def init_representation_beads_pmi2(self, m):
s = IMP.pmi.topology.System(m)
st = s.create_state()
protA = st.create_molecule("ProtA", sequence='A' * 30, chain_id='A')
protA.add_representation(protA[0:10],
resolutions=[1],
bead_default_coord=[0, 0, 0])
protA.add_representation(protA[10:20],
resolutions=[1],
bead_default_coord=[10, 0, 0])
protA.add_representation(protA[20:30],
resolutions=[1],
bead_default_coord=[20, 0, 0])
protB = st.create_molecule("ProtB", sequence='A' * 30, chain_id='B')
protB.add_representation(protB[0:10],
resolutions=[1],
bead_default_coord=[0, 0, 0])
protB.add_representation(protB[10:20],
resolutions=[1],
bead_default_coord=[10, 0, 0])
protB.add_representation(protB[20:30],
resolutions=[1],
bead_default_coord=[20, 0, 0])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(m)
dof.create_flexible_beads(protA)
dof.create_flexible_beads(protB)
return hier, dof
def test_mc_flexible_beads_disable(self):
"""Test disable of flexible beads"""
mdl = IMP.Model()
s,mol = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
fb_movers = dof.create_flexible_beads(mol.get_non_atomic_residues(),max_trans=1.0)
self.assertEqual(len(fb_movers),3)
mvs = dof.get_movers()
self.assertEqual(len(mvs),3)
particles=IMP.atom.Selection(s.hier,molecule="Prot1").get_selected_particles()
xyzs,rbs=dof.disable_movers(particles)
self.assertEqual(len(xyzs),3)
self.assertEqual(len(rbs),0)
mvs = dof.get_movers()
self.assertEqual(len(mvs),0)
dof.enable_all_movers()
particles=IMP.atom.Selection(s.hier,molecule="Prot1").get_selected_particles()
xyzs,rbs=dof.disable_movers(particles,mover_types=[IMP.core.RigidBodyMover])
self.assertEqual(len(xyzs),0)
self.assertEqual(len(rbs),0)
mvs = dof.get_movers()
self.assertEqual(len(mvs),3)
dof.enable_all_movers()
particles=IMP.atom.Selection(s.hier,molecule="Prot1").get_selected_particles()
xyzs,rbs=dof.disable_movers(particles,mover_types=[IMP.core.BallMover])
self.assertEqual(len(xyzs),3)
self.assertEqual(len(rbs),0)
mvs = dof.get_movers()
self.assertEqual(len(mvs),0)
def test_mc_flexible_beads3(self):
"""Test flex beads don't work if nothing passed"""
mdl = IMP.Model()
s,mols = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
fb_movers = dof.create_flexible_beads(mols[1].get_non_atomic_residues(),max_trans=1.0)
self.assertEqual(len(fb_movers),0)
def init_representation_beads_pmi2(self,m):
s = IMP.pmi.topology.System(m)
st = s.create_state()
protA = st.create_molecule("ProtA",sequence='A'*30,chain_id='A')
protA.add_representation(protA[0:10],resolutions=[1],bead_default_coord=[0,0,0])
protA.add_representation(protA[10:20],resolutions=[1],bead_default_coord=[10,0,0])
protA.add_representation(protA[20:30],resolutions=[1],bead_default_coord=[20,0,0])
protB = st.create_molecule("ProtB",sequence='A'*30,chain_id='B')
protB.add_representation(protB[0:10],resolutions=[1],bead_default_coord=[0,0,0])
protB.add_representation(protB[10:20],resolutions=[1],bead_default_coord=[10,0,0])
protB.add_representation(protB[20:30],resolutions=[1],bead_default_coord=[20,0,0])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(m)
dof.create_flexible_beads(protA)
dof.create_flexible_beads(protB)
return hier,dof
def test_mc_flexible_beads3(self):
"""Test flex beads don't work if nothing passed"""
mdl = IMP.Model()
s, mols = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
fb_movers = dof.create_flexible_beads(
mols[1].get_non_atomic_residues(), max_trans=1.0)
self.assertEqual(len(fb_movers), 0)
def test_mc_flexible_beads(self):
mdl = IMP.Model()
molecule = self.init_topology1(mdl)
hier = molecule.get_hierarchy()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
sel_nonrigid = IMP.atom.Selection(hier, residue_indexes=[3, 4, 10])
fbs = dof.create_flexible_beads(sel_nonrigid, max_trans=1.0)
mvs = fbs.get_movers()
self.assertEqual(len(mvs), 3)
def test_mc_flexible_beads(self):
mdl = IMP.Model()
molecule = self.init_topology1(mdl)
hier = molecule.get_hierarchy()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
sel_nonrigid = IMP.atom.Selection(hier,residue_indexes=[3,4,10])
