def test_userdefn_ValueErrors(self, universe):
# Test len(gridcenter) != 3
with pytest.raises(ValueError):
D = density.density_from_Universe(
universe,
select=self.selections['static'],
delta=self.delta,
xdim=10.0,
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters['error1'])
# Test gridcenter includes non-numeric strings
with pytest.raises(ValueError):
D = density.density_from_Universe(
universe,
select=self.selections['static'],
delta=self.delta,
xdim=10.0,
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters['error2'])
# Test xdim != int or float
with pytest.raises(ValueError):
D = density.density_from_Universe(
universe,
select=self.selections['static'],
delta=self.delta,
xdim="MDAnalysis",
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters['static_defined'])
def test_gridcenter(u1):
gridcenter = np.array([10, 10, 10])
xdim = 190
ydim = 200
zdim = 210
serial = density_from_Universe(u1,
atomselection='name OD1',
update_selection=True,
gridcenter=gridcenter,
xdim=xdim,
ydim=ydim,
zdim=zdim)
parallel = DensityAnalysis(u1.atoms,
atomselection='name OD1',
updating=True,
gridcenter=gridcenter,
xdim=xdim,
ydim=ydim,
zdim=zdim)
core_number = 4
parallel.run(n_blocks=core_number, n_jobs=core_number)
assert_almost_equal(serial.grid, parallel.density.grid)
assert_almost_equal(parallel._gridcenter, gridcenter)
assert len(parallel.density.edges[0]) == xdim + 1
assert len(parallel.density.edges[1]) == ydim + 1
assert len(parallel.density.edges[2]) == zdim + 1
def calcDensity(cutoff, **kwargs):
"""Retrive the density in Molar of density_sel"""
for k, v in kwargs.items():
exec(k + '=v')
for co in cutoff:
filenames = str(
glob.glob(results_dir +
'structures/NAC_frames-{}-{}-{}-{}-*.gro'.format(
results_dir, prot, mol, c, co)))
for f in filenames:
xtc = f[:-4] + '.xtc'
fit = f + '-fit.xtc'
ref = mda.Universe(f)
mobile = mda.Universe(f, xtc)
alignment = align.AlignTraj(mobile, ref, filename=fit)
alignment.run()
fit_u = mda.Universe(filename + '.gro', fit)
density = density_from_Universe(
fit_u, delta=0.5
) #, atomselection=density_sel, update_selection=True)
density.convert_density('Molar')
density.export(filename + '-density_Molar.dx', type=double)
def test_userdefn_boxshape(self, universe):
D = density.density_from_Universe(
universe,
select=self.selections['static'],
delta=1.0,
xdim=8.0,
ydim=12.0,
zdim=17.0,
gridcenter=self.gridcenters['static_defined'])
assert D.grid.shape == (8, 12, 17)
def test_userdefn_selwarning(self, universe):
regex = ("Atom selection does not fit grid --- "
"you may want to define a larger box")
with pytest.warns(UserWarning, match=regex):
D = density.density_from_Universe(
universe,
select=self.selections['static'],
delta=self.delta,
xdim=1.0,
ydim=2.0,
zdim=2.0,
padding=0.0,
gridcenter=self.gridcenters['static_defined'])
def test_userdefn_padding(self, universe):
regex = ("Box padding \(currently set at 1\.0\) is not used "
"in user defined grids\.")
