def align(full_base, ox_base):
theta = utils.get_angle(full_base.a3, ox_base._a3)
# if the two bases are already essentially aligned then we do nothing
if sin(theta) > 1e-3:
axis = np.cross(full_base.a3, ox_base._a3)
axis /= sqrt(np.dot(axis, axis))
R = utils.get_rotation_matrix(axis, theta)
full_base.rotate(R)
theta = utils.get_angle(full_base.a1, ox_base._a1)
if sin(theta) > 1e-3:
axis = np.cross(full_base.a1, ox_base._a1)
axis /= sqrt(np.dot(axis, axis))
R = utils.get_rotation_matrix(axis, theta)
full_base.rotate(R)
def vhelix_rotation_origami_he(direction, perp):
R = utils.get_rotation_matrix(direction, np.pi * 160. / 180)
return np.dot(R, perp)
for c in range(nbases):
#dna center of mass positions
ssdna1[c, :] = coordxyz[c, :] - CM_CENTER_DS * v_perp_ssdna1[c, :]
ssdna2[c, :] = coordxyz[c, :] + CM_CENTER_DS * v_perp_ssdna1[c, :]
#Update v_perp_ssdna1
ind_1 = c
ind = (c + 1) % nbases
alpha = top.py_ang(v_perp_ssdna1[ind_1, :], p[ind, :], dist[ind_1, :])
gamma = rot_base - alpha
#prevent change when ind=0 on open chain
if c != nbases - 1:
R = utils.get_rotation_matrix(dist[ind, :], gamma)
v_perp_ssdna1[ind, :] = np.dot(R, p[ind, :])
v_perp_ssdna2[ind, :] = -v_perp_ssdna1[ind, :]
# check LK imposed and measured
if opts.closed:
TW_measured = top.get_twist(coordxyz, ssdna1)
box = np.array([boxmax, boxmax, boxmax])
system = base.System(box)
if opts.sequence_file == None:
ssdna1_base = np.zeros(nbases, int)
for c in range(nbases):
ssdna1_base[c] = np.random.randint(0, 4)
else: