def test_multiple_amounts():
substance = Substance()
substance.add_component(Substance.Component('[Na+]'),
Substance.MoleFraction(0.75))
substance.add_component(Substance.Component('[Na+]'),
Substance.ExactAmount(1))
substance.add_component(Substance.Component('[Cl-]'),
Substance.MoleFraction(0.25))
substance.add_component(Substance.Component('[Cl-]'),
Substance.ExactAmount(1))
assert substance.number_of_components == 2
sodium_amounts = substance.get_amounts('[Na+]')
chlorine_amounts = substance.get_amounts('[Cl-]')
assert len(sodium_amounts) == 2
assert len(chlorine_amounts) == 2
molecule_counts = substance.get_molecules_per_component(6)
assert len(molecule_counts) == 2
assert molecule_counts['[Na+]'] == 4
assert molecule_counts['[Cl-]'] == 2
def test_solvate_existing_structure_protocol():
"""Tests solvating a single methanol molecule in water."""
methanol_substance = Substance()
methanol_substance.add_component(Substance.Component('CO'),
Substance.ExactAmount(1))
water_substance = Substance()
water_substance.add_component(Substance.Component('O'),
Substance.MoleFraction(1.0))
with tempfile.TemporaryDirectory() as temporary_directory:
build_methanol_coordinates = BuildCoordinatesPackmol('build_methanol')
build_methanol_coordinates.max_molecules = 1
build_methanol_coordinates.substance = methanol_substance
build_methanol_coordinates.execute(temporary_directory,
ComputeResources())
solvate_coordinates = SolvateExistingStructure('solvate_methanol')
solvate_coordinates.max_molecules = 9
solvate_coordinates.substance = water_substance
solvate_coordinates.solute_coordinate_file = build_methanol_coordinates.coordinate_file_path
solvate_coordinates.execute(temporary_directory, ComputeResources())
solvated_pdb = PDBFile(solvate_coordinates.coordinate_file_path)
assert solvated_pdb.topology.getNumResidues() == 10
def create_substance():
test_substance = Substance()
test_substance.add_component(Substance.Component('C', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
test_substance.add_component(Substance.Component('CC', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
test_substance.add_component(Substance.Component('CCC', role=Substance.ComponentRole.Receptor),
Substance.ExactAmount(1))
test_substance.add_component(Substance.Component('O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
return test_substance
def test_build_docked_coordinates_protocol():
"""Tests docking a methanol molecule into alpha-Cyclodextrin."""
ligand_substance = Substance()
ligand_substance.add_component(
Substance.Component('CO', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
# TODO: This test could likely be made substantially faster
# by storing the binary prepared receptor. Would this
# be in breach of any oe license terms?
with tempfile.TemporaryDirectory() as temporary_directory:
build_docked_coordinates = BuildDockedCoordinates('build_methanol')
build_docked_coordinates.ligand_substance = ligand_substance
build_docked_coordinates.number_of_ligand_conformers = 5
build_docked_coordinates.receptor_coordinate_file = get_data_filename(
'test/molecules/acd.mol2')
build_docked_coordinates.execute(temporary_directory,
ComputeResources())
docked_pdb = PDBFile(
build_docked_coordinates.docked_complex_coordinate_path)
assert docked_pdb.topology.getNumResidues() == 2
def test_ligand_receptor_yank_protocol():
full_substance = Substance()
full_substance.add_component(
Substance.Component(smiles='c1ccccc1',
role=Substance.ComponentRole.Receptor),
Substance.ExactAmount(1))
full_substance.add_component(
Substance.Component(smiles='C', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
full_substance.add_component(
Substance.Component(smiles='O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
solute_substance = Substance()
solute_substance.add_component(
Substance.Component(smiles='C', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
solute_substance.add_component(
Substance.Component(smiles='O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
thermodynamic_state = ThermodynamicState(temperature=298.15 * unit.kelvin,
pressure=1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
with temporarily_change_directory(directory):
force_field_path = 'ff.json'
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
complex_coordinate_path, complex_system_path = _setup_dummy_system(
'full', full_substance, 3, force_field_path)
ligand_coordinate_path, ligand_system_path = _setup_dummy_system(
'ligand', solute_substance, 2, force_field_path)
run_yank = LigandReceptorYankProtocol('yank')
run_yank.substance = full_substance
run_yank.thermodynamic_state = thermodynamic_state
run_yank.number_of_iterations = 1
run_yank.steps_per_iteration = 1
run_yank.checkpoint_interval = 1
run_yank.verbose = True
run_yank.setup_only = True
run_yank.ligand_residue_name = 'TMP'
run_yank.receptor_residue_name = 'TMP'
run_yank.solvated_ligand_coordinates = ligand_coordinate_path
run_yank.solvated_ligand_system = ligand_system_path
run_yank.solvated_complex_coordinates = complex_coordinate_path
run_yank.solvated_complex_system = complex_system_path
run_yank.force_field_path = force_field_path
result = run_yank.execute('', ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
def test_solvation_yank_protocol(solvent_smiles):
full_substance = Substance()
full_substance.add_component(
Substance.Component(smiles='CO', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
full_substance.add_component(
Substance.Component(smiles=solvent_smiles,
role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
solvent_substance = Substance()
solvent_substance.add_component(
Substance.Component(smiles=solvent_smiles,
role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
solute_substance = Substance()
solute_substance.add_component(
Substance.Component(smiles='CO', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
thermodynamic_state = ThermodynamicState(temperature=298.15 * unit.kelvin,
pressure=1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
with temporarily_change_directory(directory):
force_field_path = 'ff.json'
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
solvated_coordinate_path, solvated_system_path = _setup_dummy_system(
'full', full_substance, 2, force_field_path)
vacuum_coordinate_path, vacuum_system_path = _setup_dummy_system(
'vacuum', solute_substance, 1, force_field_path)
run_yank = SolvationYankProtocol('yank')
run_yank.solute = solute_substance
run_yank.solvent_1 = solvent_substance
run_yank.solvent_2 = Substance()
run_yank.thermodynamic_state = thermodynamic_state
run_yank.number_of_iterations = 1
run_yank.steps_per_iteration = 1
run_yank.checkpoint_interval = 1
run_yank.verbose = True
run_yank.setup_only = True
run_yank.solvent_1_coordinates = solvated_coordinate_path
run_yank.solvent_1_system = solvated_system_path
run_yank.solvent_2_coordinates = vacuum_coordinate_path
run_yank.solvent_2_system = vacuum_system_path
run_yank.electrostatic_lambdas_1 = [1.00]
run_yank.steric_lambdas_1 = [1.00]
run_yank.electrostatic_lambdas_2 = [1.00]
run_yank.steric_lambdas_2 = [1.00]
result = run_yank.execute('', ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
def _create_data_set():
"""Create a small data set of three properties taken from the
FreeSolv data set: https://github.com/mobleylab/FreeSolv.
Returns
-------
PhysicalPropertyDataSet
The data set of three select FreeSolv properties.
"""
butan_1_ol = Substance()
butan_1_ol.add_component(
Substance.Component('CCCCO', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
butan_1_ol.add_component(
Substance.Component('O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
butan_1_ol_property = SolvationFreeEnergy(
thermodynamic_state=ThermodynamicState(298.15 * unit.kelvin,
1.0 * unit.atmosphere),
phase=PropertyPhase.Liquid,
substance=butan_1_ol,
value=-4.72 * unit.kilocalorie / unit.mole,
uncertainty=0.6 * unit.kilocalorie / unit.mole,
source=MeasurementSource(doi=' 10.1021/ct050097l'))
methyl_propanoate = Substance()
methyl_propanoate.add_component(
Substance.Component('CCC(=O)OC', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
methyl_propanoate.add_component(
Substance.Component('O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
methyl_propanoate_property = SolvationFreeEnergy(
thermodynamic_state=ThermodynamicState(298.15 * unit.kelvin,
1.0 * unit.atmosphere),
phase=PropertyPhase.Liquid,
substance=methyl_propanoate,
value=-2.93 * unit.kilocalorie / unit.mole,
uncertainty=0.6 * unit.kilocalorie / unit.mole,
source=MeasurementSource(doi=' 10.1021/ct050097l'))
benzamide = Substance()
benzamide.add_component(
Substance.Component('c1ccc(cc1)C(=O)N',
role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
benzamide.add_component(
Substance.Component('O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
benzamide_property = SolvationFreeEnergy(
thermodynamic_state=ThermodynamicState(298.15 * unit.kelvin,
1.0 * unit.atmosphere),
phase=PropertyPhase.Liquid,
substance=benzamide,
value=-11.0 * unit.kilocalorie / unit.mole,
uncertainty=0.2 * unit.kilocalorie / unit.mole,
source=MeasurementSource(doi=' 10.1021/ct050097l'))
data_set = PhysicalPropertyDataSet()
data_set.properties[butan_1_ol.identifier] = [butan_1_ol_property]
data_set.properties[methyl_propanoate.identifier] = [
methyl_propanoate_property
]
data_set.properties[benzamide.identifier] = [benzamide_property]
return data_set