def test_get_fg_chain_roots(self):
'''
Test that SimulationData.get_fg_chain_roots() works correctly
'''
IMP.set_log_level(IMP.SILENT)
test_util.test_protobuf_installed(self)
cfg_file = self.get_tmp_file_name("barak_config.pb")
assign_file = self.get_tmp_file_name("barak_assign.pb")
coords = self._create_cfg_file_with_fgs(cfg_file)
print("assigning parameter ranges from config")
num=assign_ranges( cfg_file, assign_file, 0, False, 10 )
print ("Loading SimData")
sd= IMP.npctransport.SimulationData(assign_file, False)
sd.set_rmf_file( self.get_tmp_file_name("out.rmf") )
fgs = sd.get_fg_chain_roots( ) # atom.Hierarchies
print (" fgs ", fgs)
ones = 0
twos = 0
for fg in fgs:
chain = get_fg_chain(fg)
type_name = IMP.core.Typed(fg.get_child(0)).get_type().get_string()
if(type_name == "my_fg1"):
self.assert_(chain.get_number_of_beads() == 3)
ones = ones + 1
if(type_name == "my_fg2"):
self.assert_(chain.get_number_of_beads() == 6)
twos = twos + 1
self.assert_(ones == 2 and twos == 3)
def test_get_fg_chain_roots(self):
'''
Test that SimulationData.get_fg_chain_roots() works correctly
'''
IMP.set_log_level(IMP.SILENT)
test_util.test_protobuf_installed(self)
cfg_file = self.get_tmp_file_name("barak_config.pb")
assign_file = self.get_tmp_file_name("barak_assign.pb")
coords = self._create_cfg_file_with_fgs(cfg_file)
print("assigning parameter ranges from config")
num = assign_ranges(cfg_file, assign_file, 0, False, 10)
print("Loading SimData")
sd = IMP.npctransport.SimulationData(assign_file, False)
sd.set_rmf_file(self.get_tmp_file_name("out.rmf"))
fgs = sd.get_fg_chain_roots() # atom.Hierarchies
print(" fgs ", fgs)
ones = 0
twos = 0
for fg in fgs:
chain = get_fg_chain(fg)
type_name = IMP.core.Typed(fg.get_child(0)).get_type().get_string()
if (type_name == "my_fg1"):
self.assertEqual(chain.get_number_of_beads(), 3)
ones = ones + 1
if (type_name == "my_fg2"):
self.assertEqual(chain.get_number_of_beads(), 6)
twos = twos + 1
self.assertTrue(ones == 2 and twos == 3)
def test_copy_fgs(self):
test_util.test_protobuf_installed(self)
config_fname = "./config_fg_copy.pb" # self.get_tmp_file_name("simple_cfg.pb")
output_fname1 = "./output_fg_copy.pb" # self.get_tmp_file_name("test_fg_copy.pb")
output_fname2 = "./output_fg_copy.pb" # self.get_tmp_file_name("test_fg_copy.pb")
rmf_fname1 = "./rmf_fg_copy.rmf" # self.get_tmp_file_name("test_fg_copy.pb")
rmf_fname2 = "./rmf_fg_copy2.rmf" # self.get_tmp_file_name("test_fg_copy.pb")
test_util.make_simple_cfg(
config_fname,
is_slab_on=True,
n_particles_factor=3.0,
is_obstacles=True)
sd1= run_from_config(config_fname, output_fname1, rmf_fname1)
sd2= run_from_config(config_fname, output_fname2, rmf_fname2)
fg_beads1= get_fg_beads_from_simulation_data(sd1)
fg_beads2= get_fg_beads_from_simulation_data(sd2)
# Verify that not all are equal initially:
are_all_equal= True
for p1, p2 in zip(fg_beads1, fg_beads2):
if not are_rigid_body_reference_frames_equal \
( IMP.core.RigidBody(p1), IMP.core.RigidBody(p2) ):
are_all_equal=False
self.assertFalse(are_all_equal)
# Copy then verify that all are equal now:
IMP.npctransport.copy_FGs_coordinates(sd1, sd2)
for p1, p2 in zip(fg_beads1, fg_beads2):
self.assertTrue(are_rigid_body_reference_frames_equal \
( IMP.core.RigidBody(p1), IMP.core.RigidBody(p2) ) )
if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