with pytest.warns(UserWarning, match=regex):
D = density.density_from_Universe(
universe,
select=self.selections['static'],
delta=self.delta,
xdim=100.0,
ydim=100.0,
zdim=100.0,
padding=1.0,
gridcenter=self.gridcenters['static_defined'])
def test_density_values(u1, n_blocks, stop, step):
parallel = DensityAnalysis(u1.atoms,
atomselection='name OD1',
updating=True)
parallel.run(n_blocks=n_blocks,
n_jobs=n_blocks,
start=0,
stop=stop,
step=step)
serial = density_from_Universe(u1,
atomselection='name OD1',
update_selection=True,
start=0,
stop=stop,
step=step)
assert np.sum(serial.grid) == np.sum(parallel.density.grid)
assert_almost_equal(serial.grid, parallel.density.grid, decimal=17)
def check_density_from_Universe(self, atomselection, ref_meandensity,
universe, tmpdir, **kwargs):
with tmpdir.as_cwd():
D = density.density_from_Universe(universe,
select=atomselection,
delta=self.delta,
**kwargs)
assert_almost_equal(D.grid.mean(),
ref_meandensity,
err_msg="mean density does not match")
D.export(self.outfile)
D2 = density.Density(self.outfile)
assert_almost_equal(
D.grid,
D2.grid,
decimal=self.precision,
err_msg="DX export failed: different grid sizes")
base + '5us_traj_popc_protein_lipid_popc.xtc',
base + '15us_traj_protein_lipid_popc.xtc'
])
# define the contact condition in ångströms
contact_dist = 5
nearby = "name PO4 and (around " + str(
contact_dist
) + " name SC1 or around " + str(contact_dist) + " name SC2 or around " + str(
contact_dist) + " name SC3 or around " + str(contact_dist) + " name SC4)"
# write out 3D density of PO4 everywhere and near the protein in VTK Image Data
Dall = density_from_Universe(u,
delta=0.5,
atomselection="name PO4",
update_selection=True)
Dnear = density_from_Universe(u,
delta=1,
atomselection=nearby,
update_selection=True)
print('near:', Dnear.grid.shape) # should be (60, 57, 51)
grid = tvtk.tvtk.ImageData(spacing=Dnear.delta,
origin=Dnear.origin,
dimensions=Dnear.grid.shape)
grid.point_data.scalars = Dnear.grid.ravel(order='F')
grid.point_data.scalars.name = 'POPC near SC1_4'
tvtk.write_data(
grid, 'Dnear.vtk'
) # omit `vtk` extension to write newer XML VTK, otherwise legacy VTK
def test_has_DeprecationWarning(self, universe):
with pytest.warns(DeprecationWarning,
match="will be removed in release 2.0.0"):
D = density.density_from_Universe(universe,
select=self.selections['static'],
delta=self.delta)
import MDAnalysis as mda
from MDAnalysis.analysis.density import density_from_Universe
u = mda.Universe('GRO_file', 'XTC_FILE')
sto=len(u.trajectory)
for i in range(0,sto):
x=i+1
D=density_from_Universe(u, delta=1.0,start=i,stop=x,step=1, atomselection="name OH2",padding=0)
D.convert_density('TIP3P') #assuming TIP3P
D.export('water_density_convert_'+str(i)+'.dx')
import MDAnalysis as mda
from MDAnalysis.analysis.density import density_from_Universe
u = mda.Universe('../../step7_1.gro', '../../all_c_long.xtc')
sto = len(u.trajectory)
for i in range(0, sto):
x = i + 1
D = density_from_Universe(u,
delta=1.0,
start=i,
stop=x,
step=1,
atomselection="name OH2",
padding=0)
P = density_from_Universe(u,
delta=1.0,
start=i,
stop=x,
step=1,
atomselection="protein",
padding=0)
L = density_from_Universe(u,
delta=1.0,
start=i,
stop=x,
step=1,
atomselection="resname POPC",
padding=0)
D.convert_density('TIP3P') #assuming TIP3P
D.export('water_density_convert_' + str(i) + '.dx')
P.export('protein_density_notconvert_' + str(i) + '.dx')
#!/usr/bin/env python
from MDAnalysis import Universe
from MDAnalysis.analysis.density import density_from_Universe
uni = Universe("ref.gro", "./all_fit.xtc")
D = density_from_Universe(uni, delta=1.0, atomselection="name OW")
D.export("density.dx")