def test_serial():
universe = mda.Universe(waterPSF, waterDCD)
sel_string = 'all'
selection = universe.select_atoms(sel_string)
xpos = np.array([0., 0., 0., 0.0072334, 0.00473299, 0., 0., 0., 0., 0.])
ld = LinearDensity(selection, binsize=5).run()
assert_almost_equal(xpos, ld.results['x']['pos'])
def density(u, binsize, block):
'''Computes water density profile perpendicular to a surface.
Args:
u: MDAnalysis Universe object containing trajectory.
binsize: Bin size of profile (histogram).
block: Range of frames composing block.
Returns:
Linear density profile.
'''
# Select water
water = u.select_atoms('name O or name H')
# Initialize and run linear density analysis
ldens = LinearDensity(water, binsize=binsize, verbose=True)
ldens.run(start=block.start, stop=block.stop)
return ldens.results.z.pos
def test_serial(self):
ld = LinearDensity(self.selection, binsize=5).run()
assert_allclose(self.xpos, ld.results['x']['pos'], rtol=1e-6, atol=0)
def electron_density_mdanalysis(self):
'''This function calulate the charge density through MDAnalaysis'''
u = mda.Universe(self.tprpath, self.trjpath)
lipid_types_first = ''.join(self.molecules[0])
print(lipid_types_first)
self.lipid_type_items = ' '.join(self.molecules)
print(lipid_types_first)
selection = u.select_atoms('resname {}'.format(self.lipid_type_items))
ref_selection = u.select_atoms(
'resname {} and name P'.format(lipid_types_first))
print(self.times[2])
interval_of_frames = str(self.times[2])
print(interval_of_frames)
if self.times[2] == '1000':
start_frame = 100
frame_intervals = 1
end_frame = 300
else:
start_frame = 1000
frame_intervals = 10
end_frame = 3000
Idens = LinearDensity(selection,
grouping='atoms',
binsize=0.25,
start=start_frame,
step=frame_intervals,
stop=end_frame)
Idens.run()
Idens.save(description='densprof', form='txt')
# subtracting the center of geometry of the lipid from the first column of the data
# calculating center of geometry of lipids
u = self.universe
cog = []
for i_ts, ts in enumerate(u.trajectory[start_frame::frame_intervals]):
ref_selection_xyz = ref_selection.center_of_geometry()
cog.append(ref_selection_xyz[2])
centerofgeometry_z = np.mean(cog)
####
dat = np.loadtxt('{}_{}.densprof_atoms.ldens'.format(self.system,
self.temperature,
skiprows=2))
dat[:, 0] = dat[:, 0] - centerofgeometry_z
np.savetxt('{}_{}.densprof_atoms_centered.ldens'.format(
self.system, self.temperature),
dat,
delimiter=' ',
fmt='%.5f')
def test_results_warning():
universe = mda.Universe(waterPSF, waterDCD)
msg = ("The structure of the `results` dictionary will change in "
"MDAnalysis version 2.0.")
with pytest.warns(DeprecationWarning, match=msg):
LinearDensity(universe.atoms).run()
sel.append("name OW and (around %.4f resname %s) and name OW and (not \
around %.4f resname %s)" % (cation[2], cation[0], cation[1], cation[0]))
sel.append("name OW and (around %.4f resname %s)" % (anion[1], anion[0]))
sel.append("name OW and (around %.4f resname %s) and name OW and (not \
around %.4f resname %s)" % (anion[2], anion[0], anion[1], anion[0]))
# Water mass density analysis
print("#------------------------------------------------------#")
print("Start Water mass density analysis")
os.system("mkdir Mass-Density")
resid = int((u.select_atoms("resname SOL").n_atoms) / 3)
u = mda.Universe(TPR, TRR)
water = u.select_atoms("resid 0-%d" % (resid))
watermassdensity = LA(water)
watermassdensity.run()
watermassdensity.save(description='watermassdensity', form='txt')
data = np.loadtxt("nvtnemd.watermassdensity_atoms.ldens", skiprows=2)
labels = ["x", "y", "z"]
colors = ["chartreuse", "deepskyblue", "r"]
for i in range(len(labels)):
if i == 0:
plt.plot(data[:, 0] / 10.0,
data[:, i + 1],
color=colors[i],
lw=2.0,
label=labels[i])
if i == 1: