def _setup_dummy_system(directory):
"""Generate a temporary parameterized system object."""
force_field_path = path.join(directory, "ff.json")
with open(force_field_path, "w") as file:
file.write(build_tip3p_smirnoff_force_field().json())
substance = Substance.from_components("O")
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 10
build_coordinates.mass_density = 0.05 * unit.grams / unit.milliliters
build_coordinates.substance = substance
build_coordinates.execute(directory)
assign_parameters = BuildSmirnoffSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory)
return (
build_coordinates.coordinate_file_path,
assign_parameters.parameterized_system,
)
def test_solvate_existing_structure_protocol():
"""Tests solvating a single methanol molecule in water."""
import mdtraj
methanol_component = Component("CO")
methanol_substance = Substance()
methanol_substance.add_component(methanol_component, ExactAmount(1))
water_substance = Substance()
water_substance.add_component(Component("O"), 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())
methanol_residue_name = build_methanol_coordinates.assigned_residue_names[
methanol_component.identifier]
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_system = mdtraj.load_pdb(
solvate_coordinates.coordinate_file_path)
assert solvated_system.n_residues == 10
assert solvated_system.top.residue(0).name == methanol_residue_name
def test_calculate_reduced_potential_openmm():
substance = Substance.from_components("O")
thermodynamic_state = ThermodynamicState(298 * unit.kelvin,
1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
force_field_path = path.join(directory, "ff.json")
with open(force_field_path, "w") as file:
file.write(build_tip3p_smirnoff_force_field().json())
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 10
build_coordinates.mass_density = 0.05 * unit.grams / unit.milliliters
build_coordinates.substance = substance
build_coordinates.execute(directory, None)
assign_parameters = BuildSmirnoffSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory, None)
reduced_potentials = OpenMMReducedPotentials("reduced_potentials")
reduced_potentials.substance = substance
reduced_potentials.thermodynamic_state = thermodynamic_state
reduced_potentials.reference_force_field_paths = [force_field_path]
reduced_potentials.system_path = assign_parameters.system_path
reduced_potentials.trajectory_file_path = get_data_filename(
"test/trajectories/water.dcd")
reduced_potentials.coordinate_file_path = get_data_filename(
"test/trajectories/water.pdb")
reduced_potentials.kinetic_energies_path = get_data_filename(
"test/statistics/stats_pandas.csv")
reduced_potentials.high_precision = False
reduced_potentials.execute(directory, ComputeResources())
assert path.isfile(reduced_potentials.statistics_file_path)
final_array = StatisticsArray.from_pandas_csv(
reduced_potentials.statistics_file_path)
assert ObservableType.ReducedPotential in final_array
def _setup_dummy_system(directory, substance, number_of_molecules,
force_field_path):
os.makedirs(directory, exist_ok=True)
build_coordinates = BuildCoordinatesPackmol("coordinates")
build_coordinates.substance = substance
build_coordinates.max_molecules = number_of_molecules
build_coordinates.execute(directory, None)
assign_parameters = BuildSmirnoffSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory, None)
return build_coordinates.coordinate_file_path, assign_parameters.system_path
def test_build_coordinates_packmol_exact(count_exact_amount):
"""Tests that the build coordinate protocol behaves correctly for substances
with exact amounts."""
import mdtraj
substance = Substance()
substance.add_component(Component("O"), MoleFraction(1.0))
substance.add_component(Component("C"), ExactAmount(1))
max_molecule = 11 if count_exact_amount else 10
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = max_molecule
build_coordinates.count_exact_amount = count_exact_amount
build_coordinates.substance = substance
with tempfile.TemporaryDirectory() as directory:
build_coordinates.execute(directory)
built_system = mdtraj.load_pdb(build_coordinates.coordinate_file_path)
assert built_system.n_residues == 11
def test_build_coordinates_packmol(input_substance, expected):
"""Tests that the build coordinate protocols correctly report
the composition of the built system."""
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 10
build_coordinates.substance = input_substance
with tempfile.TemporaryDirectory() as directory:
build_coordinates.execute(directory)
assert build_coordinates.output_substance == expected
for component in input_substance:
assert component.identifier in build_coordinates.assigned_residue_names
if component.smiles == "O":
assigned_name = build_coordinates.assigned_residue_names[
component.identifier]
assert assigned_name[:3] == "HOH"
def test_build_tleap_system():
with tempfile.TemporaryDirectory() as directory:
force_field_path = path.join(directory, "ff.json")
with open(force_field_path, "w") as file:
file.write(TLeapForceFieldSource().json())
substance = Substance.from_components("CCCCCCCC", "O", "C(=O)N")
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 9
build_coordinates.substance = substance
build_coordinates.execute(directory, None)
assign_parameters = BuildTLeapSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory, None)
assert path.isfile(assign_parameters.system_path)
def test_build_smirnoff_system():
with tempfile.TemporaryDirectory() as directory:
force_field_path = path.join(directory, "ff.json")
with open(force_field_path, "w") as file:
file.write(build_tip3p_smirnoff_force_field().json())
substance = Substance.from_components("C", "O", "CO", "C(=O)N")
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 8
build_coordinates.substance = substance
build_coordinates.execute(directory)
assign_parameters = BuildSmirnoffSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory)
assert path.isfile(assign_parameters.parameterized_system.system_path)
def test_build_ligpargen_system(requests_mock):
force_field_source = LigParGenForceFieldSource(
request_url="http://testligpargen.com/request",
download_url="http://testligpargen.com/download",
)
substance = Substance.from_components("C", "O")
def request_callback(request, context):
context.status_code = 200
smiles = re.search(r'"smiData"\r\n\r\n(.*?)\r\n',
request.text).group(1)
cmiles_molecule = load_molecule(smiles, toolkit="rdkit")
smiles = mol_to_smiles(cmiles_molecule,
isomeric=False,
explicit_hydrogen=False,
mapped=False)
assert smiles == "C"
return 'value="/tmp/0000.xml"'
def download_callback(_, context):
context.status_code = 200
return """
<ForceField>
<AtomTypes>
<Type name="opls_802" class="H802" element="H" mass="1.008000" />
<Type name="opls_804" class="H804" element="H" mass="1.008000" />
<Type name="opls_803" class="H803" element="H" mass="1.008000" />
<Type name="opls_800" class="C800" element="C" mass="12.011000" />
<Type name="opls_801" class="H801" element="H" mass="1.008000" />
</AtomTypes>
<Residues>
<Residue name="UNK">
<Atom name="C00" type="opls_800" />
<Atom name="H01" type="opls_801" />
<Atom name="H02" type="opls_802" />
<Atom name="H03" type="opls_803" />
<Atom name="H04" type="opls_804" />
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<Bond from="0" to="3"/>
<Bond from="0" to="4"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="H801" class2="C800" length="0.109000" k="284512.000000"/>
<Bond class1="H802" class2="C800" length="0.109000" k="284512.000000"/>
<Bond class1="H803" class2="C800" length="0.109000" k="284512.000000"/>
<Bond class1="H804" class2="C800" length="0.109000" k="284512.000000"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle class1="H801" class2="C800" class3="H802" angle="1.881465" k="276.144000"/>
<Angle class1="H801" class2="C800" class3="H803" angle="1.881465" k="276.144000"/>
<Angle class1="H801" class2="C800" class3="H804" angle="1.881465" k="276.144000"/>
<Angle class1="H802" class2="C800" class3="H803" angle="1.881465" k="276.144000"/>
<Angle class1="H803" class2="C800" class3="H804" angle="1.881465" k="276.144000"/>
<Angle class1="H802" class2="C800" class3="H804" angle="1.881465" k="276.144000"/>
</HarmonicAngleForce>
<PeriodicTorsionForce>
<Improper class1="C800" class2="H801" class3="H802" class4="H803" k1="0.000000" k2="0.000000" k3="0.000000"
k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00"
phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>
<Improper class1="C800" class2="H801" class3="H802" class4="H804" k1="0.000000" k2="0.000000" k3="0.000000"
k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00"
phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>
</PeriodicTorsionForce>
<NonbondedForce coulomb14scale="0.5" lj14scale="0.5">
<Atom type="opls_803" charge="0.074800" sigma="0.250000" epsilon="0.125520" />
<Atom type="opls_802" charge="0.074800" sigma="0.250000" epsilon="0.125520" />
<Atom type="opls_800" charge="-0.299400" sigma="0.350000" epsilon="0.276144" />
<Atom type="opls_804" charge="0.074800" sigma="0.250000" epsilon="0.125520" />
<Atom type="opls_801" charge="0.074800" sigma="0.250000" epsilon="0.125520" />
</NonbondedForce>
</ForceField>
"""
requests_mock.post(force_field_source.request_url, text=request_callback)
requests_mock.post(force_field_source.download_url, text=download_callback)
with tempfile.TemporaryDirectory() as directory:
force_field_path = path.join(directory, "ff.json")
with open(force_field_path, "w") as file:
file.write(force_field_source.json())
build_coordinates = BuildCoordinatesPackmol("build_coordinates")
build_coordinates.max_molecules = 8
build_coordinates.substance = substance
build_coordinates.execute(directory, None)
assign_parameters = BuildLigParGenSystem("assign_parameters")
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory, None)
assert path.isfile(assign_parameters.system_path)