fbs = dof.create_flexible_beads(sel_nonrigid,max_trans=1.0)
mvs = fbs.get_movers()
self.assertEqual(len(mvs),3)
def test_mc_flexible_beads(self):
"""Test setup of flexible beads"""
mdl = IMP.Model()
s,mol = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
fb_movers = dof.create_flexible_beads(mol.get_non_atomic_residues(),max_trans=1.0)
self.assertEqual(len(fb_movers),3)
rex = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=s.get_hierarchy(),
monte_carlo_sample_objects = dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
def test_mc_flexible_beads(self):
"""Test setup of flexible beads"""
mdl = IMP.Model()
s, mol = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
fb_movers = dof.create_flexible_beads(mol.get_non_atomic_residues(),
max_trans=1.0)
self.assertEqual(len(fb_movers), 3)
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=s.get_hierarchy(),
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
def test_mc_flexible_beads_disable(self):
"""Test disable of flexible beads"""
mdl = IMP.Model()
s, mol = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
fb_movers = dof.create_flexible_beads(mol.get_non_atomic_residues(),
max_trans=1.0)
self.assertEqual(len(fb_movers), 3)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 3)
particles = IMP.atom.Selection(
s.hier, molecule="Prot1").get_selected_particles()
xyzs, rbs = dof.disable_movers(particles)
self.assertEqual(len(xyzs), 3)
self.assertEqual(len(rbs), 0)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 0)
dof.enable_all_movers()
particles = IMP.atom.Selection(
s.hier, molecule="Prot1").get_selected_particles()
xyzs, rbs = dof.disable_movers(particles,
mover_types=[IMP.core.RigidBodyMover])
self.assertEqual(len(xyzs), 0)
self.assertEqual(len(rbs), 0)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 3)
dof.enable_all_movers()
particles = IMP.atom.Selection(
s.hier, molecule="Prot1").get_selected_particles()
xyzs, rbs = dof.disable_movers(particles,
mover_types=[IMP.core.BallMover])
self.assertEqual(len(xyzs), 3)
self.assertEqual(len(rbs), 0)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 0)
##fname = 'test2.rmf'
##rh = RMF.create_rmf_file(fname)
##IMP.rmf.add_hierarchy(rh, root_hier)
##IMP.rmf.save_frame(rh)
##(receptor_radius,receptor_center_residue)=get_radius_center_residue(receptor)
##(ligand_radius,ligand_center_residue)=get_radius_center_residue(ligand)
##print "radius",receptor_radius +ligand_radius+5.0
## Setup degrees of freedom
## The DOF functions automatically select all resolutions
## Objects passed to nonrigid_parts move with the frame but also have their own independent movers.
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_flexible_beads(ligand_mol,max_trans = -1, resolutions_list=resolutions,move_sizes_list = move_sizes)
########################## RESTRAINTS #####################
output_objects = [] # keep a list of functions that need to be reported
display_restraints = [] # display as springs in RMF
# Connectivity keeps things connected along the backbone (ignores if inside same rigid body)
crs = []
for mol in mols:
cr = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(mol)
cr.add_to_model()
output_objects.append(cr)
crs.append(cr)
# Excluded volume - automatically more efficient due to rigid bodies
evr1 = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects = ligand_mol)
# State 2: ProtA (chainA), ProtC (chainC)
m2A = st2.create_molecule('ProtA',sequence,chain_id='A')
m2A.add_representation(m2A,resolutions=[1])
m2C = st2.create_molecule('ProtC',sequence,chain_id='C')
m2C.add_representation(m2C,resolutions=[1])
root_hier = s.build()
### Display all the states, molecules, representations
IMP.atom.show_with_representations(root_hier)
### Setup all molecules to move as flexible beads and super rigid bodies
# "Super rigid bodies" aren't really rigid, it's just a mover that moves the whole body together
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
for mol in (m1A,m1B,m1C,m2A,m2C):
dof.create_flexible_beads(mol,
max_trans=0.1)
dof.create_super_rigid_body(mol)