sd2.get_bd().optimize(1)
else:
sd2.get_bd().optimize(20000)
def test_copy_fgs(self):
test_util.test_protobuf_installed(self)
config_fname = "./config_fg_copy.pb" # self.get_tmp_file_name("simple_cfg.pb")
output_fname1 = "./output_fg_copy.pb" # self.get_tmp_file_name("test_fg_copy.pb")
output_fname2 = "./output_fg_copy.pb" # self.get_tmp_file_name("test_fg_copy.pb")
rmf_fname1 = "./rmf_fg_copy.rmf" # self.get_tmp_file_name("test_fg_copy.pb")
rmf_fname2 = "./rmf_fg_copy2.rmf" # self.get_tmp_file_name("test_fg_copy.pb")
test_util.make_simple_cfg(config_fname,
is_slab_on=True,
n_particles_factor=3.0,
is_obstacles=True)
sd1 = run_from_config(config_fname, output_fname1, rmf_fname1)
sd2 = run_from_config(config_fname, output_fname2, rmf_fname2)
fg_beads1 = get_fg_beads_from_simulation_data(sd1)
fg_beads2 = get_fg_beads_from_simulation_data(sd2)
# Verify that not all are equal initially:
are_all_equal = True
for p1, p2 in zip(fg_beads1, fg_beads2):
if not are_rigid_body_reference_frames_equal \
( IMP.core.RigidBody(p1), IMP.core.RigidBody(p2) ):
are_all_equal = False
self.assertFalse(are_all_equal)
# Copy then verify that all are equal now:
IMP.npctransport.copy_FGs_coordinates(sd1, sd2)
for p1, p2 in zip(fg_beads1, fg_beads2):
self.assertTrue(are_rigid_body_reference_frames_equal \
( IMP.core.RigidBody(p1), IMP.core.RigidBody(p2) ) )
if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
sd2.get_bd().optimize(1)
else:
sd2.get_bd().optimize(20000)
def test_fg_anchoring_through_protobuf(self):
'''
Test that FG nups can be anchored properly through protobuf file
'''
IMP.set_log_level(IMP.SILENT)
test_util.test_protobuf_installed(self)
cfg_file = self.get_tmp_file_name("barak_config.pb")
assign_file = self.get_tmp_file_name("barak_assign.pb")
coords = self._create_cfg_file_with_fg_anchors(cfg_file)
print("assigning parameter ranges from config")
num = IMP.npctransport.assign_ranges(cfg_file, assign_file, 0, False,
10)
sd = IMP.npctransport.SimulationData(assign_file, False, "")
# self.get_tmp_file_name("out.rmf"));
self._assert_anchors_in_place(sd, coords)
# verify that anchors remain intact during optimization
if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
short_init_factor = 0.00001
print("short position initialization in non-fast mode")
else:
short_init_factor = 0.1
IMP.npctransport.initialize_positions(sd, [], False, short_init_factor)
self._assert_anchors_in_place(sd, coords)
sd.get_bd().optimize(1000)
self._assert_anchors_in_place(sd, coords)
def _test_harmonic_spring_score_from_protobuf(self, n_beads=2):
'''
Test that FG nups can be anchored properly through protobuf file
'''
global NS_PER_CHUNK
IMP.set_log_level(IMP.SILENT)
test_util.test_protobuf_installed(self)
cfg_file = self.get_tmp_file_name("barak_config.pb")
# assign_file = self.get_tmp_file_name("barak_assign.pb")
assign_file = "output2.pb"
self._create_cfg_file_with_fg_anchors(cfg_file, n_beads)
print("assigning parameter ranges from config")
num = IMP.npctransport.assign_ranges(cfg_file, assign_file, 0, False,
10)
sd = IMP.npctransport.SimulationData(assign_file, False, "")
# "out2.rmf")
# self.get_tmp_file_name("out.rmf"));
# verify that anchors remain intact during optimization
if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
short_init_factor = 0.0001
