def test_restraint_probability_complex(self):
m = IMP.Model()
rcomplex = self.init_representation_complex(m)
xlc, cldb = self.setup_crosslinks_complex(rcomplex, "single_category")
# check all internals didn't change since last time
o = IMP.pmi.output.Output()
o.write_test("expensive_test_new_cross_link_ms_restraint.dat", [xlc])
passed = o.test(
self.get_input_file_name(
"expensive_test_new_cross_link_ms_restraint.dat"), [xlc])
self.assertEqual(passed, True)
rs = xlc.get_restraint()
# check the probability of cross-links
restraints = []
for xl in xlc.xl_list:
p0 = xl["Particle1"]
p1 = xl["Particle2"]
prob = xl["Restraint"].get_probability()
resid1 = xl[cldb.residue1_key]
chain1 = xl[cldb.protein1_key]
resid2 = xl[cldb.residue2_key]
chain2 = xl[cldb.protein2_key]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist = IMP.core.get_distance(d0, d1)
test_prob = get_probability([d0], [d1], [sig1], [sig2], [psi],
21.0, 0.0)
restraints.append(xl["Restraint"])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score = rs.unprotected_evaluate(None)
test_log_wrapper_score = log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score,
test_log_wrapper_score,
delta=0.00001)
for output in [
'excluded.None.xl.db',
'expensive_test_new_cross_link_ms_restraint.dat',
'included.None.xl.db', 'missing.None.xl.db'
]:
os.unlink(output)
def test_restraint_probability_complex(self):
m = IMP.Model()
rcomplex = self.init_representation_complex(m)
xlc = setup_crosslinks_complex(rcomplex, "single_category")
# check all internals didn't change since last time
o = IMP.pmi.output.Output()
o.write_test("expensive_test_cross_link_ms_restraint.dat", [xlc])
passed = o.test(
self.get_input_file_name(
"expensive_test_cross_link_ms_restraint.dat"), [xlc])
self.assertEqual(passed, True)
rs = xlc.get_restraint()
# check the probability of cross-links
restraints = []
for p in xlc.pairs:
p0 = p[0]
p1 = p[1]
prob = p[2].get_probability()
resid1 = p[3]
chain1 = p[4]
resid2 = p[5]
chain2 = p[6]
attribute = p[7]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist = IMP.core.get_distance(d0, d1)
sig1 = xlc.get_sigma(p[8])[0]
sig2 = xlc.get_sigma(p[9])[0]
psi = xlc.get_psi(p[10])[0]
test_prob = get_probability([d0], [d1], [sig1], [sig2], [psi],
21.0, 0.0)
restraints.append(p[2])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score = rs.unprotected_evaluate(None)
test_log_wrapper_score = log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score,
test_log_wrapper_score,
delta=0.00001)
for output in [
'excluded.None.xl.db',
'expensive_test_cross_link_ms_restraint.dat',
'included.None.xl.db', 'missing.None.xl.db'
]:
os.unlink(output)
def test_restraint_probability_complex(self):
m = IMP.Model()
rcomplex = self.init_representation_complex(m)
xlc, cldb = self.setup_crosslinks_complex(rcomplex, "single_category")
# check all internals didn't change since last time
o = IMP.pmi.output.Output()
o.write_test("expensive_test_new_cross_link_ms_restraint.dat", [xlc])
passed = o.test(self.get_input_file_name("expensive_test_new_cross_link_ms_restraint.dat"), [xlc])
self.assertEqual(passed, True)
rs = xlc.get_restraint()
# check the probability of cross-links
restraints = []
for xl in xlc.xl_list:
p0 = xl["Particle1"]
p1 = xl["Particle2"]
prob = xl["Restraint"].get_probability()
resid1 = xl[cldb.residue1_key]
chain1 = xl[cldb.protein1_key]
resid2 = xl[cldb.residue2_key]
chain2 = xl[cldb.protein2_key]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist = IMP.core.get_distance(d0, d1)
test_prob = get_probability([d0], [d1], [sig1], [sig2], [psi], 21.0, 0.0)
restraints.append(xl["Restraint"])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score = rs.unprotected_evaluate(None)
test_log_wrapper_score = log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score, test_log_wrapper_score, delta=0.00001)
for output in [
"excluded.None.xl.db",
"expensive_test_new_cross_link_ms_restraint.dat",
"included.None.xl.db",
"missing.None.xl.db",
]:
os.unlink(output)
def test_restraint_probability_complex(self):
m = IMP.Model()
rcomplex=self.init_representation_complex(m)
xlc=setup_crosslinks_complex(rcomplex,"single_category")
# check all internals didn't change since last time
o=IMP.pmi.output.Output()
o.write_test("expensive_test_cross_link_ms_restraint.dat", [xlc])
passed=o.test(self.get_input_file_name("expensive_test_cross_link_ms_restraint.dat"), [xlc])
self.assertEqual(passed, True)
rs=xlc.get_restraint()
# check the probability of cross-links
restraints=[]
for p in xlc.pairs:
p0 = p[0]
p1 = p[1]
prob = p[2].get_probability()
resid1 = p[3]
chain1 = p[4]
resid2 = p[5]
chain2 = p[6]
attribute = p[7]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist=IMP.core.get_distance(d0, d1)
sig1 = xlc.get_sigma(p[8])[0]
sig2 = xlc.get_sigma(p[9])[0]
psi = xlc.get_psi(p[10])[0]
test_prob=get_probability([d0],[d1],[sig1],[sig2],[psi],21.0,0.0)
restraints.append(p[2])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score=rs.unprotected_evaluate(None)
test_log_wrapper_score=log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score, test_log_wrapper_score, delta=0.00001)
for output in ['excluded.None.xl.db',
'expensive_test_cross_link_ms_restraint.dat',
'included.None.xl.db', 'missing.None.xl.db']:
os.unlink(output)
def test_restraint_probability_complex(self):
"""Test restraint gets correct probabilities"""
m = IMP.Model()
rcomplex, dof = self.init_representation_complex_pmi2(m)
xlc, cldb = self.setup_crosslinks_complex(root_hier=rcomplex,
mode="single_category")
self.assertEqual(len(dof.get_movers()), 42)
dof.get_nuisances_from_restraint(xlc)
self.assertEqual(len(dof.get_movers()), 44)
# check all internals didn't change since last time
o = IMP.pmi.output.Output()
o.write_test("expensive_test_new_cross_link_ms_restraint.dat", [xlc])
passed = o.test(
self.get_input_file_name(
"expensive_test_new_cross_link_ms_restraint.dat"), [xlc])
self.assertEqual(passed, True)
rs = xlc.get_restraint()
# check the probability of cross-links
restraints = []
for xl in xlc.xl_list:
p0 = xl["Particle1"]
p1 = xl["Particle2"]
prob = xl["Restraint"].get_probability()
resid1 = xl[cldb.residue1_key]
chain1 = xl[cldb.protein1_key]
resid2 = xl[cldb.residue2_key]
chain2 = xl[cldb.protein2_key]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist = IMP.core.get_distance(d0, d1)
test_prob = get_probability([d0], [d1], [sig1], [sig2], [psi],
21.0, 0.0)
restraints.append(xl["Restraint"])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score = rs.unprotected_evaluate(None)
test_log_wrapper_score = log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score,
test_log_wrapper_score,
delta=0.00001)
rex = IMP.pmi.macros.ReplicaExchange0(
m,
root_hier=rcomplex,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
for output in [
'excluded.None.xl.db',
'expensive_test_new_cross_link_ms_restraint.dat',
'included.None.xl.db', 'missing.None.xl.db'
]:
os.unlink(output)
def test_restraint_probability_complex(self):
"""Test restraint gets correct probabilities"""
for i in range(2):
m = IMP.Model()
print("Testing PMI version",i+1)
if i==0:
rcomplex = self.init_representation_complex(m)
xlc,cldb = self.setup_crosslinks_complex(rcomplex,"single_category")
else:
rcomplex,dof=self.init_representation_complex_pmi2(m)
xlc,cldb = self.setup_crosslinks_complex(root_hier=rcomplex,
mode="single_category")
self.assertEqual(len(dof.get_movers()),42)
dof.get_nuisances_from_restraint(xlc)
self.assertEqual(len(dof.get_movers()),44)
# check all internals didn't change since last time
o=IMP.pmi.output.Output()
o.write_test("expensive_test_new_cross_link_ms_restraint.dat", [xlc])
passed=o.test(self.get_input_file_name("expensive_test_new_cross_link_ms_restraint.dat"),
[xlc])
self.assertEqual(passed, True)
rs = xlc.get_restraint()
# check the probability of cross-links
restraints=[]
for xl in xlc.xl_list:
p0 = xl["Particle1"]
p1 = xl["Particle2"]
prob = xl["Restraint"].get_probability()
resid1 = xl[cldb.residue1_key]
chain1 = xl[cldb.protein1_key]
resid2 = xl[cldb.residue2_key]
chain2 = xl[cldb.protein2_key]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist=IMP.core.get_distance(d0, d1)
test_prob=get_probability([d0],[d1],[sig1],[sig2],[psi],21.0,0.0)
restraints.append(xl["Restraint"])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score=rs.unprotected_evaluate(None)
test_log_wrapper_score=log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score, test_log_wrapper_score, delta=0.00001)
if i==0:
rex0 = IMP.pmi.macros.ReplicaExchange0(m,
rcomplex,
monte_carlo_sample_objects=[rcomplex],
number_of_frames=2,
test_mode=True,
replica_exchange_object = rem)
rex0.execute_macro()
else:
rex = IMP.pmi.macros.ReplicaExchange0(m,
root_hier=rcomplex,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object = rem)
rex.execute_macro()
for output in ['excluded.None.xl.db',
'expensive_test_new_cross_link_ms_restraint.dat',
'included.None.xl.db', 'missing.None.xl.db']:
os.unlink(output)