def rotation_test():
print ">> running rotation test ",
sys.stdout.flush()
f = open("rotation.dat","w")
p = 4
print >>f,"# rotation test "
n = 40
alphas = []
cs = []
p = [math.sqrt(2.),math.sqrt(2.),0]
p = [0,1,0]
for i in range(n+1):
a = 2.0*math.pi*i/n
R = util.rotation(p,a)
c = np.array(util.rotate_all(R,c1))
alphas.append(a)
cs.append(c)
g0,R0 = r.distance(C1,C2)
print >>f,"# RMSD ref =",g0
print >>f,"# OGTO ref =",
o0s = []
for sig in sigmas:
d0,R0 = o.distance(c1,c2,sig)
o0s.append(d0)
print >>f,d0,
print >>f
print >>f,"# alpha d_rmsd, d_ogto @ sig=",
for sig in sigmas: print >>f, sig,
print >>f
for i in range(len(alphas)):
sys.stdout.write("*")
sys.stdout.flush()
a = alphas[i]
# optimal rot
d1,R1r = r.distance(C1,cs[i])
print >>f,"{0:8.5f} ".format(a),
print >>f,"{0:10.7f} ".format(d1),
for j in range(len(sigmas)):
sig = sigmas[j]
d0 = o0s[j]
d1,R1 = o.distance(c1,cs[i],sig)
print >>f,"{0:10.7f} ".format(d1),
# if (d1 < 0.01):
# print
# print R1r
# print R1
# no rot
d1,R1 = r.dist(C1,cs[i])
print >>f,"{0:10.7f} ".format(d1),
for j in range(len(sigmas)):
sig = sigmas[j]
d0 = o0s[j]
d1,R1 = o.dist(c1,cs[i],sig)
print >>f,"{0:10.7f} ".format(d1),
print >>f
print "done"
def rotation_test():
print ">> running rotation test ",
sys.stdout.flush()
f = open("rotation.dat", "w")
p = 4
print >> f, "# rotation test "
n = 40
alphas = []
cs = []
for i in range(n + 1):
a = 2.0 * math.pi * i / n
R = util.rotation([1, 0, 0], a)
c = np.array(util.rotate_all(R, c1))
alphas.append(a)
cs.append(c)
g0, R0 = g.distance(C1, C2)
print >> f, "# RMSD ref =", g0
print >> f, "# OGTO ref =",
o0s = []
for sig in sigmas:
d0, R0 = o.distance(c1, c2, sig)
#d0,R0 = o.dist(c1,c2,sig)
o0s.append(d0)
print >> f, d0,
print >> f
print >> f, "# alpha (d1,d2)_rmsd, _ogto @ sig=",
for sig in sigmas:
print >> f, sig,
print >> f
for i in range(len(alphas)):
sys.stdout.write("*")
sys.stdout.flush()
a = alphas[i]
d1, R1 = g.distance(C1, cs[i])
d2, R2 = g.distance(C2, cs[i])
print "RMSD\n", R1, "\n", R2
print >> f, "{0:8.5f} {1:10.7f} {2:10.7f}".format(a, d1 / g0, d2 / g0),
for j in range(len(sigmas)):
sig = sigmas[j]
d0 = o0s[j]
d1, R1 = o.distance(c1, cs[i], sig)
d2, R2 = o.distance(c2, cs[i], sig)
#d1,R1 = o.dist(c1,cs[i],sig)
#d2,R2 = o.dist(c2,cs[i],sig)
print "OGTO\n", R1, "\n", R2
print >> f, "{0:10.7f} {1:10.7f}".format(d1 / d0, d2 / d0),
print >> f
print "done"
def rotation_test():
print ">> running rotation test ",
sys.stdout.flush()
f = open("rotation.dat","w")
p = 4
print >>f,"# rotation test "
n = 40
alphas = []
cs = []
for i in range(n+1):
a = 2.0*math.pi*i/n
R = util.rotation([1,0,0],a)
c = np.array(util.rotate_all(R,c1))
alphas.append(a)
cs.append(c)
g0,R0 = g.distance(C1,C2)
print >>f,"# RMSD ref =",g0
print >>f,"# OGTO ref =",
o0s = []
for sig in sigmas:
d0,R0 = o.distance(c1,c2,sig)
#d0,R0 = o.dist(c1,c2,sig)
o0s.append(d0)
print >>f,d0,
print >>f
print >>f,"# alpha (d1,d2)_rmsd, _ogto @ sig=",
for sig in sigmas: print >>f, sig,
print >>f
for i in range(len(alphas)):
sys.stdout.write("*")
sys.stdout.flush()
a = alphas[i]
d1,R1 = g.distance(C1,cs[i])
d2,R2 = g.distance(C2,cs[i])
print "RMSD\n",R1,"\n",R2
print >>f,"{0:8.5f} {1:10.7f} {2:10.7f}".format(a,d1/g0,d2/g0),
for j in range(len(sigmas)):
sig = sigmas[j]
d0 = o0s[j]
d1,R1 = o.distance(c1,cs[i],sig)
d2,R2 = o.distance(c2,cs[i],sig)
#d1,R1 = o.dist(c1,cs[i],sig)
#d2,R2 = o.dist(c2,cs[i],sig)
print "OGTO\n",R1,"\n",R2
print >>f,"{0:10.7f} {1:10.7f}".format(d1/d0,d2/d0),
print >>f
print "done"
print >> f, " }"
print >> f, "}"
f.close()
os.system("dot -Tpdf " + tag + ".gv -o " + tag + ".pdf")
#####################################################################
## MAIN
#####################################################################
if __name__ == "__main__":
print "!!! TEST !!!"
c1 = [[1.1, 1, 1], [1, -1, -1], [-1, 1, -1], [-1, -1, 1]]
C1 = np.array(c1)
c2 = [[1.1, 1, 1], [-1, 1, -1], [1, -1, -1], [-1, -1, 1]]
#c2 = c1
C2 = np.array(c2)
g = graph()
g.from_points(c1, c2)
g.write("c12")
print "# theta d"
g.exponent = -2
for i in range(19):
theta = math.pi * i / 6
R = util.rotation([1, 0, 0], theta)
#print R
Rc2 = util.rotate_all(R, c2)
#print Rc2
g.from_points(c1, Rc2)
print "{0:10.6f} {1:10.6f}".format(theta, g.norm())
#####################################################################
## MAIN
#####################################################################
if __name__ == "__main__":
print "!!! TEST !!!"
c1 = [[1.1, 1, 1],
[1, -1, -1],
[-1, 1, -1],
[-1, -1, 1]]
C1 = np.array(c1)
c2 = [[1.1, 1, 1],
[-1, 1, -1],
[1, -1, -1],
[-1, -1, 1]]
#c2 = c1
C2 = np.array(c2)
g = graph()
g.from_points(c1,c2)
g.write("c12")
print "# theta d"
g.exponent = -2
for i in range(19):
theta = math.pi*i/6
R = util.rotation([1,0,0],theta)
#print R
Rc2 = util.rotate_all(R,c2)
#print Rc2
g.from_points(c1,Rc2)
print "{0:10.6f} {1:10.6f}".format(theta,g.norm())