def simulation_zigzag(NB=5):
mersenne_twister = flex.mersenne_twister(seed=0)
body = six_dof_body(
labels=["00", "01", "02"],
sites=matrix.col_list([
(0.3,-0.5,0),
(0.4,0.5,0),
(0,0,0)]),
bonds=[(0,2),(1,2)],
mersenne_twister=mersenne_twister)
body.parent = -1
bodies = [body]
vu = matrix.col((0,1,0)).rotate_around_origin(
axis=matrix.col((1,0,0)), angle=75, deg=True)
vr = matrix.col((0,1,0))
v = vu
pivot = matrix.col((0,0,0))
for ib in xrange(1,NB):
body = revolute_body(
labels=[str(ib)],
sites=[pivot + v*0.5],
bonds=[(-1,0)],
pivot=pivot,
normal=matrix.col((1,0,0)),
mersenne_twister=mersenne_twister)
body.parent = ib-1
bodies.append(body)
pivot += v
if (v is vu): v = vr
else: v = vu
return simulation(bodies=bodies)
def simulation_gly_with_nh():
pdb = """\
ATOM 0 N GLY A 1 10.949 12.815 15.189 0.00 0.00 N
ATOM 1 CA GLY A 1 10.405 13.954 15.917 0.00 0.00 C
ATOM 2 C GLY A 1 10.779 15.262 15.227 0.00 0.00 C
ATOM 3 O GLY A 1 9.916 16.090 14.936 0.00 0.00 O
ATOM 4 H GLY A 1 11.792 12.691 15.311 0.00 0.00 H
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(
labels=labels[:3],
sites=sites[:3],
bonds=[(0,1),(1,2)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(
labels=labels[3:4],
sites=sites[3:4],
bonds=[(-1,0)],
pivot=sites[2],
normal=(sites[2]-sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
body2 = revolute_body(
labels=labels[4:],
sites=sites[4:],
bonds=[(-3,0)],
pivot=sites[0],
normal=(sites[0]-sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body2.parent = 0
return simulation(bodies=[body0, body1, body2])
def simulation_ala_no_h():
pdb = """\
ATOM 0 N ALA A 1 10.949 12.815 15.189 0.00 0.00 N
ATOM 1 CA ALA A 1 10.405 13.954 15.917 0.00 0.00 C
ATOM 2 C ALA A 1 10.779 15.262 15.227 0.00 0.00 C
ATOM 3 CB ALA A 1 10.908 13.950 17.351 0.00 0.00 C
ATOM 4 O ALA A 1 9.916 16.090 14.936 0.00 0.00 O
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(
labels=labels[:4],
sites=sites[:4],
bonds=[(0,1),(1,2),(1,3)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(
labels=labels[4:],
sites=sites[4:],
bonds=[(-2,0)],
pivot=sites[2],
normal=(sites[2]-sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
return simulation(bodies=[body0, body1])
def simulation_gly_with_nh():
pdb = """\
ATOM 0 N GLY A 1 10.949 12.815 15.189 0.00 0.00 N
ATOM 1 CA GLY A 1 10.405 13.954 15.917 0.00 0.00 C
ATOM 2 C GLY A 1 10.779 15.262 15.227 0.00 0.00 C
ATOM 3 O GLY A 1 9.916 16.090 14.936 0.00 0.00 O
ATOM 4 H GLY A 1 11.792 12.691 15.311 0.00 0.00 H
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(labels=labels[:3],
sites=sites[:3],
bonds=[(0, 1), (1, 2)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(labels=labels[3:4],
sites=sites[3:4],
bonds=[(-1, 0)],
pivot=sites[2],
normal=(sites[2] - sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
body2 = revolute_body(labels=labels[4:],
sites=sites[4:],
bonds=[(-3, 0)],
pivot=sites[0],
normal=(sites[0] - sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body2.parent = 0