n_opt_cycles = 10
print("short position initialization in non-fast mode")
else:
n_opt_cycles = 100000
short_init_factor = 1.0
IMP.npctransport.initialize_positions(sd, [], False, short_init_factor)
print("Energy before optimization:",
sd.get_bd().get_scoring_function().evaluate(False))
print("Optimizing")
print("dT %.1f fs" % sd.get_bd().get_maximum_time_step())
sd.get_bd().optimize(n_opt_cycles)
print()
print("Energy after optimization:",
sd.get_bd().get_scoring_function().evaluate(False))
print("Report particles:")
self._do_particles_report(sd.get_model(), sd.get_beads())
print()
sim_time_ns = 500 * TAU_NS
sd.get_bd().set_current_time(0.0)
sd.activate_statistics()
print("Running for %.1f ns" % sim_time_ns)
R = test_util.optimize_in_chunks(sd, sim_time_ns, NS_PER_CHUNK)
# print(R[0:100])
self._analyze_run(assign_file, R)
def test_Avro2PBReader(self):
""" Testing whether an avro file is read properly by Avro2PBReader """
test_util.test_protobuf_installed(self)
in_avro = self.get_input_file_name("avro.sample")
print("parsing", in_avro)
a = IMP.npctransport.Avro2PBReader([in_avro])
o = IMP.npctransport.Output()
s = a.read_next()
while len(s) > 0: # while valid output
o.ParseFromString(s)
rg = o.statistics.fgs[0].radius_of_gyration
# print rg
s = a.read_next()
self.assertAlmostEqual(rg, 40.2645193868, 7)
def test_init_from_old_output_more_recent(self):
"""
Testing whether a more recent output file (Dec 2013) is loaded
at all
"""
return
print("TEST_INIT_FROM_OLD_OUTPUT_MORE_RECENT")
test_util.test_protobuf_installed(self)
IMP.set_log_level(IMP.SILENT)
rt_prev_output = self.get_input_file_name("out_more_recent.pb")
out_rmf = self.get_tmp_file_name("movie.rmf")
rt_new_output = self.get_tmp_file_name("out.pb")
print("reloading from output file ", rt_prev_output)
print("New Output: ", rt_new_output)
sd = IMP.npctransport.SimulationData(rt_prev_output, False, out_rmf,
rt_new_output)
sd.activate_statistics()
sd.set_rmf_file(out_rmf, False)
def test_init_from_old_output_more_recent(self):
"""
Testing whether a more recent output file (Dec 2013) is loaded
at all
"""
return
print("TEST_INIT_FROM_OLD_OUTPUT_MORE_RECENT")
test_util.test_protobuf_installed(self)
IMP.set_log_level(IMP.SILENT)
rt_prev_output = self.get_input_file_name("out_more_recent.pb")
out_rmf = self.get_tmp_file_name("movie.rmf")
rt_new_output = self.get_tmp_file_name("out.pb")
print("reloading from output file ", rt_prev_output)
print("New Output: ", rt_new_output)
sd = IMP.npctransport.SimulationData(rt_prev_output,
False,
out_rmf,
rt_new_output)
sd.activate_statistics()
sd.set_rmf_file(out_rmf, False)
def test_init_from_output(self):
""" Testing whether positions are loaded properly from output file """
print("TEST_INIT_FROM_OUTPUT")
test_util.test_protobuf_installed(self)
# random generator initialization
IMP.set_log_level(IMP.SILENT)
config = self.get_tmp_file_name("simple_cfg.pb")
test_util.make_simple_cfg(config,
is_slab_on=True,
n_particles_factor=1.5,
is_obstacles=True)
rt_output = self.get_tmp_file_name(
"round_trip_output.pb") # "./test.pb" #
print("Config ", config)
print("RT output: ", rt_output)
sd = self.run_from_config(config, rt_output)
print("reloading from output file ", rt_output)
sdp = IMP.npctransport.SimulationData(rt_output, False)
sdp.activate_statistics()
