import IMP.pmi.output as output
# input parameter
pdbfile = IMP.pmi.get_data_path("1WCM.pdb")
fastafile = IMP.pmi.get_data_path("1WCM.fasta.txt")
components = ["Rpb3", "Rpb3.copy", "Rpb4"]
chains = "CCD"
colors = [0., 0.5, 1.0]
beadsize = 20
fastids = tools.get_ids_from_fasta_file(fastafile)
m = IMP.Model()
simo = representation.SimplifiedModel(m)
hierarchies = {}
for n in range(len(components)):
simo.add_component_name(components[n], color=colors[n])
simo.add_component_sequence(components[n], fastafile, id=fastids[n + 2])
hierarchies[components[n]] = simo.autobuild_pdb_and_intervening_beads(
components[n], pdbfile, chains[n],
resolutions=[1, 10, 100], beadsize=beadsize)
simo.setup_component_sequence_connectivity(components[n], 1)
def check_time(stop_watch_object, threshold):
elapsed_time = float(
stop_watch_object.get_output()["Stopwatch_None_delta_seconds"])
if (elapsed_time > threshold):
print "WARNING: the calculation time of " + str(
elapsed_time) + " is above the " + str(threshold) + " threshold"
else:
print "the calculation time of " + str(
elapsed_time) + " is below the threshold"
# input parameter
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()
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')
def test_selection(self):
"""Test selection"""
# input parameter
pdbfile = self.get_input_file_name("1WCM.pdb")
fastafile = self.get_input_file_name("1WCM.fasta.txt")
components = ["Rpb3", "Rpb3.copy", "Rpb4"]
chains = "CCD"
colors = [0., 0.5, 1.0]
beadsize = 20
fastids = tools.get_ids_from_fasta_file(fastafile)
m = IMP.Model()
simo = representation.Representation(m)
hierarchies = {}
for n in range(len(components)):
simo.create_component(components[n], color=colors[n])
simo.add_component_sequence(components[n], fastafile,
id=fastids[n + 2])
hierarchies[components[n]] \
= simo.autobuild_model(
components[n], pdbfile, chains[n],
resolutions=[1, 10, 100], beadsize=beadsize)
simo.setup_component_sequence_connectivity(components[n], 1)
def test(a, b):
assert a==b, "%d != %d" % (a,b)
result_dict = {
"All": 691,
"resolution=1": 621,
"resolution=1,resid=10": 3,
"resolution=1,resid=10,name=Rpb3": 1,
"resolution=1,resid=10,name=Rpb3,ambiguous": 2,
"resolution=1,resid=10,name=Rpb4,ambiguous": 1,
"resolution=1,resrange=(10,20),name=Rpb3": 11,
"resolution=1,resrange=(10,20),name=Rpb3,ambiguous": 22,
"resolution=10,resrange=(10,20),name=Rpb3": 2,
"resolution=10,resrange=(10,20),name=Rpb3,ambiguous": 4,
"resolution=100,resrange=(10,20),name=Rpb3": 1,
"resolution=100,resrange=(10,20),name=Rpb3,ambiguous": 2,
"Rpb4_1-3_bead resolution=1": 1,
"Rpb4_1-3_bead resolution=10": 1,
"Rpb4_1-3_bead resolution=100": 1,
"Rpb4_4-76_pdb resolution=1": 73,
"Rpb4_4-76_pdb resolution=10": 0,
"Rpb4_4-76_pdb resolution=100": 0,
"Rpb4_4-76_pdb#2 resolution=1": 0,
"Rpb4_4-76_pdb#2 resolution=10": 8,
"Rpb4_4-76_pdb#2 resolution=100": 0,
"Rpb4_4-76_pdb#3 resolution=1": 0,
"Rpb4_4-76_pdb#3 resolution=10": 0,
"Rpb4_4-76_pdb#3 resolution=100": 1,
"Rpb4_77-96_bead resolution=1": 1,
"Rpb4_77-96_bead resolution=10": 1,
"Rpb4_77-96_bead resolution=100": 1,
"Rpb4_97-116_bead resolution=1": 1,
"Rpb4_97-116_bead resolution=10": 1,