###################### RESTRAINTS #####################
output_objects = [] # keep a list of functions that need to be reported
rmf_restraints = [] # display these restraints as springs in the RMF
### Crosslinks setup
# 1) Create file. This one XL has 3 ambiguity options: State1 has 2, State2 has 1
lines = '''id,mol1,res1,mol2,res2,score
1,ProtA,3,ProtC,9,1.0
'''
tf = tempfile.NamedTemporaryFile(delete=False, mode='w')
tf.write(lines)
tf.close()
def test_restraint_copy_ambiguity(self):
"""Test restraint works for systems with configuration ambiguity in PMI2"""
# setup system
m = IMP.Model()
s = IMP.pmi.topology.System(m)
st = s.create_state()
protA = st.create_molecule("ProtA",sequence='A'*30,chain_id='A')
protA.add_representation(protA[0:10],resolutions=[1],bead_default_coord=[0,0,0])
protA.add_representation(protA[10:20],resolutions=[1],bead_default_coord=[10,0,0])
protA.add_representation(protA[20:30],resolutions=[1],bead_default_coord=[20,0,0])
protA2 = protA.create_clone('C')
protB = st.create_molecule("ProtB",sequence='A'*30,chain_id='B')
protB.add_representation(protB[0:10],resolutions=[1],bead_default_coord=[0,0,0])
protB.add_representation(protB[10:20],resolutions=[1],bead_default_coord=[10,0,0])
protB.add_representation(protB[20:30],resolutions=[1],bead_default_coord=[20,0,0])
protB2 = protB.create_clone('D')
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(m)
dof.create_flexible_beads([protA,protA2,protB,protB2])
xlbeads,cldb = self.setup_crosslinks_beads(root_hier=hier,mode="single_category")
# check enough clones were created
self.assertEqual(len(cldb.data_base['1']),8)
self.assertEqual(len(cldb.data_base['2']),4)
self.assertEqual(len(cldb.data_base['3']),4)
self.assertEqual(len(cldb.data_base['4']),4)
# check score
for j in range(100):
IMP.pmi.tools.shuffle_configuration(hier,max_translation=10)
cross_link_dict={}
for xl in xlbeads.xl_list:
p0 = xl["Particle1"]
p1 = xl["Particle2"]
prob = xl["Restraint"].get_probability()
resid1 = xl[cldb.residue1_key]
chain1 = xl[cldb.protein1_key]
resid2 = xl[cldb.residue2_key]
chain2 = xl[cldb.protein2_key]
xlid=xl[cldb.unique_id_key]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
if xlid not in cross_link_dict:
cross_link_dict[xlid]=([d0],[d1],[sig1],[sig2],[psi],prob)
else:
cross_link_dict[xlid][0].append(d0)
cross_link_dict[xlid][1].append(d1)
cross_link_dict[xlid][2].append(sig1)
cross_link_dict[xlid][3].append(sig2)
cross_link_dict[xlid][4].append(psi)
for xlid in cross_link_dict:
test_prob=get_probability(cross_link_dict[xlid][0],
cross_link_dict[xlid][1],
cross_link_dict[xlid][2],
cross_link_dict[xlid][3],
cross_link_dict[xlid][4],21.0,0.01)
prob=cross_link_dict[xlid][5]
self.assertAlmostEqual(test_prob,prob, delta=0.0001)
for output in ['excluded.None.xl.db',
'included.None.xl.db', 'missing.None.xl.db']:
os.unlink(output)
for i, mol in enumerate(pol2g_mols):
# create a rigid body for each domain with structural information, the flexible beads inside are part of the rigid body, the remaining part of the
#crystal structures of RPB1 and RPB2
if i in range(12):
print(i, mol)
pol2g_unstructured = mol.get_non_atomic_residues()
pol2g_structured = mol.get_atomic_residues()
pol2g_all = mol.get_residues()
pol2g_complex.append(pol2g_all)
pol2g_complexn.append(pol2g_unstructured)
if i in [12]:
pol2g_u = mol.get_non_atomic_residues()
pol2g_rigid1 = mol.get_residues()
dof.create_flexible_beads(pol2g_rigid1,
max_trans=FLEX_MAX_TRANS,
resolution=10)
print(dof)
pol2g_molc2 = [x for x in pol2g_complex]
pol2g_molc3 = [x for x in pol2g_complexn]
dof.create_flexible_beads(pol2g_molc3, max_trans=FLEX_MAX_TRANS, resolution=10)
##############################################################
##############################################################
##############################################################
##############################################################
##############################################################
####################### RESTRAINTS #####################
