def test_fill_region_incorrect_type(self, ethane):
box1 = {"a": 1}
with pytest.raises(ValueError, match=r"expected a list of type:"):
mb.fill_region(compound=[ethane],
n_compounds=[2],
region=box1,
bounds=None)
def test_bad_args(self, h2o):
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10)
with pytest.raises(ValueError):
mb.fill_box(h2o, density=1000)
with pytest.raises(ValueError):
mb.fill_box(h2o, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10, density=1000, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(compound=[h2o, h2o], n_compounds=[10], density=1000)
with pytest.raises(ValueError):
mb.solvate(solute=h2o,
solvent=[h2o],
n_solvent=[10, 10],
box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_region(h2o,
n_compounds=[10, 10],
region=[2, 2, 2, 4, 4, 4])
with pytest.raises(ValueError):
mb.fill_box(
compound=[h2o, h2o],
n_compounds=[10],
density=1000,
fix_orientation=[True, True, True],
)
def test_fill_region_multiple(self, ethane, h2o):
filled = mb.fill_region(compound=[ethane, h2o], n_compounds=[2, 2],
region=[[2, 2, 2, 4, 4, 4], [4, 2, 2, 6, 4, 4]])
assert filled.n_particles == 2 * 8 + 2 * 3
assert filled.n_bonds == 2 * 7 + 2 * 2
assert np.max(filled.xyz[:16, 0]) < 4
assert np.min(filled.xyz[16:, 0]) > 4
def test_fill_region_box(self, h2o):
mybox = mb.Box([4, 4, 4])
filled = mb.fill_region(h2o, n_compounds=50, region=mybox)
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:,0]) >= 0
assert np.max(filled.xyz[:,2]) <= 4
def test_box_edge(self, h2o, methane):
system_box = mb.Box(lengths=(1.8, 1.8, 1.8))
packed = mb.fill_box(compound=h2o,
n_compounds=100,
box=system_box,
edge=0.2)
edge_sizes = system_box.lengths - packed.boundingbox.lengths
assert np.allclose(edge_sizes, np.array([0.4]*3), atol=0.1)
region = mb.fill_region(compound=h2o,
n_compounds=100,
region=system_box,
edge=0.2)
edge_sizes = system_box.lengths - packed.boundingbox.lengths
assert np.allclose(edge_sizes, np.array([0.4]*3), atol=0.1)
sphere = mb.fill_sphere(compound=h2o,
n_compounds=100,
sphere=[2, 2, 2, 1],
edge=0.2)
assert np.allclose(sphere.boundingbox.mins, np.array([1.2]*3), atol=0.1)
assert np.allclose(sphere.boundingbox.maxs, np.array([2.8]*3), atol=0.1)
solvated = mb.solvate(solvent=h2o,
solute=methane,
n_solvent=100,
box=system_box,
overlap=0.2)
edge_sizes = system_box.lengths - solvated.boundingbox.lengths
assert np.allclose(edge_sizes, np.array([0.4]*3), atol=0.1)
def test_fill_region_multiple(self, ethane, h2o):
filled = mb.fill_region(compound=[ethane, h2o], n_compounds=[2, 2],
region=[[2, 2, 2, 4, 4, 4], [4, 2, 2, 6, 4, 4]])
assert filled.n_particles == 2 * 8 + 2 * 3
assert filled.n_bonds == 2 * 7 + 2 * 2
assert np.max(filled.xyz[:16, 0]) < 4
assert np.min(filled.xyz[16:, 0]) > 4
def test_fill_region_box(self, h2o):
mybox = mb.Box([4, 4, 4])
filled = mb.fill_region(h2o, n_compounds=50, region=mybox)
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:, 0]) >= 0
assert np.max(filled.xyz[:, 2]) <= 4
def test_fill_region(self, h2o):
filled = mb.fill_region(h2o, n_compounds=50,
region=[3, 2, 2, 4, 4, 3])
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:,0]) >= 3
assert np.max(filled.xyz[:,2]) <= 3
def test_write_temp_file(self, h2o):
cwd = os.getcwd() # Must keep track of the temp dir that pytest creates
filled = mb.fill_box(h2o, n_compounds=10, box=[4, 4, 4], temp_file='temp_file1.pdb')
region = mb.fill_region(h2o, 10, [2, 2, 2, 4, 4, 4], temp_file='temp_file2.pdb')
solvated = mb.solvate(filled, h2o, 10, box=[4, 4, 4], temp_file='temp_file3.pdb')
assert os.path.isfile(os.path.join(cwd, 'temp_file1.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file2.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file3.pdb'))
def test_write_temp_file(self, h2o):
cwd = os.getcwd() # Must keep track of the temp dir that pytest creates
filled = mb.fill_box(h2o, n_compounds=10, box=[4, 4, 4], temp_file='temp_file1.pdb')
region = mb.fill_region(h2o, 10, [2, 2, 2, 4, 4, 4], temp_file='temp_file2.pdb')
solvated = mb.solvate(filled, h2o, 10, box=[4, 4, 4], temp_file='temp_file3.pdb')
assert os.path.isfile(os.path.join(cwd, 'temp_file1.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file2.pdb'))
assert os.path.isfile(os.path.join(cwd, 'temp_file3.pdb'))