sd.set_rmf_file(self.get_tmp_file_name("out1.rmf"), False)
print("After reload", time.ctime())
self.assert_almost_equal_sds(sd, sdp)
def test_init_from_output(self):
""" Testing whether positions are loaded properly from output file """
print("TEST_INIT_FROM_OUTPUT")
test_util.test_protobuf_installed(self)
# random generator initialization
IMP.set_log_level(IMP.SILENT)
config = self.get_tmp_file_name("simple_cfg.pb")
test_util.make_simple_cfg(
config,
is_slab_on=True,
n_particles_factor=1.5,
is_obstacles=True)
rt_output = self.get_tmp_file_name("round_trip_output.pb") # "./test.pb" #
print("Config ", config)
print("RT output: ", rt_output)
sd = self.run_from_config(config, rt_output)
print("reloading from output file ", rt_output)
sdp = IMP.npctransport.SimulationData(rt_output, False)
sdp.activate_statistics()
sd.set_rmf_file( self.get_tmp_file_name("out1.rmf"), False )
print("After reload", time.ctime())
self.assert_almost_equal_sds(sd, sdp)
def test_sites_from_simulation_data(self):
'''
Test that the site interaction glues particles together
in the context of simualtion data optimization
'''
# Prepare run:
test_util.test_protobuf_installed(self)
if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
print("SLOW MODE")
fast = False
short_init_factor=0.0001
opt_cycles_ns=0.05
n_iter = 10
n_good_thresh=1
else:
print("FAST MODE")
fast = True
short_init_factor=0.01
opt_cycles_ns=10.0
n_iter = 100
n_good_thresh=3
if(DEBUG):
opt_cycles_ns=opt_cycles_ns*200
n_iter=1
cfg_file = "barak_config.pb"
assign_file = "barak_assign.pb"
pymol_file = "sites.pym"
n_good_thresh=1
else:
cfg_file = self.get_tmp_file_name("barak_config.pb")
assign_file = self.get_tmp_file_name("barak_assign.pb")
pymol_file = self.get_tmp_file_name("sites.pym")
self._create_cfg_file_with_fg_anchors( cfg_file )
# print("assigning parameter ranges from config", cfg_file, end=' ')
# print("to file", assign_file)
num=assign_ranges( cfg_file, assign_file, 0, False, 10 );
sd= IMP.npctransport.SimulationData(assign_file, False)
if(DEBUG):
rmf_file="tmp.rmf"
else:
rmf_file = self.get_tmp_file_name("out.rmf");
print("RMF file", rmf_file)
sd.set_rmf_file(rmf_file, False)
self._assert_kap_in_place(sd, False)
# Init and run:
IMP.set_log_level(IMP.SILENT)
sd.get_bd().set_log_level(IMP.SILENT)
IMP.npctransport.initialize_positions( sd, [], False,
short_init_factor)
opt_cycles_frames=math.ceil(opt_cycles_ns*1E+6/sd.get_bd().get_maximum_time_step());
print()
print()
# IMP.set_log_level(IMP.PROGRESS)
sd.write_geometry(pymol_file)
n_good=0
timer= IMP.npctransport.timer();
sd.get_bd().set_current_time(0.0)
sd.activate_statistics()
sd.get_statistics().reset_statistics_optimizer_states()
for i in range(n_iter):
sd.get_bd().optimize(opt_cycles_frames)
sd.get_statistics().update(timer,opt_cycles_frames)
try:
self._assert_kap_in_place(sd, True)
print ("Asserted kap interacts")
print ("total energy", sd.get_bd().get_scoring_function().evaluate(False),)
print ("predr", sd.get_scoring().get_predicates_pair_restraint().evaluate(False))
self.assert_(sd.get_scoring().get_predicates_pair_restraint().evaluate(False) < -30.0)
n_good=n_good+1
print("NGOOD", n_good)
self.assert_(self.is_stats_interact_(assign_file))
print("stats interact asserted")
except AssertionError:
continue
if(n_good >= n_good_thresh):