output_objects = [] # keep a list of functions that need to be reported
pass
sys.stdout = DummyFile()
"""setting up the representation
PMI 2 representation. Creates two particles and
an harmonic distance restraints between them"""
m = IMP.Model()
s = IMP.pmi.topology.System(m)
st1 = s.create_state()
mol = st1.create_molecule("A", "GG", "A")
mol.add_representation(resolutions=[1])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mol)
dof.create_flexible_beads(mol, max_trans=3.0, resolution=1)
ps = IMP.atom.get_leaves(hier)
dr = IMP.pmi.restraints.basic.DistanceRestraint(root_hier=hier,
tuple_selection1=(1, 1, "A"),
tuple_selection2=(2, 2, "A"),
distancemin=10,
distancemax=10)
dr.add_to_model()
start_time = process_time()
rex = IMP.pmi.macros.ReplicaExchange0(
m,
root_hier=hier,
monte_carlo_sample_objects=dof.get_movers(),
def test_multistate(self):
psiv = 0.01
sigmav = 12.0
slope = 0.0
length = 21
inputx = 70
m = IMP.Model()
s = IMP.pmi.topology.System(m)
# define the particles in state 1
st1 = s.create_state()
mol1 = []
for mn in range(1, 4):
mol = st1.create_molecule("particle%d" % mn, "G" * 10,
"ABC"[mn - 1])
mol.add_representation(resolutions=[10])
mol1.append(mol)
# define the particles in state 2
st2 = s.create_state()
mol2 = []
for mn in range(1, 4):
mol = st2.create_molecule("particle%d" % mn, "G" * 10,
"ABC"[mn - 1])
mol.add_representation(resolutions=[10])
mol2.append(mol)
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(m)
# only allow particle3 in each state to move
dof.create_flexible_beads(mol1[2])
dof.create_flexible_beads(mol2[2])
pp1, pp2, pp3 = IMP.atom.get_leaves(st1.hier)
xyz11 = IMP.core.XYZ(pp1)
xyz21 = IMP.core.XYZ(pp2)
xyz31 = IMP.core.XYZ(pp3)
xyz11.set_coordinates((0, 0, 0))
print(xyz11.get_coordinates())
xyz21.set_coordinates((inputx, 0, 0))
xyz31.set_coordinates((0, 0, 0))
pp1, pp2, pp3 = IMP.atom.get_leaves(st2.hier)
xyz12 = IMP.core.XYZ(pp1)
xyz22 = IMP.core.XYZ(pp2)
xyz32 = IMP.core.XYZ(pp3)
xyz12.set_coordinates((0, 0, 0))
xyz22.set_coordinates((inputx, 0, 0))
xyz32.set_coordinates((inputx, 0, 0))
eb = IMP.pmi.restraints.basic.ExternalBarrier(hierarchies=st1.hier,
radius=1000)
eb.add_to_model()
eb = IMP.pmi.restraints.basic.ExternalBarrier(hierarchies=st2.hier,
radius=1000)
eb.add_to_model()
xldbkwc = IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter()
xldbkwc.set_protein1_key("prot1")
xldbkwc.set_protein2_key("prot2")
xldbkwc.set_residue1_key("res1")
xldbkwc.set_residue2_key("res2")
xldbkwc.set_unique_id_key("id")
cldb = IMP.pmi.io.crosslink.CrossLinkDataBase(xldbkwc)
cldb.create_set_from_file(self.get_input_file_name('multistate.csv'))
xl = IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint(
root_hier=hier,
database=cldb,
length=length,
slope=slope,
resolution=1.0)
psi = xl.psi_dictionary['PSI'][0]
psi.set_scale(psiv)
sigma = xl.sigma_dictionary['SIGMA'][0]
sigma.set_scale(sigmav)
xl.set_psi_is_sampled(False)
xl.set_sigma_is_sampled(False)
# psi.set_scale(0.1)
# xl.get_sigma(1.0)
out_dict = xl.get_output()
sorted_keys = sorted(out_dict.keys())
for entry in sorted_keys:
print(entry, out_dict[entry])
print(xyz11.get_coordinates())
xl.add_to_model()
rset = IMP.pmi.tools.get_restraint_set(m)
self.assertAlmostEqual(rset.evaluate(False), -3.03166, delta=1e-2)
o = IMP.pmi.output.Output()
o.init_rmf("trajectory.rmf3", [st1.hier, st2.hier])
print(o.dictionary_rmfs)
mc = IMP.pmi.samplers.MonteCarlo(m, dof.get_movers(), 1.0)
mc.set_simulated_annealing(min_temp=1.0,
max_temp=2.0,
min_temp_time=200,
max_temp_time=50)
o.init_stat2("modeling.stat", [mc, xl])
for i in range(1, 20):
xyz31.set_coordinates((float(i), 0, 0))
for j in range(1, 20):
xyz32.set_coordinates((float(j), 0, 0))
print(i, j, rset.evaluate(False))
o.write_stats2()
po = IMP.pmi.output.ProcessOutput("modeling.stat")
print(po.get_keys())
self.assertEqual(len(po.get_keys()), 14)
fs = po.get_fields([
'CrossLinkingMassSpectrometryRestraint_Distance_||2.1|particle1|5|particle3|5|1|PSI|',
'CrossLinkingMassSpectrometryRestraint_Distance_||1.1|particle2|5|particle3|5|1|PSI|',
'CrossLinkingMassSpectrometryRestraint_Data_Score',
