def test_perturbed_frames(self):
"""Test reading and writing particles with frames"""
for suffix in RMF.suffixes:
m= IMP.kernel.Model()
p0= IMP.kernel.Particle(m)
p1= IMP.kernel.Particle(m)
ik= IMP.IntKey("hi int")
fk= IMP.FloatKey("hi float")
p0.add_attribute(ik, 1)
p1.add_attribute(fk, 2.0)
p1.add_attribute(ik, 3)
name= self.get_tmp_file_name("particles."+suffix)
print name
rmf= RMF.create_rmf_file(name)
IMP.base.set_log_level(IMP.base.SILENT)
IMP.rmf.add_particles(rmf, [p0, p1])
IMP.rmf.save_frame(rmf, 0)
p1.set_value(ik, 5)
IMP.rmf.save_frame(rmf, 1)
del rmf
rmf= RMF.open_rmf_file_read_only(name)
cat= rmf.get_category("IMP")
print cat
keys= rmf.get_keys(cat)
print [rmf.get_name(k) for k in keys]
bps= IMP.rmf.create_particles(rmf, m)
def test_perturbed_frames(self):
"""Test reading and writing particles with frames"""
RMF.set_log_level("trace")
for suffix in IMP.rmf.suffixes:
m = IMP.kernel.Model()
p0 = IMP.kernel.Particle(m)
p1 = IMP.kernel.Particle(m)
ik = IMP.IntKey("hi int")
fk = IMP.FloatKey("hi float")
p0.add_attribute(ik, 1)
p1.add_attribute(fk, 2.0)
p1.add_attribute(ik, 3)
name = self.get_tmp_file_name("particles" + suffix)
print(name)
rmf = RMF.create_rmf_file(name)
IMP.base.set_log_level(IMP.base.SILENT)
IMP.rmf.add_particles(rmf, [p0, p1])
IMP.rmf.save_frame(rmf, str(0))
p1.set_value(ik, 5)
IMP.rmf.save_frame(rmf, str(1))
del rmf
print("closed")
rmf = RMF.open_rmf_file_read_only(name)
cat = rmf.get_category("IMP")
print(cat)
keys = rmf.get_keys(cat)
print([rmf.get_name(k) for k in keys])
bps = IMP.rmf.create_particles(rmf, m)
print("load 0")
IMP.rmf.load_frame(rmf, RMF.FrameID(0))
self.assertEqual(len(bps), 2)
print("out")
bps[0].show()
self.assertTrue(bps[0].has_attribute(ik))
self.assertEqual(bps[0].get_value(ik), 1)
self.assertTrue(bps[1].has_attribute(ik))
self.assertEqual(bps[1].get_value(ik), 3)
self.assertTrue(bps[1].has_attribute(fk))
self.assertEqual(bps[1].get_value(fk), 2.0)
IMP.rmf.load_frame(rmf, RMF.FrameID(1))
self.assertTrue(bps[1].has_attribute(ik))
self.assertEqual(bps[1].get_value(ik), 5)
def test_perturbed_frames(self):
"""Test reading and writing particles with frames"""
RMF.set_log_level("trace")
for suffix in IMP.rmf.suffixes:
m = IMP.kernel.Model()
p0 = IMP.kernel.Particle(m)
p1 = IMP.kernel.Particle(m)
ik = IMP.IntKey("hi int")
fk = IMP.FloatKey("hi float")
p0.add_attribute(ik, 1)
p1.add_attribute(fk, 2.0)
p1.add_attribute(ik, 3)
name = self.get_tmp_file_name("particles" + suffix)
print name
rmf = RMF.create_rmf_file(name)
IMP.base.set_log_level(IMP.base.SILENT)
IMP.rmf.add_particles(rmf, [p0, p1])
IMP.rmf.save_frame(rmf, str(0))
p1.set_value(ik, 5)
IMP.rmf.save_frame(rmf, str(1))
del rmf
print "closed"
rmf = RMF.open_rmf_file_read_only(name)
cat = rmf.get_category("IMP")
print cat
keys = rmf.get_keys(cat)
print[rmf.get_name(k) for k in keys]
bps = IMP.rmf.create_particles(rmf, m)
print "load 0"
IMP.rmf.load_frame(rmf, RMF.FrameID(0))
self.assertEqual(len(bps), 2)
print "out"
bps[0].show()
self.assertTrue(bps[0].has_attribute(ik))
self.assertEqual(bps[0].get_value(ik), 1)
self.assertTrue(bps[1].has_attribute(ik))
self.assertEqual(bps[1].get_value(ik), 3)
self.assertTrue(bps[1].has_attribute(fk))
self.assertEqual(bps[1].get_value(fk), 2.0)
IMP.rmf.load_frame(rmf, RMF.FrameID(1))
self.assertTrue(bps[1].has_attribute(ik))
self.assertEqual(bps[1].get_value(ik), 5)
# pass the cache to the restraint score based filter
# it will use all the restraints in the cache
rssft = IMP.domino.RestraintScoreSubsetFilterTable(rc)
s.set_subset_filter_tables([ef, rssft])