return simulation(bodies=[body0, body1, body2])
def simulation_zigzag(NB=5):
mersenne_twister = flex.mersenne_twister(seed=0)
body = six_dof_body(labels=["00", "01", "02"],
sites=matrix.col_list([(0.3, -0.5, 0), (0.4, 0.5, 0),
(0, 0, 0)]),
bonds=[(0, 2), (1, 2)],
mersenne_twister=mersenne_twister)
body.parent = -1
bodies = [body]
vu = matrix.col((0, 1, 0)).rotate_around_origin(axis=matrix.col((1, 0, 0)),
angle=75,
deg=True)
vr = matrix.col((0, 1, 0))
v = vu
pivot = matrix.col((0, 0, 0))
for ib in xrange(1, NB):
body = revolute_body(labels=[str(ib)],
sites=[pivot + v * 0.5],
bonds=[(-1, 0)],
pivot=pivot,
normal=matrix.col((1, 0, 0)),
mersenne_twister=mersenne_twister)
body.parent = ib - 1
bodies.append(body)
pivot += v
if (v is vu): v = vr
else: v = vu
return simulation(bodies=bodies)
def exercise_revolute(out, n_trials, n_dynamics_steps, delta_t=0.001):
mersenne_twister = flex.mersenne_twister(seed=0)
for i_trial in xrange(n_trials):
body = revolute_body(mersenne_twister=mersenne_twister)
body.parent = -1
sim = simulation(bodies=[body])
print >> out, "revolute:"
relative_range = exercise_sim(
out=out, n_dynamics_steps=n_dynamics_steps, delta_t=delta_t, sim=sim)
if (out is not sys.stdout):
assert relative_range < 1.e-4
def exercise_revolute(out, n_trials, n_dynamics_steps, delta_t=0.001):
mersenne_twister = flex.mersenne_twister(seed=0)
for i_trial in range(n_trials):
body = revolute_body(mersenne_twister=mersenne_twister)
body.parent = -1
sim = simulation(bodies=[body])
print("revolute:", file=out)
relative_range = exercise_sim(
out=out, n_dynamics_steps=n_dynamics_steps, delta_t=delta_t, sim=sim)
if (out is not sys.stdout):
assert relative_range < 1.e-4
def exercise_six_dof(out, n_trials, n_dynamics_steps, delta_t=0.001):
mersenne_twister = flex.mersenne_twister(seed=0)
for n_sites in xrange(1,4):
for i_trial in xrange(n_trials):
body = six_dof_body(mersenne_twister=mersenne_twister, n_sites=n_sites)
body.parent = -1
sim = simulation(bodies=[body])
print >> out, "six_dof number of sites:", n_sites
relative_range = exercise_sim(
out=out, n_dynamics_steps=n_dynamics_steps, delta_t=delta_t, sim=sim)
if (out is not sys.stdout):
assert relative_range < 1.e-4
def exercise_six_dof(out, n_trials, n_dynamics_steps, delta_t=0.001):
mersenne_twister = flex.mersenne_twister(seed=0)
for n_sites in range(1,4):
for i_trial in range(n_trials):
body = six_dof_body(mersenne_twister=mersenne_twister, n_sites=n_sites)
body.parent = -1
sim = simulation(bodies=[body])
print("six_dof number of sites:", n_sites, file=out)
relative_range = exercise_sim(
out=out, n_dynamics_steps=n_dynamics_steps, delta_t=delta_t, sim=sim)
if (out is not sys.stdout):
assert relative_range < 1.e-4
def exercise_revolute2(out, n_trials, n_dynamics_steps, delta_t=0.001):
mersenne_twister = flex.mersenne_twister(seed=0)
for i_trial in xrange(n_trials):
body1 = revolute_body(mersenne_twister=mersenne_twister)
body1.parent = -1
body2 = revolute_body(mersenne_twister=mersenne_twister, prev=body1)
