def setUp(self):
self.nrigid = 1
self.boxl = np.array([5,5,5])
# self.topology = RBTopologyBulk(self.boxl)
# self.topology.finalize_setup()
# sites = []
# for i in range(self.nrigid):
# sites.append(self.make_molecule())
# self.topology.add_sites(sites)
# self.draw_bonds = []
# for i in xrange(self.nrigid):
# # self.draw_bonds.append((2*i,2*i+1))
# self.draw_bonds.append((3*i, 3*i+1))
# self.draw_bonds.append((3*i, 3*i+2))
# #self.permlist = self.get_permlist()
import pele.angleaxis._otp_bulk as OTP
self.system = OTP.OTPBulk(self.nrigid, self.boxl, 2.5)
self.topology = self.system.aatopology
self.mindist = self.system.get_mindist()
self.transform = TransformPeriodicRigid()
self.measure = MeasurePeriodicRigid(self.topology, self.transform)
self.exact_match = ExactMatchRigidPeriodic(self.measure, accuracy=1e-5)
# self.mindist = MinPermDistBulk(self.boxl, self.measure)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
self.x2same = self.x1.copy()
self.x2trans = self.x1.copy()
trans = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, trans)
def setUp(self):
self.nrigid = 1
self.boxl = np.array([5,5,5])
# self.topology = RBTopologyBulk(self.boxl)
# self.topology.finalize_setup()
# sites = []
# for i in range(self.nrigid):
# sites.append(self.make_molecule())
# self.topology.add_sites(sites)
# self.draw_bonds = []
# for i in xrange(self.nrigid):
# # self.draw_bonds.append((2*i,2*i+1))
# self.draw_bonds.append((3*i, 3*i+1))
# self.draw_bonds.append((3*i, 3*i+2))
# #self.permlist = self.get_permlist()
import pele.angleaxis._otp_bulk as OTP
self.system = OTP.OTPBulk(self.nrigid, self.boxl, 2.5)
self.topology = self.system.aatopology
self.mindist = self.system.get_mindist()
self.transform = TransformPeriodicRigid()
self.measure = MeasurePeriodicRigid(self.topology, self.transform)
self.exact_match = ExactMatchRigidPeriodic(self.measure, accuracy=1e-5)
# self.mindist = MinPermDistBulk(self.boxl, self.measure)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
self.x2same = self.x1.copy()
self.x2trans = self.x1.copy()
trans = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, trans)
def get_mindist(self, **kwargs):
measure = MeasurePeriodicRigid(self.aatopology,
transform=TransformPeriodicRigid())
return MinDistBulkRigid(self.boxvec,
measure,
niter=10,
transform=TransformPeriodicRigid(),
verbose=False,
tol=0.01,
accuracy=0.01)
class TestExactMatchPeriodicRigid(unittest.TestCase):
def setUp(self):
self.nrigid = 1
self.boxl = np.array([5,5,5])
# self.topology = RBTopologyBulk(self.boxl)
# self.topology.finalize_setup()
# sites = []
# for i in range(self.nrigid):
# sites.append(self.make_molecule())
# self.topology.add_sites(sites)
# self.draw_bonds = []
# for i in xrange(self.nrigid):
# # self.draw_bonds.append((2*i,2*i+1))
# self.draw_bonds.append((3*i, 3*i+1))
# self.draw_bonds.append((3*i, 3*i+2))
# #self.permlist = self.get_permlist()
import pele.angleaxis._otp_bulk as OTP
self.system = OTP.OTPBulk(self.nrigid, self.boxl, 2.5)
self.topology = self.system.aatopology
self.mindist = self.system.get_mindist()
self.transform = TransformPeriodicRigid()
self.measure = MeasurePeriodicRigid(self.topology, self.transform)
self.exact_match = ExactMatchRigidPeriodic(self.measure, accuracy=1e-5)
# self.mindist = MinPermDistBulk(self.boxl, self.measure)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
self.x2same = self.x1.copy()
self.x2trans = self.x1.copy()
trans = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, trans)
#dist = self.measure.get_dist(self.x1, self.x2diff)
def make_molecule(self):
"""this constructs a single test molecule"""
molecule = RigidFragmentBulk(self.boxl)
