def bilayer_lipid():
import matplotlib.pyplot as plt
outfile = "/home/mho/Downloads/new-self-ass.h5"
n_particles_per_frame, positions, types, ids = load_trajectory_to_npy(
outfile, stride=10)
config = readdyviewer.Configuration()
t = readdy.Trajectory(outfile)
config.colors[t.particle_types['Head']] = readdyviewer.Color(
plt.cm.jet(0)[0],
plt.cm.jet(0)[1],
plt.cm.jet(0)[2])
config.radii[t.particle_types['Head']] = .7
config.colors[t.particle_types['Tail']] = readdyviewer.Color(
plt.cm.jet(1.)[0],
plt.cm.jet(1.)[1],
plt.cm.jet(1.)[2])
config.radii[t.particle_types['Tail']] = .7
config.stride = 1
config.smoothing = 5
config.cutoff = 5
config.bond_radius = .02
config.wait = 3
config.draw_periodic = True
config.set_box_size(25, 25, 25)
readdyviewer.watch_npy(positions, types, ids, n_particles_per_frame,
config) #
def more_topologies_sim():
trajfile = "/home/mho/Development/readdyviewer/tests/more_topologies_simulation.h5"
n_particles_per_frame, positions, types, ids = load_trajectory_to_npy(
trajfile)
config = readdyviewer.Configuration()
t = readdy.Trajectory(trajfile)
entries = t.read()
time, topology_records = t.read_observable_topologies()
edges = []
for timestep, tops in enumerate(topology_records):
current_edges = []
for top in tops:
for e1, e2 in top.edges:
ix1 = top.particles[e1]
ix2 = top.particles[e2]
current_edges.append((ix1, ix2))
p1 = entries[timestep][ix1]
p2 = entries[timestep][ix2]
assert p1.type == 'T' or p1.type == 'center T', "expected topology type but got {} -- {}".format(
p1, p2)
assert p2.type == 'T' or p2.type == 'center T', "expected topology type but got {} -- {}".format(
p1, p2)
edges.append(current_edges)
config.colors[t.particle_types['center T']] = readdyviewer.Color(
153. / 255., 255. / 255., 0.)
config.radii[t.particle_types['center T']] = .5
config.colors[t.particle_types['T']] = readdyviewer.Color(
255. / 255., 153. / 255., 0.)
config.radii[t.particle_types['T']] = .5
config.clearcolor = readdyviewer.Color(155. / 255., 155. / 255.,
155. / 255.)
config.stride = 1
print(positions.shape)
print("go!")
readdyviewer.watch_npy(positions, types, ids, n_particles_per_frame,
config, edges)
def to_numpy(self, name="", start=None, stop=None):
from readdy.api.utils import load_trajectory_to_npy
return load_trajectory_to_npy(self._filename, begin=start, end=stop, name=name)
