def pdbBoxString(box):
# Box vectors
u, v, w = box[0:3], box[3:6], box[6:9]
# Box vector lengths
nu, nv, nw = [math.sqrt(FUNC.norm2(i)) for i in (u, v, w)]
# Box vector angles
alpha = nv*nw == 0 and 90 or math.acos(FUNC.cos_angle(v, w))/d2r
beta = nu*nw == 0 and 90 or math.acos(FUNC.cos_angle(u, w))/d2r
gamma = nu*nv == 0 and 90 or math.acos(FUNC.cos_angle(u, v))/d2r
return pdbBoxLine % (10*FUNC.norm(u), 10*FUNC.norm(v), 10*FUNC.norm(w), alpha, beta, gamma)
def add_dummy(beads, dist=0.11, n=2):
# Generate a random vector in a sphere of -1 to +1, to add to the bead position
v = [random.random()*2.-1, random.random()*2.-1, random.random()*2.-1]
# Calculated the length of the vector and divide by the final distance of the dummy bead
norm_v = FUNC.norm(v)/dist
# Resize the vector
vn = [i/norm_v for i in v]
# m sets the direction of the added vector, currently only works when adding one or two beads.
m = 1
for j in range(n):
newName = 'SCD'
newBead = (newName, tuple([i+(m*j) for i, j in zip(beads[-1][1], vn)]), beads[-1][2])
beads.append(newBead)
m *= -2
return beads