"Rpb4_97-116_bead resolution=100": 1,
"Rpb4_117_bead resolution=1": 1,
"Rpb4_117_bead resolution=10": 1,
"Rpb4_117_bead resolution=100": 1,
"Rpb4_118-215_pdb resolution=1": 98,
"Rpb4_118-215_pdb resolution=10": 0,
"Rpb4_118-215_pdb resolution=100": 0,
"Rpb4_118-215_pdb#2 resolution=1": 0,
"Rpb4_118-215_pdb#2 resolution=10": 10,
"Rpb4_118-215_pdb#2 resolution=100": 0,
"Rpb4_118-215_pdb#3 resolution=1": 0,
"Rpb4_118-215_pdb#3 resolution=10": 0,
"Rpb4_118-215_pdb#3 resolution=100": 1,
"Rpb3.copy_1-2_bead resolution=1": 1,
"Rpb3.copy_1-2_bead resolution=10": 1,
"Rpb3.copy_1-2_bead resolution=100": 1,
"Rpb3.copy_3-177_pdb resolution=1": 175,
"Rpb3.copy_3-177_pdb resolution=10": 0,
"Rpb3.copy_3-177_pdb resolution=100": 0,
"Rpb3.copy_3-177_pdb#2 resolution=1": 0,
"Rpb3.copy_3-177_pdb#2 resolution=10": 18,
"Rpb3.copy_3-177_pdb#2 resolution=100": 0,
"Rpb3.copy_3-177_pdb#3 resolution=1": 0,
"Rpb3.copy_3-177_pdb#3 resolution=10": 0,
"Rpb3.copy_3-177_pdb#3 resolution=100": 2,
"Rpb3_1-2_bead resolution=1": 1,
"Rpb3_1-2_bead resolution=10": 1,
"Rpb3_1-2_bead resolution=100": 1,
"Rpb3_3-268_pdb resolution=1": 266,
"Rpb3_3-268_pdb resolution=10": 0,
"Rpb3_3-268_pdb resolution=100": 0,
"Rpb3_3-268_pdb#2 resolution=1": 0,
"Rpb3_3-268_pdb#2 resolution=10": 27,
"Rpb3_3-268_pdb#2 resolution=100": 0,
"Rpb3_3-268_pdb#3 resolution=1": 0,
"Rpb3_3-268_pdb#3 resolution=10": 0,
"Rpb3_3-268_pdb#3 resolution=100": 3,
"Rpb3_269-288_bead resolution=1": 1,
"Rpb3_269-288_bead resolution=10": 1,
"Rpb3_269-288_bead resolution=100": 1,
"Rpb3_289-308_bead resolution=1": 1,
"Rpb3_289-308_bead resolution=10": 1,
"Rpb3_289-308_bead resolution=100": 1,
"Rpb3_309-318_bead resolution=1": 1,
"Rpb3_309-318_bead resolution=10": 1,
"Rpb3_309-318_bead resolution=100": 1,
"Beads": 9,
"Molecule": 691,
"resolution=1,Molecule": 621,
"resolution=10,Molecule": 72,
"resolution=100,Molecule": 16,
"resolution=1,Beads": 9,
"resolution=10,Beads": 9,
"resolution=100,Beads": 9,
"resolution=2": 621,
"resolution=7": 72,
"resolution=10": 72,
"resolution=100": 16}
test(result_dict["All"], len(tools.select(simo)))
test(result_dict["resolution=1"], len(tools.select(simo, resolution=1)))
test(result_dict["resolution=1,resid=10"],
len(tools.select(simo, resolution=1, residue=10)))
test(result_dict["resolution=1,resid=10,name=Rpb3"],
len(tools.select(simo, resolution=1, name="Rpb3", residue=10)))
test(result_dict["resolution=1,resid=10,name=Rpb3,ambiguous"],
len(tools.select(simo, resolution=1, name="Rpb3",
name_is_ambiguous=True, residue=10)))
test(result_dict["resolution=1,resid=10,name=Rpb4,ambiguous"],
len(tools.select(simo, resolution=1, name="Rpb4",
name_is_ambiguous=True, residue=10)))
test(result_dict["resolution=1,resrange=(10,20),name=Rpb3"],
len(tools.select(simo, resolution=1, name="Rpb3",
first_residue=10, last_residue=20)))
test(result_dict["resolution=1,resrange=(10,20),name=Rpb3,ambiguous"],
len(tools.select(simo, resolution=1, name="Rpb3",
name_is_ambiguous=True, first_residue=10,
last_residue=20)))
test(result_dict["resolution=10,resrange=(10,20),name=Rpb3"],
len(tools.select(simo, resolution=10, name="Rpb3",
first_residue=10, last_residue=20)))