# create a subset with all the particles
# Subsets keep the particles in sorted order and so are different than
# a simple list of particles
alls = IMP.domino.Subset(ps)
# get all the assignments that fit
sts = s.get_sample_assignments(alls)
# create a temporary file to write things to
rmf = RMF.create_rmf_file(IMP.create_temporary_file_name("cache", ".rmf"))
print("saving configurations to", rmf.get_name())
IMP.rmf.add_hierarchy(rmf, h)
# the restraint cache processes the restraints to make them more efficient
# for use with domino. So we want to get back the processed restraints
# before looking at them further
domino_restraints = rc.get_restraints()
for r in domino_restraints:
IMP.show_restraint_hierarchy(r)
IMP.rmf.add_restraints(rmf, domino_restraints)
# for each assignment load it, and add the configuration to an rmf file
print("found assignments", sts)
# we don't care about messages during saving
# pass the cache to the restraint score based filter
# it will use all the restraints in the cache
rssft = IMP.domino.RestraintScoreSubsetFilterTable(rc)
s.set_subset_filter_tables([ef, rssft])
# create a subset with all the particles
# Subsets keep the particles in sorted order and so are different than
# a simple list of particles
alls = IMP.domino.Subset(ps)
# get all the assignments that fit
sts = s.get_sample_assignments(alls)
# create a temporary file to write things to
rmf = RMF.create_rmf_file(IMP.create_temporary_file_name("cache", ".rmf"))
print("saving configurations to", rmf.get_name())
IMP.rmf.add_hierarchy(rmf, h)
# the restraint cache processes the restraints to make them more efficient
# for use with domino. So we want to get back the processed restraints
# before looking at them further
domino_restraints = rc.get_restraints()
for r in domino_restraints:
IMP.show_restraint_hierarchy(r)
IMP.rmf.add_restraints(rmf, domino_restraints)
# for each assignment load it, and add the configuration to an rmf file
print("found assignments", sts)
# we don't care about messages during saving
bbss = IMP.core.BoundingBox3DSingletonScore(
IMP.core.HarmonicUpperBound(0, k), bb)
bbr = IMP.container.SingletonsRestraint(bbss, ps)
rs.append(bbr)
sf = IMP.core.RestraintsScoringFunction(rs, "SF")
bd = IMP.atom.BrownianDynamics(m)
bd.set_log_level(IMP.base.SILENT)
bd.set_scoring_function(sf)
bd.set_maximum_time_step(10)
name = IMP.base.create_temporary_file_name("brownian", ".rmf")
rmf = RMF.create_rmf_file(name)
rmf.set_description("Brownian dyanmics trajectory with 10fs timestep.\n")
IMP.rmf.add_hierarchy(rmf, h)
IMP.rmf.add_restraints(rmf, rs)
IMP.rmf.add_geometry(rmf, IMP.display.BoundingBoxGeometry(bb))
os = IMP.rmf.SaveOptimizerState(rmf)
os.update_always("initial conformation")
os.set_log_level(IMP.base.SILENT)
os.set_simulator(bd)
bd.add_optimizer_state(os)
bd.optimize(frames)
print "file is", rmf.get_name()
bbss = IMP.core.BoundingBox3DSingletonScore(
IMP.core.HarmonicUpperBound(0, k), bb)
bbr = IMP.container.SingletonsRestraint(bbss, ps)
rs.append(bbr)
sf = IMP.core.RestraintsScoringFunction(rs, "SF")
bd = IMP.atom.BrownianDynamics(m)
bd.set_log_level(IMP.SILENT)
bd.set_scoring_function(sf)
bd.set_maximum_time_step(10)
name = IMP.create_temporary_file_name("brownian", ".rmf")
rmf = RMF.create_rmf_file(name)
rmf.set_description("Brownian dyanmics trajectory with 10fs timestep.\n")
IMP.rmf.add_hierarchy(rmf, h)
IMP.rmf.add_restraints(rmf, rs)
IMP.rmf.add_geometry(rmf, IMP.display.BoundingBoxGeometry(bb))
os = IMP.rmf.SaveOptimizerState(m, rmf)
os.update_always("initial conformation")
os.set_log_level(IMP.SILENT)
os.set_simulator(bd)
bd.add_optimizer_state(os)
bd.optimize(frames)
print("file is", rmf.get_name())