print("total energy", sd.get_bd().get_scoring_function().evaluate(False), end=' ')
print("predr", sd.get_scoring().get_predicates_pair_restraint().evaluate(False), end=' ')
return True
if fast:
print("Failed to glue particles after %d iterations x %d opt frames (total %.3f ns)" \
% (n_iter, opt_cycles_frames, opt_cycles_ns*n_iter))
self.assert_(n_good >= n_good_thresh)
else:
print("Debug mode - couldn't glue particles in such short run")
def test_init_from_old_output1(self):
""" Testing whether an old output file is loaded properly """
return
print("TEST_INIT_FROM_OLD_OUTPUT1")
test_util.test_protobuf_installed(self)
expected_sites = [(3.67394e-15, 0, -30),
(17.2447, -0.377296, -24.5455),
(-1.55764, -23.0892, -19.0909),
(-19.7675, 17.9804, -13.6364),
(28.589, -3.96571, -8.18182),
(-28.2097, -9.8375, -2.72727),
(20.6227, 21.6163, 2.72727),
(-4.64461, -28.4866, 8.18182),
(-17.9874, 19.7612, 13.6364),
(17.8043, 14.7833, 19.0909),
(13.5084, 10.7259, 24.5455), (0, 0, 30)]
expected_time = 12500039289
expected_particles = [
[-253.636, -108.652, 40.4134, 1, 0, 0, 0], #trans + quaternion
[-236.08, -127.91, 27.47, 0.23, 0.33, -0.84, -0.36]
]
# random generator initialization
# RMF.set_log_level("trace")
IMP.set_log_level(IMP.SILENT)
rt_prev_output = self.get_input_file_name("out149.pb")
out_rmf = self.get_tmp_file_name("movie.rmf")
rt_new_output = self.get_tmp_file_name("out.pb")
print("reloading from output file ", rt_prev_output)
print("New Output: ", rt_new_output)
sd = IMP.npctransport.SimulationData(rt_prev_output, False, out_rmf,
rt_new_output)
sd.activate_statistics()
sd.set_rmf_file(out_rmf, False)
for i, p in enumerate(sd.get_beads()):
if (i >= len(expected_particles)):
break
pc = [x for x in IMP.core.XYZ(p).get_coordinates()]
pq = [
x for x in IMP.core.RigidBody(p).get_reference_frame().
get_transformation_to().get_rotation().get_quaternion()
]
for x, y in zip(pc + pq, expected_particles[i]):
self.assertAlmostEqual(x, y, delta=0.1)
# if(not IMP.npctransport.Transporting.get_is_setup(p)):
# continue
# pt = IMP.npctransport.Transporting(p)
# print "T: ", pt.get_is_last_entry_from_top(),
# print pt.get_last_tracked_z(),
# print pt.get_n_entries_bottom(),
# print pt.get_n_entries_top(),
# print
sites = sd.get_sites(IMP.core.ParticleType("kap"))
for i, s in enumerate(sites):
self.assertAlmostEqual(
(s.get_center() - expected_sites[i]).get_magnitude(),
0,
delta=.01)
# check timers
t = sd.get_bd().get_current_time()
self.assertAlmostEqual(t, expected_time, delta=1)
def test_init_from_rmf(self):
""" Testing whether initialize_positions_from_rmf indeed
restores the beads coordinates correctly """
IMP.set_log_level( IMP.SILENT );
test_util.test_protobuf_installed(self)
# First simulation with one seed:
output_pb1= self.get_tmp_file_name( "output1.pb" );
output_rmf1= IMP.create_temporary_file_name( "output", ".rmf" );
print("Starting first simulation with RMF file " + output_rmf1)
sd = self._make_and_run_simulation( output_pb1, output_rmf1, seed = 1)
e1 = sd.get_bd().get_scoring_function().evaluate(False)
print ("*** After first simulation")
print ("Energy %.2f" % e1)
coordsI = self._get_beads_coords( sd )
sd = None
# Second simulation with another seed:
output_pb2= self.get_tmp_file_name( "output2.pb" );
output_rmf2= IMP.create_temporary_file_name( "output2", ".rmf" );