'CrossLinkingMassSpectrometryRestraint_Linear_Score',
'CrossLinkingMassSpectrometryRestraint_Psi_PSI'
])
print(fs.keys())
o.close_rmf("trajectory.rmf3")
for output in [
'excluded.None.xl.db', 'included.None.xl.db',
'missing.None.xl.db', 'modeling.stat', 'trajectory.rmf3'
]:
os.unlink(output)
# State 2: ProtA (chainA), ProtC (chainC)
m2A = st2.create_molecule('ProtA', sequence, chain_id='A')
m2A.add_representation(m2A, resolutions=[1])
m2C = st2.create_molecule('ProtC', sequence, chain_id='C')
m2C.add_representation(m2C, resolutions=[1])
root_hier = s.build()
### Display all the states, molecules, representations
IMP.atom.show_with_representations(root_hier)
### Setup all molecules to move as flexible beads and super rigid bodies
# "Super rigid bodies" aren't really rigid, it's just a mover that moves the whole body together
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
for mol in (m1A, m1B, m1C, m2A, m2C):
dof.create_flexible_beads(mol, max_trans=0.1)
dof.create_super_rigid_body(mol)
###################### RESTRAINTS #####################
output_objects = [] # keep a list of functions that need to be reported
### Crosslinks setup
# 1) Create file. This one XL has 3 ambiguity options: State1 has 2, State2 has 1
lines = '''id,mol1,res1,mol2,res2,score
1,ProtA,3,ProtC,9,1.0
'''
tf = tempfile.NamedTemporaryFile(delete=False, mode='w')
tf.write(lines)
tf.close()
# 2) Define the columns
def test_macro_rmf_stat(self):
"""setting up the representation
PMI 2.0 representation. Creates two particles and
a harmonic distance restraint between them"""
import shutil
import itertools
m = IMP.Model()
s = IMP.pmi.topology.System(m)
st1 = s.create_state()
mol = st1.create_molecule("A", "GG", "A")
mol.add_representation(resolutions=[1])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mol)
dof.create_flexible_beads(mol, max_trans=3.0, resolution=1)
ps = IMP.atom.get_leaves(hier)
dr = IMP.pmi.restraints.basic.DistanceRestraint(root_hier=hier,
tuple_selection1=(1, 1,
"A"),
tuple_selection2=(2, 2,
"A"),
distancemin=10,
distancemax=10)
dr.add_to_model()
rex = IMP.pmi.macros.ReplicaExchange0(
m,
root_hier=hier,
monte_carlo_sample_objects=dof.get_movers(),
output_objects=None,
rmf_output_objects=[dr],
monte_carlo_temperature=1.0,
replica_exchange_minimum_temperature=1.0,
replica_exchange_maximum_temperature=2.5,
number_of_best_scoring_models=10,
monte_carlo_steps=10,
number_of_frames=100,
write_initial_rmf=True,
initial_rmf_name_suffix="initial",
stat_file_name_suffix="stat",
best_pdb_name_suffix="model",
do_clean_first=True,
do_create_directories=True,
global_output_directory="./test_replica_exchange_macro_output",
rmf_dir="rmfs/",
best_pdb_dir="pdbs/",
replica_stat_file_suffix="stat_replica",
em_object_for_rmf=None,
replica_exchange_object=None)
# check whether the directory is existing, in case remove it
try:
shutil.rmtree('./test_replica_exchange_macro_output')
except OSError:
pass
rex.execute_macro()
self.check_rmf_file('./test_replica_exchange_macro_output/rmfs/0.rmf3')
# check that each replica index is below the total number of replicas
my_index = rex.replica_exchange_object.get_my_index()
nreplicas = rex.replica_exchange_object.get_number_of_replicas()
temperatures = rex.replica_exchange_object.get_my_parameter("temp")
self.assertLess(my_index, nreplicas)
# check that each replica has a unique index
tf = open(
"./test_replica_exchange_macro_output/" + str(my_index) + ".test",
"w")
tf.write(str(my_index))
tf.close()
# sleep to synchronize
time.sleep(1)
if my_index == 0:
for k in range(nreplicas):
self.assertTrue(
os.path.isfile("./test_replica_exchange_macro_output/" +
str(k) + ".test"))
#extract the info form the stat files
rex_out_files = glob.glob(
"./test_replica_exchange_macro_output/stat_replica.*.out")
temp_key = "ReplicaExchange_CurrentTemp"
maxtf_key = "ReplicaExchange_MaxTempFrequency"
mintf_key = "ReplicaExchange_MinTempFrequency"
ssr_key = "ReplicaExchange_SwapSuccessRatio"
score_key = "score"
score_temp_dict = {}
avtemps_replicas = []
for f in rex_out_files:
