
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from propka.parameters import Parameters
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from pathlib import Path
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from pytest import approx
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TESTS = Path(__file__).resolve().parent
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def load_molecule(code):
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pdb_path = TESTS / f"pdb/{code}.pdb"
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options = [str(pdb_path)]
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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(str(pdb_path), molecule)
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return molecule
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def test_MolecularContainer_get_pi():
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molecule = load_molecule("1HPX")
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molecule.average_of_conformations()
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molecule.calculate_pka()
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pi_folded, pi_unfolded = molecule.get_pi()
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assert pi_folded == approx(9.54, abs=1e-2)
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assert pi_unfolded == approx(8.90, abs=1e-2)
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def test_MolecularContainer_top_up_conformations():
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molecule = load_molecule("conf-alt-AB")
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assert len(molecule.conformations) == 2
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assert len(molecule.conformations["1A"]) == 16
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assert len(molecule.conformations["1B"]) == 16
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molecule = load_molecule("conf-alt-BC")
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assert len(molecule.conformations) == 3
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assert len(molecule.conformations["1A"]) == 16
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assert len(molecule.conformations["1B"]) == 16
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assert len(molecule.conformations["1C"]) == 16
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molecule = load_molecule("conf-alt-AB-mutant")
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assert len(molecule.conformations) == 2
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assert len(molecule.conformations["1A"]) == 16
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assert len(molecule.conformations["1B"]) == 17
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molecule = load_molecule("conf-model-mutant")
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assert len(molecule.conformations) == 2
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assert len(molecule.conformations["1A"]) == 16
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assert len(molecule.conformations["2A"]) == 17
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molecule = load_molecule("conf-model-missing-atoms")
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assert len(molecule.conformations) == 3
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assert len(molecule.conformations["1A"]) == 17
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assert len(molecule.conformations["2A"]) == 17
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assert len(molecule.conformations["3A"]) == 17
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