def test_box_volume_from_box_vectors_3():
molsys = msm.convert(msm.demo['Met-enkephalin']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.build.solvate(molsys,
box_geometry='rhombic dodecahedral',
clearance='14.0 angstroms',
engine='PDBFixer')
box = msm.get(molsys, target='system', box=True)
volume = msm.pbc.box_volume_from_box_vectors(box)
check = np.allclose(msm.puw.get_value(volume, to_unit='nm**3'),
[21.5501970])
assert check
def test_get_distances_from_molsysmt_MolSys_5():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
list_groups_1 = msm.get(molsys,
target="group",
selection="group_index in [0,1,2,3]",
atom_index=True)
list_groups_2 = msm.get(molsys,
target="group",
selection="group_index in [4,5,6,7,8]",
atom_index=True)
distances = msm.structure.get_distances(
molsys,
groups_of_atoms=list_groups_1,
group_behavior="geometric_center",
groups_of_atoms_2=list_groups_2,
group_behavior_2="geometric_center")
check_shape = ((1, 4, 5) == distances.shape)
check_distance = np.isclose(
puw.get_value(distances[0, 2, 2], to_unit='nm'), 1.240669)
assert check_shape and check_distance
def test_get_31():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
molecule_index = msm.get(molsys,
target='entity',
indices=1,
molecule_index=True)
true_molecule_index = np.array([list(range(1, 166))], dtype=object)
check_molecule_index = np.all([
np.all(ii == jj) for ii, jj in zip(molecule_index, true_molecule_index)
])
assert check_molecule_index
def test_get_covalent_dihedral_quartetes_from_molsysmt_MolSys_3():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys')
chains = msm.topology.get_covalent_dihedral_quartets(molsys, dihedral_angle='chi5')
true_value_1 = np.array([[1572, 1573, 1574, 1575],
[1666, 1667, 1668, 1669],
[1721, 1722, 1723, 1724],
[2303, 2304, 2305, 2306],
[2428, 2429, 2430, 2431]])
n_args = msm.get(molsys, target='group', selection='group_name=="ARG"', n_groups=True)
check_shape_1 = np.all((n_args, 4)==chains.shape)
check_value_1 = np.all(true_value_1==chains[10:15])
assert check_shape_1 and check_value_1
def test_get_55():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
coordinates = msm.get(molsys,
target='atom',
indices=100,
structure_indices=0,
coordinates=True)
value = msm.puw.get_value(coordinates)
unit = msm.puw.get_unit(coordinates)
assert (unit == msm.puw.unit('nanometers')) and (np.allclose(
value, np.array([[[1.8835, 3.8271, 5.0365]]])))
def test_box_angles_from_box_vectors_3():
molsys = msm.convert(msm.demo['Met-enkephalin']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.build.solvate(molsys,
box_geometry='rhombic dodecahedral',
clearance='14.0 angstroms',
engine='PDBFixer')
box = msm.get(molsys, target='system', box=True)
angles = msm.pbc.box_angles_from_box_vectors(box)
check = np.allclose(msm.puw.get_value(angles, to_unit='degrees'),
[[60.0, 60.0, 90.000001]])
assert check
def test_get_maximum_distances_from_molsysmt_MolSys_2():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
list_atom_groups = msm.get(molsys,
target='group',
selection='all',
atom_index=True)
frames = np.arange(msm.get(molsys, n_structures=True))
max_group, max_distances = msm.structure.get_maximum_distances(
molsys,
groups_of_atoms=list_atom_groups,
group_behavior='geometric_center',
groups_of_atoms_2=list_atom_groups,
group_behavior_2='geometric_center',
structure_indices=frames[:-1],
structure_indices_2=frames[1:],
pairs=True)
check_shape_1 = ((4999, ) == max_group.shape)
check_distance = np.isclose(
puw.get_value(max_distances[1000], to_unit='nm'), 0.85040462)
assert check_shape_1 and check_distance
def test_box_lengths_from_box_vectors_2():
molsys = msm.convert(msm.demo['Met-enkephalin']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.build.solvate(molsys,
box_geometry='truncated octahedral',
clearance='14.0 angstroms',
engine='PDBFixer')
box = msm.get(molsys, target='system', box=True)
lengths = msm.pbc.box_lengths_from_box_vectors(box)
check = np.allclose(msm.puw.get_value(lengths, to_unit='nm'),
[[3.1236, 3.1236, 3.1236]])
assert check
