def test_set_docker_python(tempconfigfile):
njob = mdt._njobs
g1 = mdt.from_smiles('CC')
assert mdt._njobs == njob
mdt.compute.update_saved_config(run_remote={'openbabel':True})
clean_config()
g2 = mdt.from_smiles('CC')
assert mdt._njobs == njob + 1
def test_degrees_of_freedom_with_constraints(benzene, h2):
water = mdt.from_smiles('[OH2]')
water.residues[0].resname = 'HOH'
benzene.residues[0].resname = 'UNL'
h2.residues[0].resname = 'H2'
mol = benzene.combine(h2, water, water)
assert mol.num_atoms == 20 # assert I can count
assert mol.dynamic_dof == 3 * mol.num_atoms
full_dof = mol.dynamic_dof
def _constrain_direction():
c = mdt.geom.constraints.FixedCoordinate(mol.atoms[0], np.array([0.0, 0, 1.0]))
mol.constraints.append(c)
for constrainer, num_dof, args in ((mol.constrain_distance, 1, mol.atoms[:2]),
(mol.constrain_angle, 1, mol.atoms[:3]),
(mol.constrain_dihedral, 1, mol.atoms[:4]),
(mol.constrain_atom, 3, mol.atoms[:1]),
(mol.constrain_hbonds, 11, [True]),
(_constrain_direction, 1, [])):
constrainer(*args)
assert mol.dynamic_dof == full_dof-num_dof
mol.clear_constraints()
assert mol.dynamic_dof == full_dof
def test_constrained_dihedral_minimization(minkey):
minimizer = MINIMIZERS[minkey]
mol = mdt.from_smiles('C=C')
assert mol.atoms[0].atnum == mol.atoms[
1].atnum == 6 # make sure we're picking the right atoms
dihedral = mdt.DihedralMonitor(mol.atoms[0], mol.atoms[1])
assert dihedral.value == 0.0
dihedral.value = 45 * u.degrees
constraint = dihedral.constrain()
mol.set_energy_model(mdt.models.OpenBabelPotential, forcefield='mmff94s')
e0_1 = mol.calculate_potential_energy()
p0_1 = mol.positions.copy()
if minkey == 'bfgs': # BFGS expected to fail here
with pytest.raises(mdt.exceptions.NotSupportedError):
minimizer(mol)
return
traj = minimizer(mol, nsteps=100)
assert_something_resembling_minimization_happened(p0_1, e0_1, traj, mol)
assert constraint.error() <= 1.0 * u.degree
traj_twists = traj.dihedral(mol.atoms[0], mol.atoms[1])
assert (abs(traj_twists - 45 * u.degrees) <= 1.0 * u.degree).all()
e0_2 = mol.potential_energy
p0_2 = mol.positions.copy()
mol.clear_constraints()
traj2 = minimizer(mol, nsteps=100)
assert_something_resembling_minimization_happened(p0_2, e0_2, traj2, mol)
assert dihedral.value <= 5.0 * u.degrees
def test_constrained_dihedral_minimization(minkey):
minimizer = MINIMIZERS[minkey]
mol = mdt.from_smiles('C=C')
assert mol.atoms[0].atnum == mol.atoms[1].atnum == 6 # make sure we're picking the right atoms
dihedral = mdt.DihedralMonitor(mol.atoms[0], mol.atoms[1])
assert dihedral.value == 0.0
dihedral.value = 45 * u.degrees
constraint = dihedral.constrain()
mol.set_energy_model(mdt.models.OpenBabelPotential, forcefield='mmff94s')
e0_1 = mol.calculate_potential_energy()
p0_1 = mol.positions.copy()
if minkey == 'bfgs': # BFGS expected to fail here
with pytest.raises(mdt.exceptions.NotSupportedError):
minimizer(mol)
return
traj = minimizer(mol, nsteps=100)
assert_something_resembling_minimization_happened(p0_1, e0_1, traj, mol)
assert constraint.error() <= 1.0 * u.degree
traj_twists = traj.dihedral(mol.atoms[0], mol.atoms[1])
assert (abs(traj_twists - 45 * u.degrees) <= 1.0 * u.degree).all()
e0_2 = mol.potential_energy
p0_2 = mol.positions.copy()
mol.clear_constraints()