print("*** Starting second simulation with RMF file " + output_rmf2)
print("YYY")
sd = self._make_and_run_simulation( output_pb2, output_rmf2, seed = 2)
print("XXX")
e2 = sd.get_bd().get_scoring_function().evaluate(False)
print ("*** After second simulation")
print ("Energy %.2f" % e2)
coordsII = self._get_beads_coords( sd )
# Restoration from first simulation through rmf file:
print("*** Initializing positions from RMF file " + output_rmf1)
fl= RMF.open_rmf_file_read_only(output_rmf1)
sd.initialize_positions_from_rmf( fl )
e3 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After initializing positions from RMF file " + output_rmf1)
print("Energy %.2f" % e3)
self.assertAlmostEqual(e1, e3, delta=0.0001)
self.assertNotAlmostEqual(e1, e2, delta=0.0001)
coordsIII = self._get_beads_coords( sd )
# make sure that all coordinates were restored and as sanity
# check control, also that the second simulation is different than
# the first one:
for i in range( len( coordsI ) ):
for j in range(3):
self.assertAlmostEqual(coordsI[i][j], coordsIII[i][j], delta=0.00001)
self.assertNotAlmostEqual(coordsI[i][j], coordsII[i][j], delta=0.00001)
# Simulate more to scramble stuff
sd.get_bd().optimize( 1000 )
e4 = sd.get_bd().get_scoring_function().evaluate(False)
print ("Energy %.2f" % e4)
coordsIV = self._get_beads_coords( sd )
# Restoration from first simulation through output protobuf file:
print("*** Initializing positions from ProtoBuf file " + output_pb1)
f=open(output_pb1, "rb")
config= IMP.npctransport.Output()
config.ParseFromString(f.read())
bch = RMF.BufferConstHandle( config.rmf_conformation )
fch= RMF.open_rmf_buffer_read_only( bch )
sd.initialize_positions_from_rmf( fch )
e5 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After initializing positions from RMF file " + output_rmf1)
print("Energy %.2f" % e5)
self.assertAlmostEqual(e1, e5, delta=0.00001)
self.assertNotAlmostEqual(e1, e4, delta=0.00001)
coordsV = self._get_beads_coords( sd )
for i in range( len( coordsI ) ):
for j in range(3):
self.assertAlmostEqual(coordsI[i][j], coordsV[i][j], delta=0.00001)
self.assertNotAlmostEqual(coordsI[i][j], coordsIV[i][j], delta=0.00001)
def test_sites_from_simulation_data(self):
'''
Test that the site interaction glues particles together
in the context of simualtion data optimization
'''
# Prepare run:
test_util.test_protobuf_installed(self)
if IMP.get_check_level() >= IMP.USAGE_AND_INTERNAL:
print("SLOW MODE")
fast = False
short_init_factor = 0.0001
opt_cycles_ns = 0.05
n_iter = 10
n_good_thresh = 1
else:
print("FAST MODE")
fast = True
short_init_factor = 0.01
opt_cycles_ns = 10.0
n_iter = 100
n_good_thresh = 3
if (DEBUG):
opt_cycles_ns = opt_cycles_ns * 200
n_iter = 1
cfg_file = "barak_config.pb"
assign_file = "barak_assign.pb"
pymol_file = "sites.pym"
n_good_thresh = 1
else:
cfg_file = self.get_tmp_file_name("barak_config.pb")
assign_file = self.get_tmp_file_name("barak_assign.pb")
pymol_file = self.get_tmp_file_name("sites.pym")
self._create_cfg_file_with_fg_anchors(cfg_file)
# print("assigning parameter ranges from config", cfg_file, end=' ')
# print("to file", assign_file)
num = assign_ranges(cfg_file, assign_file, 0, False, 10)
sd = IMP.npctransport.SimulationData(assign_file, False)
if (DEBUG):
rmf_file = "tmp.rmf"
else:
rmf_file = self.get_tmp_file_name("out.rmf")
