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_symmetry_disables_movers(self):
"""Test the creation of symmetries"""
import math
mdl = IMP.Model()
s, m1, m2, m3 = self.init_topology_clones(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb1_movers, rb1 = dof.create_rigid_body(
m1, nonrigid_parts=m1.get_non_atomic_residues(), name="test RB 1")
rb2_movers, rb2 = dof.create_rigid_body(
m2, nonrigid_parts=m2.get_non_atomic_residues(), name="test RB 2")
rb3_movers, rb3 = dof.create_rigid_body(
m3, nonrigid_parts=m3.get_non_atomic_residues(), name="test RB 3")
mvs = dof.get_movers()
self.assertEqual(len(mvs), 12)
rotational_axis = IMP.algebra.Vector3D(0, 0, 1.0)
rotation_angle_12 = 2.0 * math.pi / float(3) * float(1)
rotation3D_12 = IMP.algebra.get_rotation_about_axis(
rotational_axis, rotation_angle_12)
dof.constrain_symmetry([m1], [m2], rotation3D_12, resolution='all')
rotation_angle_13 = 2.0 * math.pi / float(3) * float(2)
rotation3D_13 = IMP.algebra.get_rotation_about_axis(
rotational_axis, rotation_angle_13)
dof.constrain_symmetry([m1], [m3], rotation3D_13, resolution='all')
mvs = dof.get_movers()
mdl.update()
self.assertEqual(len(mvs), 4)
def test_mc_rigid_body(self):
"""Test creation of rigid body and nonrigid members"""
mdl = IMP.Model()
s, molecule = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
# Test do-nothing if no rigid parts were passed
self.assertEqual(dof.create_rigid_body([], [], name='test RB'), [])
rb_movers, rb = dof.create_rigid_body(
molecule,
nonrigid_parts=molecule.get_non_atomic_residues(),
name="test RB")
self.assertEqual(rb.get_name(), "test RB")
self.assertEqual(rb_movers[0].get_name(), "test RB")
mvs = dof.get_movers()
self.assertEqual(len(rb_movers), 4)
all_members = rb.get_member_indexes()
rigid_members = rb.get_rigid_members()
num_nonrigid = len(all_members) - len(rigid_members)
self.assertEqual(num_nonrigid, 3)
# r0 r1 r10
self.assertEqual(len(rigid_members), 57 + 7 + 2)
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_rigid_body(self):
"""Test creation of rigid body and nonrigid members"""
mdl = IMP.Model()
s,molecule = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
# Test do-nothing if no rigid parts were passed
self.assertEqual(dof.create_rigid_body([], [], name='test RB'), [])
rb_movers,rb = dof.create_rigid_body(molecule,
nonrigid_parts = molecule.get_non_atomic_residues(),
name="test RB")
self.assertEqual(rb.get_name(), "test RB")
self.assertEqual(rb_movers[0].get_name(), "test RB")
mvs = dof.get_movers()
self.assertEqual(len(rb_movers),4)
all_members = rb.get_member_indexes()
rigid_members = rb.get_rigid_members()
num_nonrigid = len(all_members)-len(rigid_members)
self.assertEqual(num_nonrigid,3)
# r0 r1 r10
self.assertEqual(len(rigid_members),57 + 7 + 2)
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 init_topology(self,mdl):
s = IMP.pmi.topology.System(mdl)
st1 = s.create_state()
seqs = IMP.pmi.topology.Sequences(self.get_input_file_name('seqs.fasta'),
name_map={'Protein_1':'Prot1',
'Protein_2':'Prot2',
'Protein_3':'Prot3'})
m1 = st1.create_molecule("Prot1",chain_id='A',sequence=seqs["Prot1"])
m2 = st1.create_molecule("Prot2",chain_id='B',sequence=seqs["Prot2"])
a1 = m1.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='A',res_range=(55,64),offset=-54)
a2 = m2.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='B',res_range=(180,192),offset=-179)
m1.add_representation(a1,resolutions=[0,1])
m1.add_representation(m1[:]-a1,resolutions=[1])
m2.add_representation(a2,resolutions=[0,1])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(m1,nonrigid_parts = m1.get_non_atomic_residues(),
max_trans=0.1)
dof.create_rigid_body(m2,nonrigid_parts = m2.get_non_atomic_residues(),
max_trans=0.1)
dr = IMP.pmi.restraints.basic.DistanceRestraint(root_hier = hier,
tuple_selection1=(1,1,"Prot1",0),
tuple_selection2=(1,1,"Prot2",0),
distancemin=5,
distancemax=15)
dr.add_to_model()
with IMP.allow_deprecated():
rex = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=hier,
output_objects=[dr],
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=10,
number_of_best_scoring_models=0,
global_output_directory = \
self.get_input_file_name("pmi2_sample_0/"))