def test_fill_region_multiple_types(self, ethane, h2o):
box1 = mb.Box(mins=[2, 2, 2], maxs=[4, 4, 4])
box2 = [4, 2, 2, 6, 4, 4]
filled = mb.fill_region(compound=[ethane, h2o], n_compounds=[2, 2],
region=[box1, box2])
assert filled.n_particles == 2 * 8 + 2 * 3
assert filled.n_bonds == 2 * 7 + 2 * 2
assert np.max(filled.xyz[:16, 0]) < 4
assert np.min(filled.xyz[16:, 0]) > 4
def test_bad_args(self, h2o):
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10)
with pytest.raises(ValueError):
mb.fill_box(h2o, density=1000)
with pytest.raises(ValueError):
mb.fill_box(h2o, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(h2o, n_compounds=10, density=1000, box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_box(compound=[h2o, h2o], n_compounds=[10], density=1000)
with pytest.raises(ValueError):
mb.solvate(solute=h2o, solvent=[h2o], n_solvent=[10, 10], box=[2, 2, 2])
with pytest.raises(ValueError):
mb.fill_region(h2o, n_compounds=[10, 10], region=[2, 2, 2, 4, 4, 4])
with pytest.raises(ValueError):
mb.fill_box(compound=[h2o, h2o], n_compounds=[10], density=1000,
fix_orientation=[True, True, True])
def test_fill_region_multiple_types(self, ethane, h2o):
box1 = mb.Box(mins=[2, 2, 2], maxs=[4, 4, 4])
box2 = [4, 2, 2, 6, 4, 4]
filled = mb.fill_region(compound=[ethane, h2o], n_compounds=[2, 2],
region=[box1, box2])
assert filled.n_particles == 2 * 8 + 2 * 3
assert filled.n_bonds == 2 * 7 + 2 * 2
assert np.max(filled.xyz[:16, 0]) < 4
assert np.min(filled.xyz[16:, 0]) > 4
def test_fill_region_box(self, h2o):
mybox = Box(lengths=[4, 4, 4], angles=[90.0, 90.0, 90.0])
filled = mb.fill_region(h2o,
n_compounds=50,
region=mybox,
bounds=[[0, 0, 0, 4, 4, 4]])
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:, 0]) >= 0
assert np.max(filled.xyz[:, 2]) <= 4
def test_fill_region(self, h2o):
filled = mb.fill_region(h2o, n_compounds=50, region=[3, 2, 2, 5, 5, 5])
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:, 0]) >= 3
assert np.min(filled.xyz[:, 1]) >= 2
assert np.min(filled.xyz[:, 2]) >= 2
assert np.max(filled.xyz[:, 0]) <= 5
assert np.max(filled.xyz[:, 1]) <= 5
assert np.max(filled.xyz[:, 2]) <= 5
def test_fill_region_multiple(self, ethane, h2o):
box1 = mb.Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
box2 = mb.Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
filled = mb.fill_region(
compound=[ethane, h2o],
n_compounds=[2, 2],
region=[box1, box2],
bounds=[[2, 2, 2, 4, 4, 4], [4, 2, 2, 6, 4, 4]],
)
assert filled.n_particles == 2 * 8 + 2 * 3
assert filled.n_bonds == 2 * 7 + 2 * 2
assert np.max(filled.xyz[:16, 0]) < 4
assert np.min(filled.xyz[16:, 0]) > 4
def test_fill_region(self, h2o):
filled = mb.fill_region(
h2o,
n_compounds=50,
region=Box(lengths=[2, 3, 3], angles=[90.0, 90.0, 90.0]),
bounds=[[3, 2, 2, 5, 5, 5]],
)
assert filled.n_particles == 50 * 3
assert filled.n_bonds == 50 * 2
assert np.min(filled.xyz[:, 0]) >= 3
assert np.min(filled.xyz[:, 1]) >= 2
assert np.min(filled.xyz[:, 2]) >= 2
assert np.max(filled.xyz[:, 0]) <= 5
assert np.max(filled.xyz[:, 1]) <= 5
assert np.max(filled.xyz[:, 2]) <= 5
def test_box_edge(self, h2o, methane):
system_box = mb.Box(lengths=(1.8, 1.8, 1.8))
packed = mb.fill_box(compound=h2o,
n_compounds=100,
box=system_box,
edge=0.2)
edge_sizes = np.subtract(system_box.lengths,
packed.get_boundingbox().lengths)
assert np.allclose(edge_sizes, np.array([0.4] * 3), atol=0.1)
region = mb.fill_region(
compound=h2o,
n_compounds=100,
region=system_box,
edge=0.2,
bounds=[system_box],
)
edge_sizes = np.subtract(system_box.lengths,
packed.get_boundingbox().lengths)
assert np.allclose(edge_sizes, np.array([0.4] * 3), atol=0.1)
edge = 0.2
bounds = [2, 2, 2, 1]
sphere = mb.fill_sphere(compound=h2o,
n_compounds=100,
sphere=bounds,
edge=edge)
target_diameter = (bounds[3] - edge) * 2
assert np.allclose(sphere.maxs - sphere.mins,
np.array([target_diameter] * 3),
atol=0.1)
solvated = mb.solvate(
solvent=h2o,
solute=methane,
n_solvent=100,
box=system_box,
overlap=0.2,
)
edge_sizes = np.subtract(system_box.lengths,
solvated.get_boundingbox().lengths)
assert np.allclose(edge_sizes, np.array([0.4] * 3), atol=0.1)
def test_box_no_bound(self, ethane):
box1 = Box(lengths=[2, 2, 2], angles=[90.0, 90.0, 90.0])
mb.fill_region(compound=[ethane],
n_compounds=[2],
region=box1,
bounds=None)