print("RMF file", rmf_file)
sd.set_rmf_file(rmf_file, False)
self._assert_kap_in_place(sd, False)
# Init and run:
IMP.set_log_level(IMP.SILENT)
sd.get_bd().set_log_level(IMP.SILENT)
IMP.npctransport.initialize_positions(sd, [], False, short_init_factor)
opt_cycles_frames = math.ceil(opt_cycles_ns * 1E+6 /
sd.get_bd().get_maximum_time_step())
print()
print()
# IMP.set_log_level(IMP.PROGRESS)
sd.write_geometry(pymol_file)
n_good = 0
timer = IMP.npctransport.timer()
sd.get_bd().set_current_time(0.0)
sd.activate_statistics()
sd.get_statistics().reset_statistics_optimizer_states()
for i in range(n_iter):
sd.get_bd().optimize(opt_cycles_frames)
sd.get_statistics().update(timer, opt_cycles_frames)
try:
self._assert_kap_in_place(sd, True)
print("Asserted kap interacts")
print(
"total energy",
sd.get_bd().get_scoring_function().evaluate(False),
)
ppr = sd.get_scoring().get_predicates_pair_restraint()
print("predr", ppr.evaluate(False))
self.assertLess(ppr.evaluate(False), -30.0)
n_good = n_good + 1
print("NGOOD", n_good)
self.assertTrue(self.is_stats_interact_(assign_file))
print("stats interact asserted")
except AssertionError:
continue
if (n_good >= n_good_thresh):
print("total energy",
sd.get_bd().get_scoring_function().evaluate(False),
end=' ')
print(
"predr",
sd.get_scoring().get_predicates_pair_restraint().evaluate(
False),
end=' ')
return True
if fast:
print("Failed to glue particles after %d iterations x %d opt frames (total %.3f ns)" \
% (n_iter, opt_cycles_frames, opt_cycles_ns*n_iter))
self.assertGreaterEqual(n_good, n_good_thresh)
else:
print("Debug mode - couldn't glue particles in such short run")
def test_init_from_old_output1(self):
""" Testing whether an old output file is loaded properly """
return
print("TEST_INIT_FROM_OLD_OUTPUT1")
test_util.test_protobuf_installed(self)
expected_sites = [ (3.67394e-15, 0, -30),
(17.2447, -0.377296, -24.5455),
(-1.55764, -23.0892, -19.0909),
(-19.7675, 17.9804, -13.6364),
(28.589, -3.96571, -8.18182),
(-28.2097, -9.8375, -2.72727),
(20.6227, 21.6163, 2.72727),
(-4.64461, -28.4866, 8.18182),
(-17.9874, 19.7612, 13.6364),
(17.8043, 14.7833, 19.0909),
(13.5084, 10.7259, 24.5455),
(0, 0, 30) ]
expected_time = 12500039289
expected_particles=[ [-253.636, -108.652, 40.4134, 1, 0, 0, 0], #trans + quaternion
[-236.08, -127.91, 27.47, 0.23, 0.33, -0.84, -0.36] ]
# random generator initialization
# RMF.set_log_level("trace")
IMP.set_log_level(IMP.SILENT)
rt_prev_output = self.get_input_file_name("out149.pb")
out_rmf = self.get_tmp_file_name("movie.rmf")
rt_new_output = self.get_tmp_file_name("out.pb")
print("reloading from output file ", rt_prev_output)
print("New Output: ", rt_new_output)
sd = IMP.npctransport.SimulationData(rt_prev_output,
False,
out_rmf,
rt_new_output)
sd.activate_statistics()
sd.set_rmf_file(out_rmf, False)
for i,p in enumerate(sd.get_beads()):
if( i >= len(expected_particles) ):
break
pc= [x for x in IMP.core.XYZ(p).get_coordinates()]
pq = [x for x in IMP.core.RigidBody(p
).get_reference_frame(
).get_transformation_to(
).get_rotation(
).get_quaternion() ]
for x,y in zip(pc+pq, expected_particles[i]):
self.assertAlmostEqual(x,y, delta=0.1)
