def test_distance(self):
for i in range(100):
coords1 = np.random.random(6 * self.nrigid) * 4
coords2 = np.random.random(6 * self.nrigid) * 4
coords1[:3 * self.nrigid] = 0
coords2[:3 * self.nrigid] = 0
measure1 = am.MeasureAngleAxisCluster(self.topology)
measure2 = am.MeasureRigidBodyCluster(self.topology)
#print
self.assertAlmostEqual(measure1.get_dist(coords1, coords2),
measure2.get_dist(coords1, coords2))
break
fin.readline()
coords = np.zeros([26, 3])
for i in range(26):
x = [float(x) for x in fin.readline().split()[1:]]
coords[i] = x
path_xyz.append(coords)
print("length of path:", len(path_xyz))
path = [map_to_aa(xyz) for xyz in path_xyz]
# this block aligns the images
transform = aamindist.TransformAngleAxisCluster(system.aasystem)
measure = aamindist.MeasureAngleAxisCluster(system.aasystem,
transform=transform)
com = measure.get_com(path[0])
transform.translate(path[0], -com)
for i in range(1, len(path)):
com = measure.get_com(path[i])
transform.translate(path[i], -com)
dist, rot = measure.find_rotation(path[i - 1], path[i])
transform.rotate(path[i], rot)
#p#ath = [ x for x in IntterpolatedPath(db.minima[19], )]
#path = [ x for x in InterpolatedPath(path[0].copy(), path[-1].copy(), 34) ]
traj = open("traj.xyz", "w")
#for x in path:
# #export_xyz(traj, x)
# #ret = quench.mylbfgs(x, pot.getEnergyGradient)