body2.parent = 0
sim = simulation(bodies=[body1, body2])
print >> out, "revolute2:"
relative_range = exercise_sim(out=out,
n_dynamics_steps=n_dynamics_steps,
delta_t=delta_t,
sim=sim)
if (out is not sys.stdout):
assert relative_range < 1.e-4
def simulation_ala_with_h():
pdb = """\
ATOM 0 N ALA A 1 10.949 12.815 15.189 0.00 0.00 N
ATOM 1 CA ALA A 1 10.405 13.954 15.917 0.00 0.00 C
ATOM 2 C ALA A 1 10.779 15.262 15.227 0.00 0.00 C
ATOM 3 HA ALA A 1 9.428 13.887 15.936 0.00 0.00 H
ATOM 4 O ALA A 1 9.916 16.090 14.936 0.00 0.00 O
ATOM 5 H ALA A 1 11.792 12.691 15.311 0.00 0.00 H
ATOM 6 CB ALA A 1 10.908 13.950 17.351 0.00 0.00 C
ATOM 7 HB1 ALA A 1 10.627 13.138 17.778 0.00 0.00 H
ATOM 8 HB2 ALA A 1 10.540 14.707 17.813 0.00 0.00 H
ATOM 9 HB3 ALA A 1 11.867 14.004 17.346 0.00 0.00 H
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(
labels=labels[:4],
sites=sites[:4],
bonds=[(0,1),(1,2),(1,3)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(
labels=labels[4:5],
sites=sites[4:5],
bonds=[(-2,0)],
pivot=sites[2],
normal=(sites[2]-sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
body2 = revolute_body(
labels=labels[5:6],
sites=sites[5:6],
bonds=[(-4,0)],
pivot=sites[0],
normal=(sites[0]-sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body2.parent = 0
body3 = revolute_body(
labels=labels[6:],
sites=sites[6:],
bonds=[(-3,0),(0,1),(0,2),(0,3)],
pivot=sites[6],
normal=(sites[6]-sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body3.parent = 0
return simulation(bodies=[body0, body1, body2, body3])
def exercise_six_dof2(out, n_trials, n_dynamics_steps, delta_t=0.001):
mersenne_twister = flex.mersenne_twister(seed=1)
for n_sites in xrange(1, 4):
for i_trial in xrange(n_trials):
body1 = six_dof_body(mersenne_twister=mersenne_twister,
n_sites=n_sites)
body1.parent = -1
body2 = six_dof_body(mersenne_twister=mersenne_twister,
n_sites=n_sites)
body2.parent = 0
sim = simulation(bodies=[body1, body2])
print >> out, "six_dof2 number of sites:", n_sites
relative_range = exercise_sim(out=out,
n_dynamics_steps=n_dynamics_steps,
delta_t=delta_t,
sim=sim)
if (out is not sys.stdout):
assert relative_range < 1.e-4
def simulation_ala_with_h():
pdb = """\
ATOM 0 N ALA A 1 10.949 12.815 15.189 0.00 0.00 N
ATOM 1 CA ALA A 1 10.405 13.954 15.917 0.00 0.00 C
ATOM 2 C ALA A 1 10.779 15.262 15.227 0.00 0.00 C
ATOM 3 HA ALA A 1 9.428 13.887 15.936 0.00 0.00 H
ATOM 4 O ALA A 1 9.916 16.090 14.936 0.00 0.00 O
ATOM 5 H ALA A 1 11.792 12.691 15.311 0.00 0.00 H
ATOM 6 CB ALA A 1 10.908 13.950 17.351 0.00 0.00 C
ATOM 7 HB1 ALA A 1 10.627 13.138 17.778 0.00 0.00 H
ATOM 8 HB2 ALA A 1 10.540 14.707 17.813 0.00 0.00 H
ATOM 9 HB3 ALA A 1 11.867 14.004 17.346 0.00 0.00 H
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(labels=labels[:4],
sites=sites[:4],
bonds=[(0, 1), (1, 2), (1, 3)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(labels=labels[4:5],
sites=sites[4:5],
bonds=[(-2, 0)],
pivot=sites[2],