# if(not IMP.npctransport.Transporting.get_is_setup(p)):
# continue
# pt = IMP.npctransport.Transporting(p)
# print "T: ", pt.get_is_last_entry_from_top(),
# print pt.get_last_tracked_z(),
# print pt.get_n_entries_bottom(),
# print pt.get_n_entries_top(),
# print
sites = sd.get_sites(IMP.core.ParticleType("kap"))
for i,s in enumerate(sites):
self.assertAlmostEqual(
( s.get_center() - expected_sites[i]).get_magnitude(),
0, delta=.01 )
# check timers
t = sd.get_bd().get_current_time()
self.assertAlmostEqual(t, expected_time, delta=1)
def test_init_from_rmf(self):
""" Testing whether initialize_positions_from_rmf indeed
restores the beads coordinates correctly """
IMP.set_log_level(IMP.SILENT)
test_util.test_protobuf_installed(self)
# First simulation with one seed:
output_pb1 = self.get_tmp_file_name("output1.pb")
output_rmf1 = IMP.create_temporary_file_name("output", ".rmf")
print("Starting first simulation with RMF file " + output_rmf1)
sd = self._make_and_run_simulation(output_pb1, output_rmf1, seed=1)
e1 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After first simulation")
print("Energy %.2f" % e1)
coordsI = self._get_beads_coords(sd)
sd = None
# Second simulation with another seed:
output_pb2 = self.get_tmp_file_name("output2.pb")
output_rmf2 = IMP.create_temporary_file_name("output2", ".rmf")
print("*** Starting second simulation with RMF file " + output_rmf2)
print("YYY")
sd = self._make_and_run_simulation(output_pb2, output_rmf2, seed=2)
print("XXX")
e2 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After second simulation")
print("Energy %.2f" % e2)
coordsII = self._get_beads_coords(sd)
# Restoration from first simulation through rmf file:
print("*** Initializing positions from RMF file " + output_rmf1)
fl = RMF.open_rmf_file_read_only(output_rmf1)
sd.initialize_positions_from_rmf(fl)
e3 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After initializing positions from RMF file " + output_rmf1)
print("Energy %.2f" % e3)
self.assertAlmostEqual(e1, e3, delta=0.0001)
self.assertNotAlmostEqual(e1, e2, delta=0.0001)
coordsIII = self._get_beads_coords(sd)
# make sure that all coordinates were restored and as sanity
# check control, also that the second simulation is different than
# the first one:
for i in range(len(coordsI)):
for j in range(3):
self.assertAlmostEqual(coordsI[i][j],
coordsIII[i][j],
delta=0.00001)
self.assertNotAlmostEqual(coordsI[i][j],
coordsII[i][j],
delta=0.00001)
# Simulate more to scramble stuff
sd.get_bd().optimize(1000)
e4 = sd.get_bd().get_scoring_function().evaluate(False)
print("Energy %.2f" % e4)
coordsIV = self._get_beads_coords(sd)
# Restoration from first simulation through output protobuf file:
print("*** Initializing positions from ProtoBuf file " + output_pb1)
f = open(output_pb1, "rb")
config = IMP.npctransport.Output()
config.ParseFromString(f.read())
bch = RMF.BufferConstHandle(config.rmf_conformation)
fch = RMF.open_rmf_buffer_read_only(bch)
sd.initialize_positions_from_rmf(fch)
e5 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After initializing positions from RMF file " + output_rmf1)
print("Energy %.2f" % e5)
self.assertAlmostEqual(e1, e5, delta=0.00001)
self.assertNotAlmostEqual(e1, e4, delta=0.00001)
coordsV = self._get_beads_coords(sd)
for i in range(len(coordsI)):
for j in range(3):
self.assertAlmostEqual(coordsI[i][j],
coordsV[i][j],
delta=0.00001)
self.assertNotAlmostEqual(coordsI[i][j],
coordsIV[i][j],
delta=0.00001)