rex.execute_macro()
trans = IMP.algebra.Transformation3D(IMP.algebra.Vector3D(10,10,10))
for rb in dof.rigid_bodies:
IMP.core.transform(rb,trans)
with IMP.allow_deprecated():
rex2 = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=hier,
output_objects=[dr],
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=10,
number_of_best_scoring_models=0,
global_output_directory = \
self.get_input_file_name("pmi2_sample_1/"),
replica_exchange_object = rex.get_replica_exchange_object())
rex2.execute_macro()
def init_topology(self,mdl):
s = IMP.pmi.topology.System(mdl)
st1 = s.create_state()
seqs = IMP.pmi.topology.Sequences(self.get_input_file_name('seqs.fasta'),
name_map={'Protein_1':'Prot1',
'Protein_2':'Prot2',
'Protein_3':'Prot3'})
m1 = st1.create_molecule("Prot1",chain_id='A',sequence=seqs["Prot1"])
m2 = st1.create_molecule("Prot2",chain_id='B',sequence=seqs["Prot2"])
a1 = m1.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='A',res_range=(55,64),offset=-54)
a2 = m2.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='B',res_range=(180,192),offset=-179)
m1.add_representation(a1,resolutions=[0,1])
m1.add_representation(m1[:]-a1,resolutions=[1])
m2.add_representation(a2,resolutions=[0,1])
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(m1,nonrigid_parts = m1.get_non_atomic_residues(),
max_trans=0.1)
dof.create_rigid_body(m2,nonrigid_parts = m2.get_non_atomic_residues(),
max_trans=0.1)
dr = IMP.pmi.restraints.basic.DistanceRestraint(root_hier = hier,
tuple_selection1=(1,1,"Prot1",0),
tuple_selection2=(1,1,"Prot2",0),
distancemin=5,
distancemax=15)
dr.add_to_model()
rex = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=hier,
output_objects=[dr],
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=10,
number_of_best_scoring_models=0,
global_output_directory = \
self.get_input_file_name("pmi2_sample_0/"))
rex.execute_macro()
trans = IMP.algebra.Transformation3D(IMP.algebra.Vector3D(10,10,10))
for rb in dof.rigid_bodies:
IMP.core.transform(rb,trans)
rex2 = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=hier,
output_objects=[dr],
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=10,
number_of_best_scoring_models=0,
global_output_directory = \
self.get_input_file_name("pmi2_sample_1/"),
replica_exchange_object = rex.get_replica_exchange_object())
rex2.execute_macro()
def test_rex_multistate(self):
"""Test you can do multi-state replica exchange"""
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
st1 = s.create_state()
m1 = st1.create_molecule("Prot1")
atomic_res = m1.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='A',res_range=(55,63),offset=-54,
soft_check=True)
m1.add_representation(m1,resolutions=[1])
st2 = s.create_state()
m2 = st2.create_molecule("Prot1")
atomic_res2 = m2.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='A',res_range=(55,63),offset=-54,
soft_check=True)
m2.add_representation(m2,resolutions=[1])
hier = s.build()
self.assertEqual(len(IMP.atom.get_by_type(hier,IMP.atom.STATE_TYPE)),2)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(m1,nonrigid_parts = atomic_res)
dof.create_rigid_body(m2,nonrigid_parts = atomic_res2)
rex = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=hier,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
def test_gaussian_rb(self):
mdl = IMP.Model()
s, m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(
densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
gem_xtal.get_restraint_set().set_was_used(True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
movers, rb = dof.create_rigid_body(em_rb)
# Check assigning of names to existing rigid bodies
self.assertEqual(movers[0].get_name(), 'created rigid body')
movers, rb = dof.create_rigid_body(em_rb, name='foo')
self.assertEqual(movers[0].get_name(), 'foo')
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 2)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 2)
def test_mc_rigid_body_disable(self):
"""Test creation of rigid body and nonrigid members"""
mdl = IMP.Model()
s, molecule = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb_movers, rb = dof.create_rigid_body(
molecule,
nonrigid_parts=molecule.get_non_atomic_residues(),
name="test RB")
mvs = dof.get_movers()
self.assertEqual(len(mvs), 4)
#fixing all particles
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), 1)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 0)
#enabling everything
dof.enable_all_movers()
mvs = dof.get_movers()
self.assertEqual(len(mvs), 4)
#IMP.atom.show_molecular_hierarchy(s.hier)
#fixing the rb
particles = IMP.atom.Selection(
s.hier, molecule="Prot1",
residue_indexes=[1]).get_selected_particles()
xyzs, rbs = dof.disable_movers(particles)
self.assertEqual(len(xyzs), 0)
self.assertEqual(len(rbs), 1)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 3)
#fixing one bead and the corresponding rb
dof.enable_all_movers()
particles = IMP.atom.Selection(
s.hier, molecule="Prot1",
residue_indexes=[10]).get_selected_particles()
xyzs, rbs = dof.disable_movers(particles)
self.assertEqual(len(xyzs), 1)
self.assertEqual(len(rbs), 1)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 2)
def test_mc_rigid_body_disable(self):
"""Test creation of rigid body and nonrigid members"""
mdl = IMP.Model()
s,molecule = self.init_topology1(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb_movers,rb = dof.create_rigid_body(molecule,
nonrigid_parts = molecule.get_non_atomic_residues(),
name="test RB")
mvs = dof.get_movers()
self.assertEqual(len(mvs),4)
#fixing all particles
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),1)
mvs = dof.get_movers()
self.assertEqual(len(mvs),0)
#enabling everything
dof.enable_all_movers()
mvs = dof.get_movers()
self.assertEqual(len(mvs),4)
#IMP.atom.show_molecular_hierarchy(s.hier)
#fixing the rb
particles=IMP.atom.Selection(s.hier,molecule="Prot1",residue_indexes=[1]).get_selected_particles()
xyzs,rbs=dof.disable_movers(particles)
self.assertEqual(len(xyzs),0)
self.assertEqual(len(rbs),1)
mvs = dof.get_movers()
self.assertEqual(len(mvs),3)
#fixing one bead and the corresponding rb
dof.enable_all_movers()
particles=IMP.atom.Selection(s.hier,molecule="Prot1",residue_indexes=[10]).get_selected_particles()
xyzs,rbs=dof.disable_movers(particles)
self.assertEqual(len(xyzs),1)
self.assertEqual(len(rbs),1)
mvs = dof.get_movers()
self.assertEqual(len(mvs),2)
def test_mc_rigid_body_helix(self):
"""Test creation of rigid body and nonrigid members"""
mdl = IMP.Model()
s,molecule = self.init_topology_helix(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb_movers,rb = dof.create_rigid_body(molecule,
nonrigid_parts = molecule.get_non_atomic_residues(),
name="test RB")
mvs = dof.get_movers()
all_members = rb.get_member_indexes()
rigid_members = rb.get_rigid_members()
num_nonrigid = len(all_members)-len(rigid_members)
rex = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=s.get_hierarchy(),
monte_carlo_sample_objects = dof.get_movers(),
number_of_frames=1,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
def test_symmetry_disables_movers(self):
"""Test the creation of symmetries"""
import math
mdl = IMP.Model()
s,m1,m2,m3 = self.init_topology_clones(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb1_movers,rb1 = dof.create_rigid_body(m1,
nonrigid_parts = m1.get_non_atomic_residues(),
name="test RB 1")
rb2_movers,rb2 = dof.create_rigid_body(m2,
nonrigid_parts = m2.get_non_atomic_residues(),
name="test RB 2")
rb3_movers,rb3 = dof.create_rigid_body(m3,
nonrigid_parts = m3.get_non_atomic_residues(),
name="test RB 3")
mvs = dof.get_movers()
self.assertEqual(len(mvs),12)
rotational_axis=IMP.algebra.Vector3D(0, 0, 1.0)
rotation_angle_12 = 2.0 * math.pi / float(3) * float(1)
rotation3D_12 = IMP.algebra.get_rotation_about_axis(rotational_axis, rotation_angle_12)
dof.constrain_symmetry(
[m1],
[m2],
rotation3D_12,
resolution='all')
rotation_angle_13 = 2.0 * math.pi / float(3) * float(2)
rotation3D_13 = IMP.algebra.get_rotation_about_axis(rotational_axis, rotation_angle_13)
dof.constrain_symmetry(
[m1],
[m3],
rotation3D_13,
resolution='all')
mvs = dof.get_movers()
mdl.update()
self.assertEqual(len(mvs),4)
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_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_rigid_body_helix(self):
"""Test creation of rigid body and nonrigid members"""
mdl = IMP.Model()
s, molecule = self.init_topology_helix(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb_movers, rb = dof.create_rigid_body(