traj2 = minimizer(mol, nsteps=100)
assert_something_resembling_minimization_happened(p0_2, e0_2, traj2, mol)
assert dihedral.value <= 5.0 * u.degrees
def h2params():
mol = mdt.from_smiles('[H][H]')
mol.atoms[0].name = 'HA'
mol.atoms[1].name = 'HB'
mol.residues[0].name = 'H2'
params = mdt.create_ff_parameters(mol, charges='gasteiger')
return mol, params
def scrambled():
mol = mdt.from_smiles('C=C')
mol.set_energy_model(mdt.models.OpenBabelPotential, forcefield='mmff94s')
mol.com = [0, 0, 0] * u.angstrom
_apply_noise(mol, scale=5.0)
e0 = mol.calculate_potential_energy()
p0 = mol.positions.copy()
return mol, e0, p0
def h2params():
mol = mdt.from_smiles('[H][H]')
mol.atoms[0].name = 'HA'
mol.atoms[1].name = 'HB'
mol.residues[0].name = 'H2'
params = mdt.create_ff_parameters(mol, charges='gasteiger')
return mol, params
def scrambled():
mol = mdt.from_smiles('C=C')
mol.set_energy_model(mdt.models.OpenBabelPotential, forcefield='mmff94s')
mol.com = [0, 0, 0] * u.angstrom
_apply_noise(mol, scale=5.0)
e0 = mol.calculate_potential_energy()
p0 = mol.positions.copy()
return mol, e0, p0
def test_parameterize_multiple_identical_small_molecules():
m1 = mdt.from_smiles('O')
params = mdt.create_ff_parameters(m1, charges='am1-bcc')
assert params is not None
m2 = m1.copy()
m2.translate([4.0, 0.0, 0.0] * mdt.units.angstrom)
mol = m1.combine(m2)
ff = mdt.forcefields.DefaultAmber()
ff.add_ff(params)
ff.assign(mol)
_test_succesful_parameterization(mol)
def test_parameterize_multiple_identical_small_molecules():
m1 = mdt.from_smiles('O')
params = mdt.create_ff_parameters(m1, charges='am1-bcc')
assert params is not None
m2 = m1.copy()
m2.translate([4.0, 0.0, 0.0] * mdt.units.angstrom)
mol = m1.combine(m2)
ff = mdt.forcefields.DefaultAmber()
ff.add_ff(params)
ff.assign(mol)
_test_succesful_parameterization(mol)
def test_pmi_reorientation_on_linear_molecule():
# note that this will fail if the generated polymer is not perfectly linear
mol = mdt.from_smiles('C#CC#CC#C')
original_distmat = mol.calc_distance_array().defunits_value()
for i in range(5):
_randomize_orientation(mol)
# calculate PMI and reorient
pmi = geom.alignment.PrincipalMomentsOfInertia(mol)
pmi.reorient(mol)
# Check that everything lies along the z-axis
np.testing.assert_allclose(mol.positions[:, :2], 0.0, atol=1e-12)
# Check that distance matrix was unchanged under the transformation
newdistmat = mol.calc_distance_array()
np.testing.assert_allclose(newdistmat.defunits_value(),
original_distmat)
def test_pmi_reorientation_on_linear_molecule():
# note that this will fail if the generated polymer is not perfectly linear
mol = mdt.from_smiles('C#CC#CC#C')
original_distmat = mol.calc_distance_array().defunits_value()
for i in range(5):
_randomize_orientation(mol)
# calculate PMI and reorient
pmi = geom.alignment.PrincipalMomentsOfInertia(mol)
pmi.reorient(mol)
# Check that everything lies along the z-axis
np.testing.assert_allclose(mol.positions[:,:2], 0.0, atol=1e-12)
# Check that distance matrix was unchanged under the transformation
newdistmat = mol.calc_distance_array()
np.testing.assert_allclose(newdistmat.defunits_value(),
original_distmat)
def test_degrees_of_freedom_with_integrator_constraints(benzene):
water = mdt.from_smiles('[OH2]')