def test_center_molsysmt_MolSys_1():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
n_structures = msm.get(molsys, n_structures=True)
origin = np.zeros([n_structures, 1, 3]) * msm.puw.unit('nanometers')
molsys = msm.structure.center(molsys)
distance = msm.structure.get_distances(molsys,
group_behavior='geometric_center',
molecular_system_2=origin)
true_distance = np.zeros([n_structures, 1, 1]) * msm.puw.unit('nanometers')
check = np.allclose(distance, true_distance)
assert check
def test_get_neighbors_from_molsysmt_MolSys_7():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atoms_in_residues_chain_0 = msm.get(
molsys,
target='group',
selection="molecule_type=='protein' and chain_index==0",
atom_index=True)
atoms_in_residues_chain_1 = msm.get(
molsys,
target='group',
selection="molecule_type=='protein' and chain_index==1",
atom_index=True)
neighbors, distances = msm.structure.get_neighbors(
molsys,
groups_of_atoms=atoms_in_residues_chain_0,
group_behavior='geometric_center',
groups_of_atoms_2=atoms_in_residues_chain_1,
group_behavior_2='geometric_center',
threshold=1.2 * puw.unit('nanometers'))
check_n_contacts = (18 == len(neighbors[0, 11]))
assert check_n_contacts
def test_get_24():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
group_indices = msm.get(molsys,
target='molecule',
indices=[0, 1],
group_index=True)
true_group_indices = np.array(
[np.array(range(497)), np.array([497])], dtype=object)
check_group_indices = np.all([
np.all(ii == jj) for ii, jj in zip(group_indices, true_group_indices)
])
assert check_group_indices
def test_get_neighbors_from_molsysmt_MolSys_3():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atoms_in_residues_chain_0 = msm.get(
molsys,
target='group',
selection="molecule_type=='protein' and chain_index==0",
atom_index=True)
atoms_in_residues_chain_1 = msm.get(
molsys,
target='group',
selection="molecule_type=='protein' and chain_index==1",
atom_index=True)
neighbors, distances = msm.structure.get_neighbors(
molsys,
groups_of_atoms=atoms_in_residues_chain_0,
group_behavior='geometric_center',
num_neighbors=8)
check_shape_1 = ((1, 248, 8) == neighbors.shape)
check_neighbors = (2 == neighbors[0, 0, 7])
check_distance = np.isclose(
puw.get_value(distances[0, 0, 7], to_unit='nm'), 0.86807833)
assert check_shape_1 and check_neighbors and check_distance
def n_entities_from_system(item, indices='all'):
from molsysmt import get
entity_index_from_atom = get(item,
target='atom',
indices='all',
entity_index=True)
if entity_index_from_atom[0] is None:
n_entities = 0
else:
output = np.unique(entity_index_from_atom)
n_entities = output.shape[0]
return n_entities
def test_get_distances_from_molsysmt_MolSys_11():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
list_atom_groups = msm.get(molsys,
target='group',
selection='all',
atom_index=True)
distances = msm.structure.get_distances(molsys,
groups_of_atoms=list_atom_groups,
group_behavior='geometric_center')
check_shape = ((5000, 7, 7) == distances.shape)
check_distance = np.isclose(
puw.get_value(distances[1000, 2, 3], to_unit='nm'), 0.4240467)
assert check_shape and check_distance
def test_get_distances_from_molsysmt_MolSys_10():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
n_structures = msm.get(molsys, n_structures=True)
all_structure_indices = np.arange(n_structures)
displacements = msm.structure.get_distances(
molsys,
selection="all",
structure_indices=np.zeros(n_structures),
structure_indices_2=all_structure_indices)
check_shape = ((5000, 62, 62) == displacements.shape)
check_distance = np.isclose(
puw.get_value(displacements[1000, 30, 30], to_unit='nm'), 0.4517681)
assert check_shape and check_distance
def test_wrap_to_pbc_molsysmt_MolSys_1():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.pbc.wrap_to_mic(
molsys, center_of_selection='molecule_type=="peptide"')
lengths = msm.get(molsys, target='system', box_lengths=True)
distances = msm.structure.get_distances(
molsys,
molecular_system_2=[[0.0, 0.0, 0.0]] * msm.puw.unit('nm'),
pbc=False)
max_dist_cube = np.sqrt(3.0 * (lengths[0, 0] / 2.0)**2)
