def main():
time_start = time.time()
print "-- create the universe"
m = IMP.Model()
m.set_log_level(IMP.SILENT)
# m.set_log_level(IMP.TERSE)
# m.set_log_level(IMP.VERBOSE)
m.set_maximum_score(model_max_score)
tfiihInfos = build_TFIIH_subunits_info(m)
print "-- read the cover spheres"
coverSpheres = read_cover_spheres(myBallsFileName)
print "-- create and inject the EM sticking restraints"
rs = get_enveloppe_restraints(coverSpheres, tfiihInfos.get_particles())
for r in rs:
m.add_restraint(r)
# print "spheres :";
# for s in coverSpheres : print s
bb = get_bbox_from_cover_spheres(coverSpheres)
print "BBOX:", bb
HGM.helpers.mute_all_restraints(m)
times = HGM.times.Times()
mcs = HGM.representation.MyConfigurationSet(tfiihInfos)
print "-- generate sample"
loop_i = 1
for i in sample_indexes:
time_loop_start = time.time()
# generate_sample_md(i,tfiihInfos,mcs,bb)
generate_sample_mccg(i, tfiihInfos, mcs, bb)
time_loop_stop = time.time()
elapse_time = int(time_loop_stop - time_loop_start)
times.set_sample_time(i, elapse_time)
print "{0:d}({1:d}s)..".format(i, elapse_time),
if loop_i % 40 == 0: print ""
sys.stdout.flush()
loop_i += 1
time_stop = time.time()
print "full sample generated in {0:d}s".format(int(time_stop - time_start))
def main():
time_start = time.time()
m = IMP.Model()
m.set_log_level(IMP.SILENT)
tfiihInfos = build_TFIIH_subunits_info(m)
HGM.helpers.mute_all_restraints(m)
times = HGM.times.Times()
# For an unexplained reason, it seems that the MD motor loses speed during the game, I thus will use different motors for each sampling
# smd = HGM.sampling.SamplerSimpleMD(tfiihInfos,md_type,T,tau,sampling_step)
mcs = HGM.representation.MyConfigurationSet(tfiihInfos)
print "-- generate sample"
for i in sample_indexes:
time_loop_start = time.time()
smd = HGM.sampling.SamplerSimpleMD(tfiihInfos, md_type, T, tau,
sampling_step)
smd.do_generate_sample(dryRun_size) # a dry run before
cs = smd.do_generate_sample(sample_size,
False) # actually generating the sample
saveName = savePrefix + "--" + str(i) + ".txt"
mcs.read_configurationSet(cs)
mcs.save_all_configs_to_file(os.path.join(saveDirSample, saveName))
mcs.delete_all_configs()
time_loop_stop = time.time()
elapse_time = int(time_loop_stop - time_loop_start)
times.set_sample_time(i, elapse_time)
print "{0:d}({1:d}s)..".format(i, elapse_time),
sys.stdout.flush()
time_stop = time.time()
print "full sample generated in {0:d}s".format(int(time_stop - time_start))
def main(argv, seed):
r = IMP.random_number_generator
r.seed(seed)
sample_indexes = [argv]
time_start = time.time()
print "-- create the universe"
m = IMP.Model()
m.set_log_level(IMP.SILENT)
# m.set_log_level(IMP.TERSE)
# m.set_log_level(IMP.VERBOSE)
m.set_maximum_score(model_max_score)
tfiihInfos = build_subunits_info(m)
bbEM = tfiihInfos.emSpheres.compute_bbox()
print "BBOX EM:", bbEM
v = bbEM.get_corner(1) - bbEM.get_corner(0)
bb = IMP.algebra.BoundingBox3D(
bbEM.get_corner(0) - v / 2.,
bbEM.get_corner(1) + v / 2.)
HGM.helpers.mute_all_restraints(m)
times = HGM.times.Times()
# mcs = HGM.representation.MyConfigurationSet(tfiihInfos)
print "-- generate sample"
loop_i = 1
for i in sample_indexes:
time_loop_start = time.time()
# generate_sample_md(i,tfiihInfos,mcs,bb)
# generate_sample_mymccg(i,tfiihInfos,mcs,bb)
print "MCCG SAMPLING ", "-" * 10
mcs = generate_sample_mccg(tfiihInfos, bb)
# mc = HGM.representation.MyConfigurationSet(tfiihInfos)
# mc.save_current_config()
print "MCCG REFINING ", "-" * 10
mcsr = refine_sample_mccg(tfiihInfos, mcs)
# mcsr = refine_sample_mccg(tfiihInfos,mc)
configs = [(800, 100, 2), (600, 200, 1.5), (400, 300, 1.5),
(200, 500, 1)]
# configs = [ (800,100,2),(600,50,1.5),(400,100,1.5),(200,500,1)]
# mc = HGM.representation.MyConfigurationSet(tfiihInfos)
# mc.save_current_config()
print "MCCG SUBUNITS REFINING ", "-" * 10
mcsr2 = refine_sample_mccg_per_subunits(tfiihInfos, mcsr, configs)
# mcsr2 = refine_sample_mccg_per_subunits(tfiihInfos,mc,configs)
print "MCCG SUBUNITS REREFINING ", "-" * 10
# mc = HGM.representation.MyConfigurationSet(tfiihInfos)
# mc.save_current_config()
configs = [(400, 200, 1.5), (300, 400, 1), (100, 600, .5)]
# mcsr3 = refine_sample_mccg_per_subunits(tfiihInfos,mc,configs)
mcsr3 = refine_sample_mccg_per_subunits(tfiihInfos, mcsr2, configs)
# mcs.read_configurationSet(mcsr)
# mcs.read_configurationSet(mcsr2)
# mcs.read_configurationSet(mcsr3)
print "SAVE ", "-" * 10
print " ", mcs.get_number_of_configurations(), "configurations"
save_sample(mcsr3, i)
# save_sample(mcsr,i)
time_loop_stop = time.time()
elapse_time = int(time_loop_stop - time_loop_start)
times.set_sample_time(i, elapse_time)
print "{0:d}({1:d}s)..".format(i, elapse_time),
if loop_i % 40 == 0: print ""
sys.stdout.flush()
loop_i += 1
mcs.delete_all_configs()
time_stop = time.time()
print "full sample generated in {0:d}s".format(int(time_stop - time_start))