water.residues[0].resname = 'HOH'
mol = benzene.combine(water)
full_dof = mol.dynamic_dof
assert full_dof == 3 * mol.num_atoms
mol.set_energy_model(mdt.models.OpenMMPotential)
mol.set_integrator(mdt.integrators.OpenMMLangevin)
mol.integrator.params.remove_translation = False
mol.integrator.params.remove_rotation = False
mol.integrator.params.constrain_hbonds = False
mol.integrator.params.constrain_water = False
assert mol.dynamic_dof == full_dof
mol.integrator.params.constrain_hbonds = True
mol.integrator.params.constrain_water = False
assert mol.dynamic_dof == full_dof - 8
mol.integrator.params.constrain_hbonds = False
mol.integrator.params.constrain_water = True
assert mol.dynamic_dof == full_dof - 3
mol.integrator.params.constrain_hbonds = True
mol.integrator.params.constrain_water = True
assert mol.dynamic_dof == full_dof - 9
mol.clear_constraints() # does nothing, constraints are in the integrator
assert mol.dynamic_dof == full_dof - 9
mol.integrator.params.constrain_hbonds = False
mol.integrator.params.constrain_water = False
assert mol.dynamic_dof == full_dof
mol.integrator.params.remove_translation = True
mol.integrator.params.remove_rotation = True
mol.integrator.params.constrain_hbonds = True
mol.integrator.params.constrain_water = True
assert mol.dynamic_dof == full_dof - 9 - 6
def bipyridine_smiles():
return mdt.from_smiles('c1ccnc(c1)c2ccccn2')
def ammonium_charged():
return mdt.from_smiles('[NH4+]')
def small_molecule():
return mdt.from_smiles('c1ccccc1')
def small_molecule():
return mdt.from_smiles('c1ccccc1')
import moldesign as mdt
mol = mdt.from_smiles('CC')
mol.draw()
def cached_acetylene_dft_631g():
mol = mdt.from_smiles('C#C')
mol.set_energy_model(mdt.models.B3LYP, basis='6-31g')
mol.calculate()
return mol
def c2_no_hydrogen_from_smiles():
mymol = mdt.from_smiles('[CH0][CH0]')
return mymol
def ammonium_nocharge():
return mdt.from_smiles('[NH4]')
def cached_small_molecule():
mol = mdt.from_smiles('CNCOS(=O)C')
mol.positions += 0.001*np.random.random(mol.positions.shape)*u.angstrom # move out of minimum
return mol
def c2_no_hydrogen_from_smiles():
mymol = mdt.from_smiles('[CH0][CH0]')
return mymol
def ammonium_nocharge():
return mdt.from_smiles('[NH4]')
def cached_small_molecule():
mol = mdt.from_smiles('CNCOS(=O)C')
mol.positions += 0.001 * np.random.random(
mol.positions.shape) * u.angstrom # move out of minimum
return mol
def cached_ethylene():
return mdt.from_smiles('C=C')
def cached_benzene():
return mdt.from_smiles('c1ccccc1')
def ethylene_waterbox_2na_2cl():
mol = mdt.from_smiles('C=C')
solvated = mdt.add_water(mol, padding=15.0*u.angstrom, ion_concentration=0.6*u.molar)
return solvated
def bipyridine_smiles():
return mdt.from_smiles('c1ccnc(c1)c2ccccn2')
def cached_benzene():
return mdt.from_smiles('c1ccccc1')
def cached_ethylene():
return mdt.from_smiles('C=C')
def ammonium_charged():
return mdt.from_smiles('[NH4+]')
def cached_acetylene_dft_631g():
mol = mdt.from_smiles('C#C')
mol.set_energy_model(mdt.models.B3LYP, basis='6-31g')
mol.calculate()
return mol
def mol_from_smiles():
return mdt.from_smiles('CC')
def ethylene_waterbox_2na_2cl():
mol = mdt.from_smiles('C=C')
solvated = mdt.add_water(mol,
padding=15.0 * u.angstrom,
ion_concentration=0.6 * u.molar)
return solvated