normal=(sites[2] - sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
body2 = revolute_body(labels=labels[5:6],
sites=sites[5:6],
bonds=[(-4, 0)],
pivot=sites[0],
normal=(sites[0] - sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body2.parent = 0
body3 = revolute_body(labels=labels[6:],
sites=sites[6:],
bonds=[(-3, 0), (0, 1), (0, 2), (0, 3)],
pivot=sites[6],
normal=(sites[6] - sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body3.parent = 0
return simulation(bodies=[body0, body1, body2, body3])
def simulation_ala_no_h():
pdb = """\
ATOM 0 N ALA A 1 10.949 12.815 15.189 0.00 0.00 N
ATOM 1 CA ALA A 1 10.405 13.954 15.917 0.00 0.00 C
ATOM 2 C ALA A 1 10.779 15.262 15.227 0.00 0.00 C
ATOM 3 CB ALA A 1 10.908 13.950 17.351 0.00 0.00 C
ATOM 4 O ALA A 1 9.916 16.090 14.936 0.00 0.00 O
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(labels=labels[:4],
sites=sites[:4],
bonds=[(0, 1), (1, 2), (1, 3)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(labels=labels[4:],
sites=sites[4:],
bonds=[(-2, 0)],
pivot=sites[2],
normal=(sites[2] - sites[1]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
return simulation(bodies=[body0, body1])
def simulation_tyr_with_h():
pdb = """\
ATOM 0 CG TYR A 1 11.007 9.417 9.446 1.00 0.79 C
ATOM 1 CD1 TYR A 1 9.923 10.155 8.940 1.00 1.42 C
ATOM 2 CD2 TYR A 1 10.765 8.288 10.238 1.00 1.41 C
ATOM 3 CE1 TYR A 1 8.612 9.760 9.229 1.00 1.61 C
ATOM 4 CE2 TYR A 1 9.453 7.895 10.525 1.00 1.42 C
ATOM 5 CZ TYR A 1 8.377 8.631 10.021 1.00 1.11 C
ATOM 6 HD1 TYR A 1 10.092 11.024 8.328 1.00 2.14 H
ATOM 7 HD2 TYR A 1 11.596 7.718 10.630 1.00 2.21 H
ATOM 8 HE1 TYR A 1 7.780 10.329 8.841 1.00 2.44 H
ATOM 9 HE2 TYR A 1 9.270 7.023 11.135 1.00 2.13 H
ATOM 10 OH TYR A 1 7.083 8.244 10.304 1.00 1.32 O
ATOM 11 HH TYR A 1 6.494 8.723 9.717 1.00 2.00 H
ATOM 12 CB TYR A 1 12.440 9.818 9.148 1.00 0.74 C
ATOM 13 HB2 TYR A 1 12.827 9.193 8.358 1.00 0.78 H
ATOM 14 HB3 TYR A 1 13.036 9.677 10.037 1.00 0.78 H
ATOM 15 N TYR A 1 11.593 12.101 9.550 1.00 0.82 N
ATOM 16 CA TYR A 1 12.527 11.286 8.721 1.00 0.75 C
ATOM 17 C TYR A 1 12.160 11.413 7.239 1.00 0.76 C
ATOM 18 HA TYR A 1 13.536 11.638 8.870 1.00 0.85 H
ATOM 19 O TYR A 1 12.298 12.462 6.643 1.00 0.83 O
ATOM 20 H TYR A 1 10.948 12.701 9.122 1.00 0.88 H
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(
labels=labels[:11],
sites=sites[:11],
bonds=[(0,1),(0,2),(1,3),(2,4),(3,5),(4,5),(5,10),(1,6),(2,7),(3,8),(4,9)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(
labels=labels[11:12],
sites=sites[11:12],
bonds=[(-1,0)],
pivot=sites[10],
normal=(sites[10]-sites[5]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
body2 = revolute_body(
labels=labels[12:15],
sites=sites[12:15],
bonds=[(-11,0),(0,1),(0,2)],
pivot=sites[12],
normal=(sites[12]-sites[0]).normalize(),
mersenne_twister=mersenne_twister)
body2.parent = 0
body3 = revolute_body(
labels=labels[15:19],
sites=sites[15:19],
bonds=[(-3,1),(0,1),(1,2),(1,3)],
pivot=sites[16],
normal=(sites[16]-sites[12]).normalize(),
