def test_get_structure_alignment_molsysmt_MolSys_1():
molsys_1 = msm.convert(msm.demo['T4 lysozyme L99A']['181l.msmpk'],
to_form='molsysmt.MolSys')
molsys_1 = msm.extract(molsys_1, selection='molecule_type=="protein"')
molsys_2 = msm.convert(msm.demo['T4 lysozyme L99A']['1l17.msmpk'],
to_form='molsysmt.MolSys')
molsys_2 = msm.convert(molsys_2,
to_form='molsysmt.MolSys',
selection='molecule_type=="protein"')
molsys_2on1 = msm.structure.align(molsys_2,
selection='backbone',
reference_molecular_system=molsys_1,
reference_selection='backbone')
identity, int2, int1 = msm.topology.get_sequence_identity(
molsys_2, reference_molecular_system=molsys_1)
aux1 = msm.select(molsys_1, selection='group_index==@int1')
sel1 = msm.select(molsys_1, selection='backbone', mask=aux1)
aux2 = msm.select(molsys_2, selection='group_index==@int2')
sel2 = msm.select(molsys_2, selection='backbone', mask=aux2)
rmsd = msm.structure.get_rmsd(molsys_2on1,
selection=sel2,
reference_molecular_system=molsys_1,
reference_selection=sel1)
check = math.isclose(0.021332505947,
msm.puw.get_value(rmsd, to_unit='nm')[0])
print(msm.puw.get_value(rmsd, to_unit='nm')[0])
assert check
def set_parameters(self, selection='atom_type!="H"', syntaxis='MolSysMT'):
from molsysmt import select
self._selection = selection
self._syntaxis = syntaxis
self._atom_indices = select(self._explorer, selection=selection, syntaxis=syntaxis)
def test_select_12():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys, 'molecule_type=="water" and molecule_index==[100,101]')
true_output = np.array([3917, 3918])
assert np.all(output == true_output)
def test_select_9():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
'atom_name!=["CA","CB","C"] and group_index==[2,3]')
true_output = np.array([16, 19, 21, 22, 23, 24, 25, 28, 30, 31])
assert np.all(output == true_output)
def _initialize(self, exploration_campaign):
topology = exploration_campaign.explorer.topology
if self._selection is not 'all':
self._atom_indices = msm.select(topology,
selection=self._selection,
syntaxis=self._syntaxis)
self.topology = msm.convert(topology,
to_form='molsysmt.Topology',
selection=self._atom_indices)
else:
self._atom_indices = 'all'
self.topology = msm.convert(topology, to_form='molsysmt.Topology')
if self._step:
self.step = []
if self._coordinates:
self.coordinates = [] * unit.nanometers
if self._boxVectors:
self.box = [] * unit.nanometers
if self._potentialEnergy:
self.potential_energy = [] * unit.kilojoules_per_mole
self._initialized = True
def test_select_32():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys, 'chain_id=="A" within 0.3 nm with pbc of chain_id=="B"')
true_output = np.array([89, 480, 527, 547, 550, 552, 554, 566, 723, 734])
assert np.all(output == true_output)
def test_select_5():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys, 'atom_name in ["CA","CB"] and group_index == [0,1,2,3]')
true_output = np.array([1, 4, 10, 13, 17, 20, 26, 29])
assert np.all(output == true_output)
def test_select_18():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
indices = list(range(10, 30))
output = msm.select(molsys, 'atom_name=="C" and atom_index in @indices')
true_output = np.array([11, 18, 27])
assert np.all(output == true_output)
def test_select_19():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
indices = [0, 100, 200]
output = msm.select(molsys, 'group_index==@indices', target='group')
true_output = np.array([0, 100, 200])
assert np.all(output == true_output)
def test_select_15():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
indices = [10, 11, 12]
output = msm.select(molsys, 'group_index==@indices and atom_name=="N"')
true_output = np.array([77, 86, 92])
assert np.all(output == true_output)
def test_select_4():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
'atom_name == "C" and group_index == [0,1,2,3]')
true_output = np.array([2, 11, 18, 27])
assert np.all(output == true_output)
def test_select_30():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys, 'chain_id=="A" not within 7.8 nanometers of chain_id=="B"')
true_output = np.array([1521, 1522, 1723, 1724])
assert np.all(output == true_output)
def test_select_3():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
target='molecule',
selection=[3900, 3910, 3920])
