def p6(c3a, c3b):
''' prep unit cell for P6 propogation '''
c3a_com = com(c3a)
c3b_com = com(c3b)
center = (c3b_com + c3a_com) / 2
center_tuple = center.tuple()
xy_center = [center_tuple[0], center_tuple[1], 0.0]
# print 'xy_center', xy_center
# print 'np.linalg.norm(xy_center)', np.linalg.norm(xy_center)
if np.linalg.norm(xy_center) > 0.00001:
'move to origin'
trans(c3a, -Vec(xy_center))
trans(c3b, -Vec(xy_center))
else:
'close enough'
c3a_com = com(c3a).tuple()
c3b_com = com(c3b).tuple()
c3_dist = (np.abs(c3a_com[0] - c3b_com[0])**2 +
np.abs(c3a_com[1] - c3b_com[1])**2)**0.5
### Angle between c3 centers must be 30 degrees
## 30, 60 degrees
## 0.523599, 1.5708
angle_to_c3a = np.arctan(c3a_com[1] / c3a_com[0])
# print np.degrees(angle_to_c3a), 'np.degrees(angle_to_c3a)'
angle_correction = float(np.degrees(angle_to_c3a - 0.523599))
# print angle_correction,'angle_correction'
rotz(c3a, -1 * angle_correction)
rotz(c3b, -1 * angle_correction)
### one of c3 centers must be along y-axis
c3a_com = com(c3a)
c3b_com = com(c3b)
# print 'c3_dist', c3_dist
# disp_to_c3a = Vec(0.0, float(c3_dist), 0.0) - c3a_com
# disp_to_c3b = Vec(0.0, float(c3_dist), 0.0) - c3b_com
if c3a_com.tuple()[1] > c3b_com.tuple()[1]:
# print 'A'
displacement = (Vec(0.0, float(c3_dist), 0.0) - c3a_com).tuple()
else:
# print 'B'
displacement = (Vec(0.0, float(c3_dist), 0.0) - c3b_com).tuple()
displacement = Vec([displacement[0], displacement[1], 0.0])
trans(c3a, displacement)
trans(c3b, displacement)
# print 'c3_dist', c3_dist
unit_cell = c3_dist * 1.73205080756887729352744634150587236694280525381038062805580
# print 'unit_cell', unit_cell
CRYST1 = 'CRYST1{0}{0} 999.000 90.00 90.00 120.00 P 6 2'.format(
str(unit_cell.round(3)).rjust(9))
print CRYST1
def show(self, points=[Vec(7, 12, 13), Vec(33, 34, 35)]):
v = pymol.cmd.get_view()
CGO = list()
for x in self.frames:
x.t = 100.0 * x.t
assert self.celltype == "CUBIC"
for p in points:
for i, j, k in itertools.product(range(-1, 2), range(-1, 2),
range(-1, 2)):
CGO.extend(cgo_sphere(x * p + Vec(i, j, k) * 100.0))
pymol.cmd.load_cgo(CGO, self.name)
cube(Vec(0, 0, 0), Vec(100, 100, 100))
pymol.cmd.set_view(v)
def op2xform(self, op):
Xop, Yop, Zop = op.split(",")
# print op
X, Tx = self.op2vec(Xop)
Y, Ty = self.op2vec(Yop)
Z, Tz = self.op2vec(Zop)
# print X
# print Y
# print Z
# print Tx,Ty,Tz
# print
return Xform(Mat(X.x, X.y, X.z, Y.x, Y.y, Y.z, Z.x, Z.y, Z.z),
Vec(Tx, Ty, Tz))
def hexgrid(n, w, maxang, sigma):
global max_sinh, max_asinh
dotthresh = cos(radians(maxang))
# if sigma != 0.0:
# w = w / sigma
X = w * Vec(1, 0, 0)
Y = w * Vec(0.5, sqrt(3.0) / 2, 0)
points = []
for i in range(-n, n + 1):
for j in range(-n, n + 1):
p = i * X + j * Y + Vec(0, 0, 1)
old = max_sinh, max_asinh
if sigma != 0.0:
p.x = mysinh(p.x * sigma) / sigma
p.y = mysinh(p.y * sigma) / sigma
p2 = p
p = p / p.length()
if p.z >= dotthresh:
points.append((p, p2))
else:
# restore if not accepted
max_sinh, max_asinh = old
return points
def op2vec(self, op):
op = op.replace(" ", "")
v, t = Vec(), 0
for o in op.replace("-", "+-").strip("+").split("+"):
if o == 'X': v += Ux
elif o == '-X': v -= Ux
elif o == 'Y': v += Uy
elif o == '-Y': v -= Uy
elif o == 'Z': v += Uz
elif o == '-Z': v -= Uz
elif o.count("/"):
n, d = o.split("/")
t += float(n) / float(d)
else:
raise ValueError
return v, t
def hcp(i, j, k, r=1.0):
return r * Vec(2.0 * i + (j % 2) + (k % 2),
(j + (k % 2) / 3.0) * sqrt(3.0),
k * sqrt(6.0) / 3.0 * 2.0)