# molecule.add_atom("O", np.array([-0.25,0.0,0.0]), 1.)
# molecule.add_atom("O", np.array([0.25,0.,0.]), 1.)
# Note: need to change setup of self.draw_bonds also.
molecule.add_atom("O", np.array([0.0, old_div(-2.,3) * np.sin( 7.*pi/24.), 0.0]), 1.)
molecule.add_atom("O", np.array([cos( 7.*pi/24.), 1./3. * sin( 7.* pi/24.), 0.0]), 1.)
molecule.add_atom("O", np.array([-cos( 7.* pi/24.), 1./3. * sin( 7.*pi/24), 0.0]), 1.)
molecule.finalize_setup()
return molecule
def randomly_permute(self, x):
import random
x = x.reshape(-1,3)
xnew = x.copy()
for atomlist in self.permlist:
permutation = copy.copy(atomlist)
random.shuffle(permutation)
xnew[atomlist,:] = x[permutation,:]
return xnew.flatten()
def get_random_configuration(self):
x = np.zeros([self.nrigid*2,3])
for i in range(self.nrigid):
for j in range(3):
x[i][j] = np.random.uniform(-self.boxl[j]/2., self.boxl[j]/2.)
for i in range(self.nrigid,2*self.nrigid):
x[i] = 5.*np.random.random(3)
#print "x.flatten()", x.flatten()
return x.flatten()
def test_exact_match(self):
self.assertTrue(self.exact_match(self.x1, self.x2trans))
def test_no_exact_match(self):
self.assertFalse(self.exact_match(self.x1, self.x2diff))
def test_exact_match_periodic(self):
self.x2same[:3] += self.topology.boxvec
self.assertTrue(self.exact_match(self.x1, self.x2same))
def test_align_translate(self):
np.random.seed(4)
n = self.nrigid
fail_counter = 0
for i in range(10000):
# if (i%100 == 0):
# print i
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
try:
dist, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
pass
if self.exact_match(self.x2diff,x2) is False:
fail_counter += 1
self.assertFalse(fail_counter, "bond lengths were changed %d times" % fail_counter)
def test_align_match(self):
np.random.seed(2)
fail_counter = 0
for i in range(1):
# if (i%100 == 0):
# print i
self.x1 = self.get_random_configuration()
self.x2trans = self.x1
translate = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, translate)
try:
dist, x1, x2 = self.mindist(self.x1, self.x2trans)
except RuntimeError:
pass
if (dist>1e-5):
fail_counter+=1
print(dist)
self.assertFalse(fail_counter, "structure matching failed %d times" % fail_counter)
def test_align_permutation(self):
np.random.seed(4)
fail_counter = 0
for i in range(1):
if (i%100 == 0):
print(i)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
try:
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
fail_counter+=1
self.assertFalse(fail_counter, "rotational alignment failed %d times" % fail_counter)
def test_align_improvement(self, verbose = True):
np.random.seed(6)
max_step = 10000
fail_counter = 0
ave = 0
ave_inc = 0
for i in range(max_step):
if (i%100 == 0):
print(i)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
dist = self.measure.get_dist(self.x1, self.x2diff)
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
if(dist2 > dist):
# if(i==10):
fail_counter += 1
ave_inc += dist2 - dist
if(verbose):
print("x1", x1)
print("old x2", self.x2diff)
print("new x2", x2)
# print "atomistic x1", self.topology.to_atomistic(x1).flatten()
# print "atomistic x2", self.topology.to_atomistic(self.x2diff)
# print "new atomistic x2", self.topology.to_atomistic(x2)
print("dist", dist)