o = IMP.pmi.output.ProcessOutput(f)
d = o.get_fields(
[temp_key, maxtf_key, mintf_key, ssr_key, score_key])
temps = [float(f) for f in d[temp_key]]
scores = [float(f) for f in d[score_key]]
avtemp = sum(temps) / len(temps)
avtemps_replicas.append(avtemp)
for n, t in enumerate(temps):
s = scores[n]
if t not in score_temp_dict:
score_temp_dict[t] = [s]
else:
score_temp_dict[t].append(s)
# test that the average temperature per replica are similar
for c in itertools.combinations(avtemps_replicas, 2):
self.assertAlmostEqual(c[0], c[1], delta=0.05)
for t in score_temp_dict:
avscore = sum(score_temp_dict[t]) / len(score_temp_dict[t])
#check that the score is the energy of an 1D harmonic oscillator
self.assertAlmostEqual(avscore, t / 2, delta=0.1)
rex_out_file = "./test_replica_exchange_macro_output/rmfs/" + str(
my_index) + ".rmf3"
dist_key = "DistanceRestraint_Score"
mc_nframe_key = "MonteCarlo_Nframe"
mc_temp_key = "MonteCarlo_Temperature"
rex_temp_key = "ReplicaExchange_CurrentTemp"
rex_max_temp_key = "ReplicaExchange_MaxTempFrequency"
rex_min_temp_key = "ReplicaExchange_MinTempFrequency"
rex_swap_key = "ReplicaExchange_SwapSuccessRatio"
rex_score_key = "Total_Score"
rmf_file_key = "rmf_file"
rmf_file_index = "rmf_frame_index"
o = IMP.pmi.output.ProcessOutput(rex_out_file)
d = o.get_fields([
dist_key, mc_temp_key, mc_nframe_key, rex_temp_key,
rex_max_temp_key, rex_min_temp_key, rex_swap_key, rex_score_key,
rmf_file_key, rmf_file_index
])
nframes = len(d[mc_nframe_key])
self.assertNotEqual(float(d[mc_nframe_key][-1]), 0)
self.assertEqual(list(map(float, d[mc_temp_key])), [1.0] * nframes)
self.assertGreater(float(d[rex_min_temp_key][-1]), 0.0)
# Create a symmetry constraint
# A constrant is invariant: IMP will automatically move all clones to match the reference
# If instead you want some more flexiblity, consider IMP.pmi.restraints.stereochemistry.SymmetryRestraint
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
center = IMP.algebra.Vector3D([50,0,0])
for nc in range(7):
rot = IMP.algebra.get_rotation_about_axis([0,0,1],2*math.pi*(nc+1)/8)
transform = IMP.algebra.get_rotation_about_point(center,rot)
dof.constrain_symmetry(mols[0],mols[nc+1],transform)
mdl.update() # propagates coordinates
############ Make stuff look cool with restraints ###########
# set up the original molecule as flexible beads
dof.create_flexible_beads(mols[0])
# Create a connectivity restraint for the first molecule
cr = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(objects=mol)
cr.add_to_model()
# Create excluded volume for all particles
evr = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects=mols)
evr.add_to_model()
# Quickly move all flexible beads into place
dof.optimize_flexible_beads(100)
# write a single-frame RMF to view the helix
out = IMP.pmi.output.Output()
out.init_rmf("example_symmetry.rmf3",hierarchies=[hier])
# Create a symmetry constraint
# A constrant is invariant: IMP will automatically move all clones to match the reference
# If instead you want some more flexiblity, consider IMP.pmi.restraints.stereochemistry.SymmetryRestraint
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
center = IMP.algebra.Vector3D([50,0,0])
for nc in range(7):
rot = IMP.algebra.get_rotation_about_axis([0,0,1],2*math.pi*(nc+1)/8)
transform = IMP.algebra.get_rotation_about_point(center,rot)
dof.constrain_symmetry(mols[0],mols[nc+1],transform)
mdl.update() # propagates coordinates
############ Make stuff look cool with restraints ###########
# set up the original molecule as flexible beads
dof.create_flexible_beads(mols[0])
# Create a connectivity restraint for the first molecule
cr = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(objects=mol)
cr.add_to_model()
# Create excluded volume for all particles
evr = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects=mols)
evr.add_to_model()
# Quickly move all flexible beads into place
dof.optimize_flexible_beads(100)
# write a single-frame RMF to view the helix
out = IMP.pmi.output.Output()
out.init_rmf("example_symmetry.rmf3",hierarchies=[hier])
