def test_loop_reconstruction(self):
"""Test loop reconstruction"""
# input parameter
pdbfile = self.get_input_file_name(
"loop_reconstruction/starting.structure.pdb")
fastafile = self.get_input_file_name(
"loop_reconstruction/sequence.fasta")
fastids = tools.get_ids_from_fasta_file(fastafile)
missing_bead_size = 1
# Component pdbfile chainid rgb color fastafile sequence id
# in fastafile
data = [("chainA", pdbfile, "A", 0.00000000, (fastafile, 0)),
("chainB", pdbfile, "B", 0.50000000, (fastafile, 0))]
# create the representation
log_objects = []
optimizable_objects = []
sw = tools.Stopwatch()
log_objects.append(sw)
m = IMP.Model()
r = representation.Representation(m)
hierarchies = {}
for d in data:
component_name = d[0]
pdb_file = d[1]
chain_id = d[2]
color_id = d[3]
fasta_file = d[4][0]
fasta_file_id = d[4][1]
# avoid adding a component with the same name
r.create_component(component_name, color=color_id)
r.add_component_sequence(component_name,
fasta_file,
id=fastids[fasta_file_id])
hierarchies = r.autobuild_model(component_name, pdb_file,
chain_id, resolutions=[1, 10],
missingbeadsize=missing_bead_size)
r.show_component_table(component_name)
rbAB = r.set_rigid_bodies(["chainA", "chainB"])
r.set_floppy_bodies()
r.fix_rigid_bodies([rbAB])
r.setup_bonds()
log_objects.append(r)
listofexcludedpairs = []
lof = [(1, 12, "chainA"), (1, 12, "chainB"),
(294, 339, "chainA"), (294, 339, "chainB"),
(686, 701, "chainA"), (686, 701, "chainB"),
(454, 464, "chainA"), (454, 464, "chainB"),
(472, 486, "chainA"), (472, 486, "chainB"),
(814, 859, "chainA"), (814, 859, "chainB")]
# add bonds and angles
for l in lof:
rbr = IMP.pmi.restraints.stereochemistry.ResidueBondRestraint(r, l)
rbr.add_to_model()
listofexcludedpairs += rbr.get_excluded_pairs()
log_objects.append(rbr)
rar = IMP.pmi.restraints.stereochemistry.ResidueAngleRestraint(r, l)
rar.add_to_model()
listofexcludedpairs += rar.get_excluded_pairs()
log_objects.append(rar)
# add excluded volume
ev = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(
r, resolution=10.0)
ev.add_excluded_particle_pairs(listofexcludedpairs)
ev.add_to_model()
log_objects.append(ev)
mc = samplers.MonteCarlo(m, [r], 1.0)
log_objects.append(mc)
o = output.Output()
print("Starting test")
o.write_test("test.current.dict", log_objects)
o.test(self.get_input_file_name(
"loop_reconstruction/test.IMP-ee1763c6.PMI-4669cfca.dict"),
log_objects)
os.unlink('test.current.dict')
pdbfile = IMP.pmi.get_data_path("benchmark_starting_structure.pdb")
fastafile = IMP.pmi.get_data_path("benchmark_sequence.fasta")
fastids = tools.get_ids_from_fasta_file(fastafile)
missing_bead_size = 1
# Component pdbfile chainid rgb color fastafile sequence id
# in fastafile
data = [("chainA", pdbfile, "A", 0.00000000, (fastafile, 0)),
("chainB", pdbfile, "B", 0.50000000, (fastafile, 0))]
# create the representation
log_objects = []
optimizable_objects = []
sw = tools.Stopwatch()
log_objects.append(sw)
m = IMP.Model()
r = representation.Representation(m)
hierarchies = {}
for d in data:
component_name = d[0]
pdb_file = d[1]
chain_id = d[2]
color_id = d[3]
fasta_file = d[4][0]
fasta_file_id = d[4][1]
# avoid to add a component with the same name
def test_loop_reconstruction(self):
"""Test loop reconstruction"""
# input parameter
pdbfile = self.get_input_file_name(
"loop_reconstruction/starting.structure.pdb")
fastafile = self.get_input_file_name(
"loop_reconstruction/sequence.fasta")
sequences = IMP.pmi.topology.Sequences(fastafile)
# create the representation
log_objects = []
optimizable_objects = []
sw = tools.Stopwatch()
log_objects.append(sw)
m = IMP.Model()
s = IMP.pmi.topology.System(m)
st = s.create_state()
cA = st.create_molecule("chainA", sequence=sequences[0])
atomic = cA.add_structure(pdbfile, chain_id='A')
cA.add_representation(atomic, resolutions=[1, 10], color=0.)
cA.add_representation(cA.get_non_atomic_residues(),
resolutions=[1],
color=0.)
cB = st.create_molecule("chainB", sequence=sequences[0])
atomic = cB.add_structure(pdbfile, chain_id='B')
cB.add_representation(atomic, resolutions=[1, 10], color=0.5)
cB.add_representation(cB.get_non_atomic_residues(),
resolutions=[1],
color=0.)
root_hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(m)
dof.create_rigid_body(cA)
dof.create_rigid_body(cB)
cr = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(
root_hier)
cr.add_to_model()
log_objects.append(cr)
listofexcludedpairs = []
lof = [
cA[:12], cB[:12], cA[293:339], cB[293:339], cA[685:701],
cB[685:701], cA[453:464], cB[453:464], cA[471:486], cB[471:486],
cA[813:859], cB[813:859]
]
# add bonds and angles
for l in lof:
print(l)
rbr = IMP.pmi.restraints.stereochemistry.ResidueBondRestraint(
objects=l)
rbr.add_to_model()
listofexcludedpairs += rbr.get_excluded_pairs()
log_objects.append(rbr)
rar = IMP.pmi.restraints.stereochemistry.ResidueAngleRestraint(
objects=l)
rar.add_to_model()
listofexcludedpairs += rar.get_excluded_pairs()
log_objects.append(rar)
# add excluded volume
ev = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(
included_objects=root_hier, resolution=10.0)
ev.add_excluded_particle_pairs(listofexcludedpairs)
ev.add_to_model()
log_objects.append(ev)
mc = samplers.MonteCarlo(m, dof.get_movers(), 1.0)
log_objects.append(mc)
o = output.Output()
print("Starting test")
o.write_test("test.current.dict", log_objects)
o.test(
self.get_input_file_name(
"loop_reconstruction/test.IMP-ee1763c6.PMI-4669cfca.dict"),
log_objects)
os.unlink('test.current.dict')