print("dist2", dist2)
print("i", i)
try:
import pele.utils.pymolwrapper as pym
pym.start()
x1 = self.topology.to_atomistic(x1)
x2 = self.topology.to_atomistic(x2)
self.x2diff = self.topology.to_atomistic(self.x2diff)
pym.draw_rigid(x1, "A", 0.1, (1,0,0), self.system.draw_bonds)
pym.draw_rigid(self.x2diff, "B", 0.1, (0,1,0), self.system.draw_bonds)
pym.draw_rigid(x2, "C", 0.1, (0,0,1), self.system.draw_bonds)
pym.draw_box(self.boxl, "D", 0.1)
# pym.draw_rigid(x1[:self.nrigid*3], "A", 0.1, (1,0,0))
# pym.draw_rigid(self.x2diff[:self.nrigid*3], "B", 0.1, (0,1,0))
# pym.draw_rigid(x2[:self.nrigid*3], "C", 0.1, (0,0,1))
# pym.draw_box(self.boxl, "D", 0.1)
except:
print("Could not draw using pymol, skipping this step")
else:
ave += dist - dist2
ave = old_div(ave,max_step)
if (fail_counter>0): ave_inc = old_div(ave_inc, fail_counter)
print("average decrease in distance", ave)
print("average increase in distance", ave_inc)
self.assertFalse(fail_counter, "alignment failed %d times" % fail_counter)
class TestExactMatchPeriodicRigid(unittest.TestCase):
def setUp(self):
self.nrigid = 1
self.boxl = np.array([5,5,5])
# self.topology = RBTopologyBulk(self.boxl)
# self.topology.finalize_setup()
# sites = []
# for i in range(self.nrigid):
# sites.append(self.make_molecule())
# self.topology.add_sites(sites)
# self.draw_bonds = []
# for i in xrange(self.nrigid):
# # self.draw_bonds.append((2*i,2*i+1))
# self.draw_bonds.append((3*i, 3*i+1))
# self.draw_bonds.append((3*i, 3*i+2))
# #self.permlist = self.get_permlist()
import pele.angleaxis._otp_bulk as OTP
self.system = OTP.OTPBulk(self.nrigid, self.boxl, 2.5)
self.topology = self.system.aatopology
self.mindist = self.system.get_mindist()
self.transform = TransformPeriodicRigid()
self.measure = MeasurePeriodicRigid(self.topology, self.transform)
self.exact_match = ExactMatchRigidPeriodic(self.measure, accuracy=1e-5)
# self.mindist = MinPermDistBulk(self.boxl, self.measure)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
self.x2same = self.x1.copy()
self.x2trans = self.x1.copy()
trans = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, trans)
#dist = self.measure.get_dist(self.x1, self.x2diff)
def make_molecule(self):
"""this constructs a single test molecule"""
molecule = RigidFragmentBulk(self.boxl)
# molecule.add_atom("O", np.array([-0.25,0.0,0.0]), 1.)
# molecule.add_atom("O", np.array([0.25,0.,0.]), 1.)
# Note: need to change setup of self.draw_bonds also.
molecule.add_atom("O", np.array([0.0, -2./3 * np.sin( 7.*pi/24.), 0.0]), 1.)
molecule.add_atom("O", np.array([cos( 7.*pi/24.), 1./3. * sin( 7.* pi/24.), 0.0]), 1.)
molecule.add_atom("O", np.array([-cos( 7.* pi/24.), 1./3. * sin( 7.*pi/24), 0.0]), 1.)
molecule.finalize_setup()
return molecule
def randomly_permute(self, x):
import random
x = x.reshape(-1,3)
xnew = x.copy()
for atomlist in self.permlist:
permutation = copy.copy(atomlist)
random.shuffle(permutation)
xnew[atomlist,:] = x[permutation,:]
return xnew.flatten()
def get_random_configuration(self):
x = np.zeros([self.nrigid*2,3])
for i in range(self.nrigid):
for j in range(3):
x[i][j] = np.random.uniform(-self.boxl[j]/2., self.boxl[j]/2.)