max_dist = np.max(distances)
check = (max_dist < max_dist_cube)
assert check
def test_get_minimum_distances_from_molsysmt_MolSys_1():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atoms_groups_component_0 = msm.get(molsys,
target='group',
selection='component_index==0',
atom_index=True)
atoms_groups_component_1 = msm.get(molsys,
target='group',
selection='component_index==1',
atom_index=True)
min_pairs, min_distances = msm.structure.get_minimum_distances(
molsys,
groups_of_atoms=atoms_groups_component_0,
group_behavior='geometric_center',
groups_of_atoms_2=atoms_groups_component_1,
group_behavior_2='geometric_center')
check_shape_1 = ((1, 2) == min_pairs.shape)
check_shape_2 = ((1, ) == min_distances.shape)
check_pairs = np.all(min_pairs[0] == np.array([69, 12]))
check_distance = np.isclose(puw.get_value(min_distances[0], to_unit='nm'),
0.38221311)
assert check_shape_1 and check_shape_2 and check_pairs and check_distance
def test_append_structures_molsysmt_MolSys():
molsys_1 = msm.convert(msm.demo['proline dipeptide']['vacuum.msmpk'],
to_form='molsysmt.MolSys')
molsys_2 = msm.structure.translate(
molsys_1, translation='[0.1, 0.1, 0.1] nanometers')
molsys_3 = msm.structure.translate(
molsys_1, translation='[0.2, 0.2, 0.2] nanometers')
n_atoms_1, n_structures_1 = msm.get(molsys_1,
target='system',
n_atoms=True,
n_structures=True)
n_structures_2 = msm.get(molsys_2, target='system', n_structures=True)
n_structures_3 = msm.get(molsys_3, target='system', n_structures=True)
msm.append_structures(molsys_1, [molsys_2, molsys_3])
n_atoms, n_structures = msm.get(molsys_1,
target='system',
n_atoms=True,
n_structures=True)
check = ('molsysmt.MolSys' == msm.get_form(molsys_1))
check_n_atoms = (n_atoms == n_atoms_1)
check_n_structures = (n_structures == n_structures_1 + n_structures_2 +
n_structures_3)
assert check and check_n_atoms and check_n_structures
def test_get_6():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
indices, component_indices = msm.get(molsys,
target='group',
indices=[550, 551, 552],
index=True,
component_index=True)
true_indices = np.array([550, 551, 552])
true_component_indices = np.array([55, 56, 57])
check_indices = np.all(indices == true_indices)
check_component_indices = np.all(
component_indices == true_component_indices)
assert check_indices and check_component_indices
def test_get_46():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
inner_bonded_atoms = msm.get(molsys,
target='atom',
indices=[0, 1, 2, 3, 4, 5],
inner_bonded_atoms=True)
true_inner_bonded_atoms = np.array([[1, 0], [2, 1], [3, 2], [4, 1], [5,
4]])
check_bonded_index = np.all([
np.all(ii == jj)
for ii, jj in zip(inner_bonded_atoms, true_inner_bonded_atoms)
])
assert check_bonded_index
def test_get_12():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atom_names, atom_indices = msm.get(molsys,
target='atom',
selection='group_index==20',
name=True,
index=True)
true_atom_names = np.array(['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD'],
dtype=object)
true_atom_indices = np.array([148, 149, 150, 151, 152, 153, 154])
check_atom_names = np.all(atom_names == true_atom_names)
check_atom_indices = np.all(atom_indices == true_atom_indices)
assert check_atom_names and check_atom_indices
def test_get_32():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
molecule_types = msm.get(molsys,
target='molecule',
indices=range(1, 10),
molecule_type=True)
true_molecule_types = np.array([
'water', 'water', 'water', 'water', 'water', 'water', 'water', 'water',
'water'
],
dtype=object)
check_molecule_types = np.all(molecule_types == true_molecule_types)
assert check_molecule_types
def test_get_distances_from_molsysmt_MolSys_7():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
list_groups_1 = msm.get(molsys,
target="group",
selection="all",
atom_index=True)
distances = msm.structure.get_distances(molsys,
groups_of_atoms=list_groups_1,
group_behavior="geometric_center",
structure_indices=3000)
check_shape = ((1, 7, 7) == distances.shape)
check_distance = np.isclose(