def test_shuffle_deep(self):
"""Test moving rbs, fbs"""
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
seqs = IMP.pmi.topology.Sequences(
self.get_input_file_name('chainA.fasta'))
st1 = s.create_state()
mol = st1.create_molecule("GCP2_YEAST",
sequence=seqs["GCP2_YEAST"][:100],
chain_id='A')
atomic_res = mol.add_structure(self.get_input_file_name('chainA.pdb'),
chain_id='A',
res_range=(1, 100))
mol.add_representation(mol.get_atomic_residues(), resolutions=[10])
mol.add_representation(mol.get_non_atomic_residues(), resolutions=[10])
mol2 = mol.create_clone('B')
mol3 = st1.create_molecule("GCP2_YEAST_BEADS",
sequence=seqs["GCP2_YEAST"][:100],
chain_id='C')
mol3.add_representation(mol3.get_non_atomic_residues(),
resolutions=[10])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(mol,
nonrigid_parts=mol.get_non_atomic_residues())
dof.create_rigid_body(mol2,
nonrigid_parts=mol2.get_non_atomic_residues())
dof.create_flexible_beads(mol3.get_non_atomic_residues(),
max_trans=1.0)
rbs, fbs = IMP.pmi.tools.get_rbs_and_beads([hier])
rbs_trans_before = {}
fbs_position_before = {}
rbs_trans_after = {}
fbs_position_after = {}
for rb in rbs:
rbs_trans_before[rb] = rb.get_reference_frame(
).get_transformation_to()
for fb in fbs:
if IMP.core.NonRigidMember.get_is_setup(fb):
fbs_position_before[fb] = \
IMP.core.NonRigidMember(fb).get_internal_coordinates()
else:
fbs_position_before[fb] = IMP.core.XYZ(fb).get_coordinates()
IMP.pmi.tools.shuffle_configuration(hier)
for rb in rbs:
rbs_trans_after[rb] = rb.get_reference_frame(
).get_transformation_to()
for fb in fbs:
if IMP.core.NonRigidMember.get_is_setup(fb):
fbs_position_after[fb] = \
IMP.core.NonRigidMember(fb).get_internal_coordinates()
else:
fbs_position_after[fb] = IMP.core.XYZ(fb).get_coordinates()
for fb in fbs:
position_after = fbs_position_after[fb]
position_before = fbs_position_before[fb]
for i in [0, 1, 2]:
self.assertNotEqual(position_after[i], position_before[i])
for rb in rbs:
position_after = rbs_trans_after[rb].get_translation()
position_before = rbs_trans_before[rb].get_translation()
rotation_after = rbs_trans_after[rb].get_rotation(
) * IMP.algebra.Vector3D(1, 1, 1)
rotation_before = rbs_trans_before[rb].get_rotation(
) * IMP.algebra.Vector3D(1, 1, 1)
for i in [0, 1, 2]:
self.assertNotEqual(position_after[i], position_before[i])
self.assertNotEqual(rotation_after[i], rotation_before[i])
TREM2_mol.append(mol)
elif 'Abeta' in molname:
crA = IMP.pmi.restraints.stereochemistry.ConnectivityRestraint(mol, scale=2.0)
crA.add_to_model()
output_objects.append(crA)
sample_objects.append(crA)
crs.append(crA)
atomic = mol.get_atomic_residues()
dof.create_rigid_body(atomic,
max_trans=0,
max_rot=0,
resolution='all')
dof.create_flexible_beads(mol.get_non_atomic_residues(),
max_trans=1.0,
resolution=1)
active_tri_mol.append(mol)
# ______Composite Restraint for Fibril___________________________________________________________________
shuffle_exclude_rbs = dof.get_rigid_bodies()[:-1]
# Constrain the fibril trimer unit copies with z-trans. symmetry ### This is very important
for i in range(0, len(chains)):
for t in range(0, len(fibril_transforms)):
threefold_trans = fibril_transforms[t]
dof.constrain_symmetry(protofil_mols[i][0], protofil_mols[i][t + 1], threefold_trans)
mdl.update()
print("||||| All sym constraints added |||||")
def test_restraint_copy_ambiguity(self):
"""Test restraint works for systems with configuration ambiguity in PMI2"""
# setup system
m = IMP.Model()
s = IMP.pmi.topology.System(m)
st = s.create_state()
protA = st.create_molecule("ProtA", sequence='A' * 30, chain_id='A')
protA.add_representation(protA[0:10],
resolutions=[1],
bead_default_coord=[0, 0, 0])
protA.add_representation(protA[10:20],
resolutions=[1],
bead_default_coord=[10, 0, 0])
protA.add_representation(protA[20:30],
resolutions=[1],
bead_default_coord=[20, 0, 0])
protA2 = protA.create_clone('C')
protB = st.create_molecule("ProtB", sequence='A' * 30, chain_id='B')
protB.add_representation(protB[0:10],
resolutions=[1],
bead_default_coord=[0, 0, 0])