for i in range(self.nrigid,2*self.nrigid):
x[i] = 5.*np.random.random(3)
#print "x.flatten()", x.flatten()
return x.flatten()
def test_exact_match(self):
self.assertTrue(self.exact_match(self.x1, self.x2trans))
def test_no_exact_match(self):
self.assertFalse(self.exact_match(self.x1, self.x2diff))
def test_exact_match_periodic(self):
self.x2same[:3] += self.topology.boxvec
self.assertTrue(self.exact_match(self.x1, self.x2same))
def test_align_translate(self):
np.random.seed(4)
n = self.nrigid
fail_counter = 0
for i in range(10000):
# if (i%100 == 0):
# print i
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
try:
dist, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
pass
if self.exact_match(self.x2diff,x2) is False:
fail_counter += 1
self.assertFalse(fail_counter, "bond lengths were changed %d times" % fail_counter)
def test_align_match(self):
np.random.seed(2)
fail_counter = 0
for i in range(1):
# if (i%100 == 0):
# print i
self.x1 = self.get_random_configuration()
self.x2trans = self.x1
translate = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, translate)
try:
dist, x1, x2 = self.mindist(self.x1, self.x2trans)
except RuntimeError:
pass
if (dist>1e-5):
fail_counter+=1
print(dist)
self.assertFalse(fail_counter, "structure matching failed %d times" % fail_counter)
def test_align_permutation(self):
np.random.seed(4)
fail_counter = 0
for i in range(1):
if (i%100 == 0):
print(i)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
try:
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
fail_counter+=1
self.assertFalse(fail_counter, "rotational alignment failed %d times" % fail_counter)
def test_align_improvement(self, verbose = True):
np.random.seed(6)
max_step = 10000
fail_counter = 0
ave = 0
ave_inc = 0
for i in range(max_step):
if (i%100 == 0):
print(i)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
dist = self.measure.get_dist(self.x1, self.x2diff)
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
if(dist2 > dist):
# if(i==10):
fail_counter += 1
ave_inc += dist2 - dist
if(verbose):
print("x1", x1)
print("old x2", self.x2diff)
print("new x2", x2)
# print "atomistic x1", self.topology.to_atomistic(x1).flatten()
# print "atomistic x2", self.topology.to_atomistic(self.x2diff)
# print "new atomistic x2", self.topology.to_atomistic(x2)
print("dist", dist)
print("dist2", dist2)
print("i", i)
try:
import pele.utils.pymolwrapper as pym
pym.start()
x1 = self.topology.to_atomistic(x1)
x2 = self.topology.to_atomistic(x2)
self.x2diff = self.topology.to_atomistic(self.x2diff)
pym.draw_rigid(x1, "A", 0.1, (1,0,0), self.system.draw_bonds)
pym.draw_rigid(self.x2diff, "B", 0.1, (0,1,0), self.system.draw_bonds)
pym.draw_rigid(x2, "C", 0.1, (0,0,1), self.system.draw_bonds)
pym.draw_box(self.boxl, "D", 0.1)
# pym.draw_rigid(x1[:self.nrigid*3], "A", 0.1, (1,0,0))
# pym.draw_rigid(self.x2diff[:self.nrigid*3], "B", 0.1, (0,1,0))
# pym.draw_rigid(x2[:self.nrigid*3], "C", 0.1, (0,0,1))
# pym.draw_box(self.boxl, "D", 0.1)
except:
print("Could not draw using pymol, skipping this step")
else:
ave += dist - dist2
ave = ave/max_step
if (fail_counter>0): ave_inc = ave_inc / fail_counter
print("average decrease in distance", ave)
print("average increase in distance", ave_inc)
self.assertFalse(fail_counter, "alignment failed %d times" % fail_counter)