puw.get_value(distances[0, 2, 4], to_unit='nm'), 0.681850)
assert check_shape and check_distance
def test_get_distances_from_molsysmt_MolSys_9():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
n_structures = msm.get(molsys, n_structures=True)
all_structure_indices = np.arange(n_structures)
displacements = msm.structure.get_distances(
molsys,
selection="group_index==0",
group_behavior="geometric_center",
structure_indices=all_structure_indices[:-1],
structure_indices_2=all_structure_indices[1:])
check_shape = ((4999, 1, 6) == displacements.shape)
check_distance = np.isclose(
puw.get_value(displacements[1000, 0, 3], to_unit='nm'), 0.84082184)
assert check_shape and check_distance
def test_get_21():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atom_indices = msm.get(molsys,
target='group',
indices=[0, 1],
atom_index=True)
true_atom_indices = np.array([
np.array([0, 1, 2, 3, 4, 5, 6, 7, 8]),
np.array([9, 10, 11, 12, 13, 14, 15])
],
dtype=object)
check_atom_indices = np.all(
[np.all(ii == jj) for ii, jj in zip(atom_indices, true_atom_indices)])
assert check_atom_indices
def test_get_2():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
names, group_indices, group_names = msm.get(molsys,
target='atom',
indices=[32, 33, 34],
name=True,
group_index=True,
group_name=True)
true_names = np.array(['N', 'CA', 'C'], dtype=object)
true_group_indices = np.array([4, 4, 4])
true_group_names = np.array(['ILE', 'ILE', 'ILE'], dtype=object)
assert np.all(names == true_names) and np.all(
group_indices == true_group_indices) and np.all(
group_names == true_group_names)
def test_get_8():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
indices, component_indices = msm.get(molsys,
target='component',
indices=[55, 56, 57],
index=True,
group_index=True)
true_indices = np.array([55, 56, 57])
true_component_indices = np.array([[550], [551], [552]], dtype=object)
check_indices = np.all(true_indices == indices)
check_component_indices = np.all([
np.all(ii == jj)
for ii, jj in zip(component_indices, true_component_indices)
])
assert check_indices and check_component_indices
def test_get_center_molsysmt_MolSys_1():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
list_CAs = msm.select(molsys, selection='atom_name=="CA"')
n_atoms_CAs = list_CAs.shape[0]
center = msm.structure.get_center(molsys,
selection=list_CAs,
weights=np.ones(n_atoms_CAs))
n_structures = msm.get(molsys, target='system', n_structures=True)
check_shape = np.all((n_structures, 1, 3) == center.shape)
true_values = np.array([[[0.79670861, 1.07878454, -0.02861541]],
[[0.83204994, 1.10665931, -0.06361365]],
[[0.77414551, 0.99350907, 0.01043041]]])
check_values = np.allclose(
true_values, msm.puw.get_value(center[1007:1010], to_unit='nm'))
assert check_shape and check_values
def test_get_maximum_distances_from_molsysmt_MolSys_1():
molsys = msm.convert(msm.demo['pentalanine']['traj.h5'],
to_form='molsysmt.MolSys')
list_atom_groups = msm.get(molsys,
target='group',
selection='all',
atom_index=True)
max_pairs, max_distances = msm.structure.get_maximum_distances(
molsys,
groups_of_atoms=list_atom_groups,
group_behavior='geometric_center')
check_shape_1 = ((5000, 2) == max_pairs.shape)
check_shape_2 = ((5000, ) == max_distances.shape)
check_pairs = np.all(max_pairs[0] == np.array([0, 6]))
check_distance = np.isclose(
puw.get_value(max_distances[1000], to_unit='nm'), 2.05848188)
assert check_shape_1 and check_shape_2 and check_pairs and check_distance
def test_get_neighbors_from_molsysmt_MolSys_5():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
atoms_in_residues_chain_1 = msm.get(
molsys,
target='group',
selection="molecule_type=='protein' and chain_index==1",
atom_index=True)
neighbors, distances = msm.structure.get_neighbors(
molsys,
selection=100,
groups_of_atoms_2=atoms_in_residues_chain_1,
group_behavior_2='geometric_center',
num_neighbors=4)
check_neighbors = (77 == neighbors[0, 0, 3])
check_distance = np.isclose(
puw.get_value(distances[0, 0, 3], to_unit='nm'), 0.8498448)
assert check_neighbors and check_distance