mersenne_twister=mersenne_twister)
body3.parent = 2
body4 = revolute_body(
labels=labels[19:20],
sites=sites[19:20],
bonds=[(-2,0)],
pivot=sites[17],
normal=(sites[17]-sites[16]).normalize(),
mersenne_twister=mersenne_twister)
body4.parent = 3
body5 = revolute_body(
labels=labels[20:21],
sites=sites[20:21],
bonds=[(-4,0)],
pivot=sites[15],
normal=(sites[15]-sites[16]).normalize(),
mersenne_twister=mersenne_twister)
body5.parent = 3
return simulation(bodies=[body0, body1, body2, body3, body4, body5])
def simulation_tyr_with_h():
pdb = """\
ATOM 0 CG TYR A 1 11.007 9.417 9.446 1.00 0.79 C
ATOM 1 CD1 TYR A 1 9.923 10.155 8.940 1.00 1.42 C
ATOM 2 CD2 TYR A 1 10.765 8.288 10.238 1.00 1.41 C
ATOM 3 CE1 TYR A 1 8.612 9.760 9.229 1.00 1.61 C
ATOM 4 CE2 TYR A 1 9.453 7.895 10.525 1.00 1.42 C
ATOM 5 CZ TYR A 1 8.377 8.631 10.021 1.00 1.11 C
ATOM 6 HD1 TYR A 1 10.092 11.024 8.328 1.00 2.14 H
ATOM 7 HD2 TYR A 1 11.596 7.718 10.630 1.00 2.21 H
ATOM 8 HE1 TYR A 1 7.780 10.329 8.841 1.00 2.44 H
ATOM 9 HE2 TYR A 1 9.270 7.023 11.135 1.00 2.13 H
ATOM 10 OH TYR A 1 7.083 8.244 10.304 1.00 1.32 O
ATOM 11 HH TYR A 1 6.494 8.723 9.717 1.00 2.00 H
ATOM 12 CB TYR A 1 12.440 9.818 9.148 1.00 0.74 C
ATOM 13 HB2 TYR A 1 12.827 9.193 8.358 1.00 0.78 H
ATOM 14 HB3 TYR A 1 13.036 9.677 10.037 1.00 0.78 H
ATOM 15 N TYR A 1 11.593 12.101 9.550 1.00 0.82 N
ATOM 16 CA TYR A 1 12.527 11.286 8.721 1.00 0.75 C
ATOM 17 C TYR A 1 12.160 11.413 7.239 1.00 0.76 C
ATOM 18 HA TYR A 1 13.536 11.638 8.870 1.00 0.85 H
ATOM 19 O TYR A 1 12.298 12.462 6.643 1.00 0.83 O
ATOM 20 H TYR A 1 10.948 12.701 9.122 1.00 0.88 H
"""
labels, sites = pdb_extract(pdb=pdb)
mersenne_twister = flex.mersenne_twister(seed=0)
body0 = six_dof_body(labels=labels[:11],
sites=sites[:11],
bonds=[(0, 1), (0, 2), (1, 3), (2, 4), (3, 5), (4, 5),
(5, 10), (1, 6), (2, 7), (3, 8), (4, 9)],
mersenne_twister=mersenne_twister)
body0.parent = -1
body1 = revolute_body(labels=labels[11:12],
sites=sites[11:12],
bonds=[(-1, 0)],
pivot=sites[10],
normal=(sites[10] - sites[5]).normalize(),
mersenne_twister=mersenne_twister)
body1.parent = 0
body2 = revolute_body(labels=labels[12:15],
sites=sites[12:15],
bonds=[(-11, 0), (0, 1), (0, 2)],
pivot=sites[12],
normal=(sites[12] - sites[0]).normalize(),
mersenne_twister=mersenne_twister)
body2.parent = 0
body3 = revolute_body(labels=labels[15:19],
sites=sites[15:19],
bonds=[(-3, 1), (0, 1), (1, 2), (1, 3)],
pivot=sites[16],
normal=(sites[16] - sites[12]).normalize(),
mersenne_twister=mersenne_twister)
body3.parent = 2
body4 = revolute_body(labels=labels[19:20],
sites=sites[19:20],
bonds=[(-2, 0)],
pivot=sites[17],
normal=(sites[17] - sites[16]).normalize(),
mersenne_twister=mersenne_twister)
body4.parent = 3
body5 = revolute_body(labels=labels[20:21],
sites=sites[20:21],
bonds=[(-4, 0)],
pivot=sites[15],
normal=(sites[15] - sites[16]).normalize(),
mersenne_twister=mersenne_twister)
body5.parent = 3
return simulation(bodies=[body0, body1, body2, body3, body4, body5])