true_output = np.array([83, 93, 103])
assert np.all(output == true_output)
def test_select_22():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
'chain_id==["A","C"] and molecule_type!="water"',
target='group')
true_output = np.array(list(range(248)))
assert np.all(output == true_output)
def test_select_20():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
'group_name=="ALA" and group_index==[2,3,4,5,6,7]',
target='group')
true_output = np.array([5, 6, 7])
assert np.all(output == true_output)
def test_select_2():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
target='group',
selection=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11])
true_output = np.array([0, 1])
assert np.all(output == true_output)
def test_select_16():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
indices = list(range(10, 20))
atoms = ["CA", "C", "O", "N"]
output = msm.select(molsys, 'atom_name==@atoms & atom_index==@indices')
true_output = np.array([10, 11, 12, 16, 17, 18, 19])
assert np.all(output == true_output)
def test_select_13():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'molecule_type=="protein" and atom_type!="H" and group_index==3')
true_output = np.array([25, 26, 27, 28, 29, 30, 31])
assert np.all(output == true_output)
def test_select_39():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
selection='group_index==[3,4,5]',
to_syntaxis='NGLView')
true_output = '@25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44'
assert np.all(output == true_output)
def test_select_8():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'atom_type=="C" and not atom_name=="CA" and group_index==[2,3]')
true_output = np.array([18, 20, 21, 22, 27, 29, 30, 31])
assert np.all(output == true_output)
def test_select_40():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
selection='group_index==[3,4,5]',
to_syntaxis='MDTraj')
true_output = 'index 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44'
assert np.all(output == true_output)
def test_select_34():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'(atom_name=="CA" and chain_id=="A") within 0.5 nm of (atom_name=="CA" and chain_id=="B")',
target='group')
true_output = np.array([10, 42, 62, 72, 73])
assert np.all(output == true_output)
def test_select_28():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
'group_index in [0,1,2,3,4]',
mask=[0, 1, 2],
target='group')
true_output = np.array([0, 1, 2])
assert np.all(output == true_output)
def test_select_42():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
target='group',
selection='group_index==[3,4,5]',
to_syntaxis='MDTraj')
true_output = 'resid 3 4 5'
assert np.all(output == true_output)
def test_select_41():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(molsys,
target='group',
selection='group_index==[3,4,5]',
to_syntaxis='NGLView')
true_output = '7:A 8:A 9:A'
assert np.all(output == true_output)
def test_select_14():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'group_name==["GLY","ALA","VAL"] and chain_id=="A" and group_index==[2,3,4,5,6]'
)
true_output = np.array([40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
assert np.all(output == true_output)
def test_select_38():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'((atom_name=="N" and chain_id=="A") bonded to atom_type=="C") within 3 angstroms of (atom_type=="O" and molecule_type=="water")'
)
true_output = np.array([119, 213, 473, 531, 654, 696, 799, 1049])
assert np.all(output == true_output)
def test_select_37():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'((atom_type=="O" and chain_id=="A") bonded to (atom_type=="C" and chain_id=="A")) and group_index==[3,4]'
)
true_output = np.array([28, 35])
assert np.all(output == true_output)
def test_select_36():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'(all not bonded to atom_type==["H","N","C","O"]) and molecule_type=="protein"'
)
true_output = np.array([363, 1714, 2275, 3626])
assert np.all(output == true_output)
def test_select_35():
molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'],
to_form='molsysmt.MolSys')
output = msm.select(
molsys,
'(atom_name=="N" bonded to atom_type=="C") and group_index==[10, 11, 12]'
)
true_output = np.array([77, 86, 92])
assert np.all(output == true_output)