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# example script to viualise how mobile all atoms from a trajectory are
# it creates a sphere for every atoms
# the radius is proportional to the mobility and the color is
# interpolated between blue (no movement at all) and red (very mobile)
dcd = DCDFile("test.dcd")
system = getSystems()[0]
number_ss = dcd.getNumberOfSnapShots()
ssm = SnapShotManager(system, getMolecularStructure().getForceField(), dcd)
rep = Representation()
positions = []
distances = []
nr_atoms = 0
for atom in atoms(system):
positions.append(Vector3())
distances.append(0)
nr_atoms += 1
# calculate the median position of every atom
while ssm.applyNextSnapShot():
i = 0
for atom in atoms(system):
positions[i] = positions[i] + atom.getPosition()
i = i + 1
for position in positions:
position /= number_ss
ssm.applyFirstSnapShot()
# calculate the medium difference in position for every atom
while ssm.applyNextSnapShot():
i = 0
for atom in atoms(system):
distances[i] = distances[i] + (atom.getPosition() - positions[i]).getLength()
i = i + 1
#normalize distances
max_distance = 0
for distance in distances:
if distance > max_distance:
max_distance = distance
i = 0
while i < nr_atoms:
distances[i] = distances[i] / max_distance
i = i + 1
# create the spheres
i = 0
while i < nr_atoms:
sphere = Sphere()
sphere.setPosition(positions[i])
sphere.setRadius(distances[i])
sphere.setColor(ColorRGBA(distances[i], 0, 1 -distances[i]))
rep.insert(sphere)
i = i + 1
# set the atoms to their median position
i = 0
for atom in atoms(system):
atom.setPosition(positions[i])
i = i + 1
getMainControl().insert(rep)
getMainControl().update(rep)
getMainControl().update(system)
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