test(result_dict["resolution=10,resrange=(10,20),name=Rpb3,ambiguous"],
len(tools.select(simo, resolution=10, name="Rpb3",
name_is_ambiguous=True, first_residue=10,
last_residue=20)))
test(result_dict["resolution=100,resrange=(10,20),name=Rpb3"],
len(tools.select(simo, resolution=100, name="Rpb3",
first_residue=10, last_residue=20)))
test(result_dict["resolution=100,resrange=(10,20),name=Rpb3,ambiguous"],
len(tools.select(simo, resolution=100, name="Rpb3",
name_is_ambiguous=True, first_residue=10,
last_residue=20)))
for key in hierarchies:
seen = {}
for h in hierarchies[key]:
# Handle duplicate names
if h.get_name() in seen:
name = h.get_name() + "#%d" % seen[h.get_name()]
seen[h.get_name()] += 1
else:
name = h.get_name()
seen[h.get_name()] = 2
test(result_dict[name + " resolution=1"],
len(tools.select(simo, resolution=1, hierarchies=[h])))
test(result_dict[name + " resolution=10"],
len(tools.select(simo, resolution=10, hierarchies=[h])))
test(result_dict[name + " resolution=100"],
len(tools.select(simo, resolution=100, hierarchies=[h])))
test(result_dict["Beads"],
len(tools.select(simo, representation_type="Beads")))
test(result_dict["Molecule"],
len(tools.select(simo, representation_type="Molecule")))
test(result_dict["resolution=1,Molecule"],
len(tools.select(simo, resolution=1,
representation_type="Molecule")))
test(result_dict["resolution=10,Molecule"],
len(tools.select(simo, resolution=10,
representation_type="Molecule")))
test(result_dict["resolution=100,Molecule"],
len(tools.select(simo, resolution=100,
representation_type="Molecule")))
test(result_dict["resolution=1,Beads"],
len(tools.select(simo, resolution=1, representation_type="Beads")))
test(result_dict["resolution=10,Beads"],
len(tools.select(simo, resolution=10,
representation_type="Beads")))
test(result_dict["resolution=100,Beads"],
len(tools.select(simo, resolution=100,
representation_type="Beads")))
test(result_dict["resolution=2"], len(tools.select(simo, resolution=2)))
test(result_dict["resolution=7"],
len(tools.select(simo, resolution=7)))
test(result_dict["resolution=10"],
len(tools.select(simo, resolution=10)))
test(result_dict["resolution=100"],
len(tools.select(simo, resolution=100)))
def test_selection(self):
"""Test selection"""
# input parameter
pdbfile = self.get_input_file_name("1WCM.pdb")
fastafile = self.get_input_file_name("1WCM.fasta.txt")
components = ["Rpb3", "Rpb3.copy", "Rpb4"]
chains = "CCD"
colors = [0., 0.5, 1.0]
beadsize = 20
fastids = tools.get_ids_from_fasta_file(fastafile)
m = IMP.Model()
simo = representation.Representation(m)
hierarchies = {}
for n in range(len(components)):
simo.create_component(components[n], color=colors[n])
simo.add_component_sequence(components[n],
fastafile,
id=fastids[n + 2])
hierarchies[components[n]] \
= simo.autobuild_model(
components[n], pdbfile, chains[n],
resolutions=[1, 10, 100], beadsize=beadsize)
simo.setup_component_sequence_connectivity(components[n], 1)
def test(a, b):
assert a == b, "%d != %d" % (a, b)
result_dict = {
"All": 691,
"resolution=1": 621,
"resolution=1,resid=10": 3,
"resolution=1,resid=10,name=Rpb3": 1,
"resolution=1,resid=10,name=Rpb3,ambiguous": 2,
"resolution=1,resid=10,name=Rpb4,ambiguous": 1,
"resolution=1,resrange=(10,20),name=Rpb3": 11,
"resolution=1,resrange=(10,20),name=Rpb3,ambiguous": 22,
"resolution=10,resrange=(10,20),name=Rpb3": 2,
"resolution=10,resrange=(10,20),name=Rpb3,ambiguous": 4,
"resolution=100,resrange=(10,20),name=Rpb3": 1,
"resolution=100,resrange=(10,20),name=Rpb3,ambiguous": 2,
"Rpb4_1-3_bead resolution=1": 1,
"Rpb4_1-3_bead resolution=10": 1,
"Rpb4_1-3_bead resolution=100": 1,
"Rpb4_4-76_pdb resolution=1": 73,
"Rpb4_4-76_pdb resolution=10": 0,
"Rpb4_4-76_pdb resolution=100": 0,
"Rpb4_4-76_pdb#2 resolution=1": 0,
"Rpb4_4-76_pdb#2 resolution=10": 8,
"Rpb4_4-76_pdb#2 resolution=100": 0,
"Rpb4_4-76_pdb#3 resolution=1": 0,
"Rpb4_4-76_pdb#3 resolution=10": 0,
"Rpb4_4-76_pdb#3 resolution=100": 1,
"Rpb4_77-96_bead resolution=1": 1,
"Rpb4_77-96_bead resolution=10": 1,
"Rpb4_77-96_bead resolution=100": 1,
"Rpb4_97-116_bead resolution=1": 1,
"Rpb4_97-116_bead resolution=10": 1,
"Rpb4_97-116_bead resolution=100": 1,
"Rpb4_117_bead resolution=1": 1,
"Rpb4_117_bead resolution=10": 1,
"Rpb4_117_bead resolution=100": 1,
"Rpb4_118-215_pdb resolution=1": 98,
"Rpb4_118-215_pdb resolution=10": 0,
"Rpb4_118-215_pdb resolution=100": 0,
"Rpb4_118-215_pdb#2 resolution=1": 0,
"Rpb4_118-215_pdb#2 resolution=10": 10,
"Rpb4_118-215_pdb#2 resolution=100": 0,
"Rpb4_118-215_pdb#3 resolution=1": 0,
"Rpb4_118-215_pdb#3 resolution=10": 0,
"Rpb4_118-215_pdb#3 resolution=100": 1,
"Rpb3.copy_1-2_bead resolution=1": 1,
"Rpb3.copy_1-2_bead resolution=10": 1,
"Rpb3.copy_1-2_bead resolution=100": 1,
"Rpb3.copy_3-177_pdb resolution=1": 175,
"Rpb3.copy_3-177_pdb resolution=10": 0,
"Rpb3.copy_3-177_pdb resolution=100": 0,
"Rpb3.copy_3-177_pdb#2 resolution=1": 0,
"Rpb3.copy_3-177_pdb#2 resolution=10": 18,
"Rpb3.copy_3-177_pdb#2 resolution=100": 0,
"Rpb3.copy_3-177_pdb#3 resolution=1": 0,
"Rpb3.copy_3-177_pdb#3 resolution=10": 0,
"Rpb3.copy_3-177_pdb#3 resolution=100": 2,
"Rpb3_1-2_bead resolution=1": 1,
"Rpb3_1-2_bead resolution=10": 1,
"Rpb3_1-2_bead resolution=100": 1,
"Rpb3_3-268_pdb resolution=1": 266,
"Rpb3_3-268_pdb resolution=10": 0,
"Rpb3_3-268_pdb resolution=100": 0,
"Rpb3_3-268_pdb#2 resolution=1": 0,
"Rpb3_3-268_pdb#2 resolution=10": 27,
"Rpb3_3-268_pdb#2 resolution=100": 0,
"Rpb3_3-268_pdb#3 resolution=1": 0,
"Rpb3_3-268_pdb#3 resolution=10": 0,
"Rpb3_3-268_pdb#3 resolution=100": 3,
"Rpb3_269-288_bead resolution=1": 1,
"Rpb3_269-288_bead resolution=10": 1,
"Rpb3_269-288_bead resolution=100": 1,
"Rpb3_289-308_bead resolution=1": 1,
"Rpb3_289-308_bead resolution=10": 1,
"Rpb3_289-308_bead resolution=100": 1,
"Rpb3_309-318_bead resolution=1": 1,
"Rpb3_309-318_bead resolution=10": 1,
"Rpb3_309-318_bead resolution=100": 1,
"Beads": 9,
"Molecule": 691,
"resolution=1,Molecule": 621,
"resolution=10,Molecule": 72,
"resolution=100,Molecule": 16,
"resolution=1,Beads": 9,
"resolution=10,Beads": 9,
"resolution=100,Beads": 9,
"resolution=2": 621,
"resolution=7": 72,
"resolution=10": 72,
"resolution=100": 16
}
test(result_dict["All"], len(tools.select(simo)))
test(result_dict["resolution=1"], len(tools.select(simo,
resolution=1)))
test(result_dict["resolution=1,resid=10"],