protB.add_representation(protB[10:20],
resolutions=[1],
bead_default_coord=[10, 0, 0])
protB.add_representation(protB[20:30],
resolutions=[1],
bead_default_coord=[20, 0, 0])
protB2 = protB.create_clone('D')
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(m)
dof.create_flexible_beads([protA, protA2, protB, protB2])
xlbeads, cldb = self.setup_crosslinks_beads(root_hier=hier,
mode="single_category")
# check enough clones were created
self.assertEqual(len(cldb.data_base['1']), 8)
self.assertEqual(len(cldb.data_base['2']), 4)
self.assertEqual(len(cldb.data_base['3']), 4)
self.assertEqual(len(cldb.data_base['4']), 4)
# check score
for j in range(100):
IMP.pmi.tools.shuffle_configuration(hier, max_translation=10)
cross_link_dict = {}
for xl in xlbeads.xl_list:
p0 = xl["Particle1"]
p1 = xl["Particle2"]
prob = xl["Restraint"].get_probability()
resid1 = xl[cldb.residue1_key]
chain1 = xl[cldb.protein1_key]
resid2 = xl[cldb.residue2_key]
chain2 = xl[cldb.protein2_key]
xlid = xl[cldb.unique_id_key]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
if xlid not in cross_link_dict:
cross_link_dict[xlid] = ([d0], [d1], [sig1], [sig2], [psi],
prob)
else:
cross_link_dict[xlid][0].append(d0)
cross_link_dict[xlid][1].append(d1)
cross_link_dict[xlid][2].append(sig1)
cross_link_dict[xlid][3].append(sig2)
cross_link_dict[xlid][4].append(psi)
for xlid in cross_link_dict:
test_prob = get_probability(cross_link_dict[xlid][0],
cross_link_dict[xlid][1],
cross_link_dict[xlid][2],
cross_link_dict[xlid][3],
cross_link_dict[xlid][4], 21.0,
0.01)
prob = cross_link_dict[xlid][5]
self.assertAlmostEqual(test_prob, prob, delta=0.0001)
for output in [
'excluded.None.xl.db', 'included.None.xl.db',
'missing.None.xl.db'
]:
os.unlink(output)
def test_shuffle_deep(self):
"""Test moving rbs, fbs"""
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
seqs = IMP.pmi.topology.Sequences(self.get_input_file_name('chainA.fasta'))
st1 = s.create_state()
mol = st1.create_molecule("GCP2_YEAST",sequence=seqs["GCP2_YEAST"][:100],chain_id='A')
atomic_res = mol.add_structure(self.get_input_file_name('chainA.pdb'),
chain_id='A',
res_range=(1,100))
mol.add_representation(mol.get_atomic_residues(),resolutions=[10])
mol.add_representation(mol.get_non_atomic_residues(), resolutions=[10])
mol2 = mol.create_clone('B')
mol3 = st1.create_molecule("GCP2_YEAST_BEADS",sequence=seqs["GCP2_YEAST"][:100],chain_id='C')
mol3.add_representation(mol3.get_non_atomic_residues(), resolutions=[10])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(mol, nonrigid_parts=mol.get_non_atomic_residues())
dof.create_rigid_body(mol2, nonrigid_parts=mol2.get_non_atomic_residues())
dof.create_flexible_beads(mol3.get_non_atomic_residues(),max_trans=1.0)
rbs,fbs = IMP.pmi.tools.get_rbs_and_beads([hier])
rbs_trans_before={}
fbs_position_before={}
rbs_trans_after={}
fbs_position_after={}
for rb in rbs:
rbs_trans_before[rb]=rb.get_reference_frame().get_transformation_to()
for fb in fbs:
if IMP.core.NonRigidMember.get_is_setup(fb):
fbs_position_before[fb] = \
IMP.core.NonRigidMember(fb).get_internal_coordinates()
else:
fbs_position_before[fb]=IMP.core.XYZ(fb).get_coordinates()
IMP.pmi.tools.shuffle_configuration(hier)
for rb in rbs:
rbs_trans_after[rb]=rb.get_reference_frame().get_transformation_to()
for fb in fbs:
if IMP.core.NonRigidMember.get_is_setup(fb):
fbs_position_after[fb] = \
IMP.core.NonRigidMember(fb).get_internal_coordinates()
else:
fbs_position_after[fb]=IMP.core.XYZ(fb).get_coordinates()
for fb in fbs:
position_after=fbs_position_after[fb]
position_before=fbs_position_before[fb]
for i in [0,1,2]:
self.assertNotEqual(position_after[i],position_before[i])
for rb in rbs:
position_after=rbs_trans_after[rb].get_translation()
position_before=rbs_trans_before[rb].get_translation()
rotation_after=rbs_trans_after[rb].get_rotation()*IMP.algebra.Vector3D(1,1,1)
rotation_before=rbs_trans_before[rb].get_rotation()*IMP.algebra.Vector3D(1,1,1)
for i in [0,1,2]:
self.assertNotEqual(position_after[i],position_before[i])
self.assertNotEqual(rotation_after[i],rotation_before[i])