len(tools.select(simo, resolution=1, residue=10)))
test(result_dict["resolution=1,resid=10,name=Rpb3"],
len(tools.select(simo, resolution=1, name="Rpb3", residue=10)))
test(
result_dict["resolution=1,resid=10,name=Rpb3,ambiguous"],
len(
tools.select(simo,
resolution=1,
name="Rpb3",
name_is_ambiguous=True,
residue=10)))
test(
result_dict["resolution=1,resid=10,name=Rpb4,ambiguous"],
len(
tools.select(simo,
resolution=1,
name="Rpb4",
name_is_ambiguous=True,
residue=10)))
test(
result_dict["resolution=1,resrange=(10,20),name=Rpb3"],
len(
tools.select(simo,
resolution=1,
name="Rpb3",
first_residue=10,
last_residue=20)))
test(
result_dict["resolution=1,resrange=(10,20),name=Rpb3,ambiguous"],
len(
tools.select(simo,
resolution=1,
name="Rpb3",
name_is_ambiguous=True,
first_residue=10,
last_residue=20)))
test(
result_dict["resolution=10,resrange=(10,20),name=Rpb3"],
len(
tools.select(simo,
resolution=10,
name="Rpb3",
first_residue=10,
last_residue=20)))
test(
result_dict["resolution=10,resrange=(10,20),name=Rpb3,ambiguous"],
len(
tools.select(simo,
resolution=10,
name="Rpb3",
name_is_ambiguous=True,
first_residue=10,
last_residue=20)))
test(
result_dict["resolution=100,resrange=(10,20),name=Rpb3"],
len(
tools.select(simo,
resolution=100,
name="Rpb3",
first_residue=10,
last_residue=20)))
test(
result_dict["resolution=100,resrange=(10,20),name=Rpb3,ambiguous"],
len(
tools.select(simo,
resolution=100,
name="Rpb3",
name_is_ambiguous=True,
first_residue=10,
last_residue=20)))
for key in hierarchies:
seen = {}
for h in hierarchies[key]:
# Handle duplicate names
if h.get_name() in seen:
name = h.get_name() + "#%d" % seen[h.get_name()]
seen[h.get_name()] += 1
else:
name = h.get_name()
seen[h.get_name()] = 2
test(result_dict[name + " resolution=1"],
len(tools.select(simo, resolution=1, hierarchies=[h])))
test(result_dict[name + " resolution=10"],
len(tools.select(simo, resolution=10, hierarchies=[h])))
test(result_dict[name + " resolution=100"],
len(tools.select(simo, resolution=100, hierarchies=[h])))
test(result_dict["Beads"],
len(tools.select(simo, representation_type="Beads")))
test(result_dict["Molecule"],
len(tools.select(simo, representation_type="Molecule")))
test(
result_dict["resolution=1,Molecule"],
len(
tools.select(simo,
resolution=1,
representation_type="Molecule")))
test(
result_dict["resolution=10,Molecule"],
len(
tools.select(simo,
resolution=10,
representation_type="Molecule")))
test(
result_dict["resolution=100,Molecule"],
len(
tools.select(simo,
resolution=100,
representation_type="Molecule")))
test(
result_dict["resolution=1,Beads"],
len(tools.select(simo, resolution=1, representation_type="Beads")))
test(
result_dict["resolution=10,Beads"],
len(tools.select(simo, resolution=10,
representation_type="Beads")))
test(
result_dict["resolution=100,Beads"],
len(tools.select(simo, resolution=100,
representation_type="Beads")))
test(result_dict["resolution=2"], len(tools.select(simo,
resolution=2)))
test(result_dict["resolution=7"], len(tools.select(simo,
resolution=7)))
test(result_dict["resolution=10"],
len(tools.select(simo, resolution=10)))
test(result_dict["resolution=100"],
len(tools.select(simo, resolution=100)))