molecule,
nonrigid_parts=molecule.get_non_atomic_residues(),
name="test RB")
mvs = dof.get_movers()
all_members = rb.get_member_indexes()
rigid_members = rb.get_rigid_members()
num_nonrigid = len(all_members) - len(rigid_members)
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=s.get_hierarchy(),
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=1,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
def test_mc_super_rigid_body(self):
mdl = IMP.Model()
s,mols = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb1_mov,rb1 = dof.create_rigid_body(mols[0],
nonrigid_parts = mols[0].get_non_atomic_residues())
rb2_mov,rb2 = dof.create_rigid_body(mols[1],
nonrigid_parts = mols[1].get_non_atomic_residues())
rb3_mov,rb3 = dof.create_rigid_body(mols[2],
nonrigid_parts = mols[2].get_non_atomic_residues())
srb_mover = dof.create_super_rigid_body(mols,chain_min_length=2,
chain_max_length=2)
### rbX = dof.create_rigid_body([mols[0],mols[1]]) should fail
# rb1:4, rb2:1, rb3:4, srbs:2
mvs = dof.get_movers()
self.assertEqual(len(mvs),11)
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_super_rigid_body(self):
mdl = IMP.Model()
s, mols = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb1_mov, rb1 = dof.create_rigid_body(
mols[0], nonrigid_parts=mols[0].get_non_atomic_residues())
rb2_mov, rb2 = dof.create_rigid_body(
mols[1], nonrigid_parts=mols[1].get_non_atomic_residues())
rb3_mov, rb3 = dof.create_rigid_body(
mols[2], nonrigid_parts=mols[2].get_non_atomic_residues())
srb_mover = dof.create_super_rigid_body(mols,
chain_min_length=2,
chain_max_length=2)
### rbX = dof.create_rigid_body([mols[0],mols[1]]) should fail
# rb1:4, rb2:1, rb3:4, srbs:2
mvs = dof.get_movers()
self.assertEqual(len(mvs), 11)
def test_pdb_from_rex(self):
"""Test PDB writing in PMI2 from replica exchange"""
mdl = IMP.Model()
pdb_file = self.get_input_file_name("mini.pdb")
fasta_file = self.get_input_file_name("mini.fasta")
seqs = IMP.pmi.topology.Sequences(fasta_file)
s = IMP.pmi.topology.System(mdl)
st = s.create_state()
molA = st.create_molecule("P1",seqs[0],chain_id='A')
aresA = molA.add_structure(pdb_file,chain_id='A',soft_check=True)
molA.add_representation(aresA,[1])
molA.add_representation(molA[:]-aresA,20)
molB = st.create_molecule("P2",seqs[1],chain_id='B')
aresB = molB.add_structure(pdb_file,chain_id='B',soft_check=True)
molB.add_representation(aresB,[10])
molB.add_representation(molB[:]-aresB,20)
molC = molB.create_copy(chain_id='C')
aresC = molC.add_structure(pdb_file,chain_id='B',soft_check=True)
molC.add_representation(aresC,[1,10])
molC.add_representation(molC[:]-aresC,2)
root_hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb_movers = dof.create_rigid_body([molA,molB,molC],
name="test RB")
rex = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=root_hier,
monte_carlo_sample_objects = dof.get_movers(),
number_of_frames=3,
monte_carlo_steps=10,
number_of_best_scoring_models=3,
global_output_directory='pdb_test/',
replica_exchange_object = rem)
rex.execute_macro()
for i in range(3):
self.assertTrue(os.path.isfile('pdb_test/pdbs/model.%i.pdb'%i))
mhtest = IMP.atom.read_pdb('pdb_test/pdbs/model.0.pdb',mdl)
self.assertEqual(len(IMP.core.get_leaves(mhtest)),17)
shutil.rmtree("pdb_test/")
def test_gaussian_rb(self):
mdl = IMP.Model()
m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(em_rb)
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 1)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 1)
def test_pdb_from_rex(self):
"""Test PDB writing in PMI2 from replica exchange"""
mdl = IMP.Model()
pdb_file = self.get_input_file_name("mini.pdb")
fasta_file = self.get_input_file_name("mini.fasta")
seqs = IMP.pmi.topology.Sequences(fasta_file)
s = IMP.pmi.topology.System(mdl)
st = s.create_state()
molA = st.create_molecule("P1", seqs[0], chain_id='A')
aresA = molA.add_structure(pdb_file, chain_id='A', soft_check=True)
molA.add_representation(aresA, [1])
molA.add_representation(molA[:] - aresA, 20)
molB = st.create_molecule("P2", seqs[1], chain_id='B')
aresB = molB.add_structure(pdb_file, chain_id='B', soft_check=True)
molB.add_representation(aresB, [10])
molB.add_representation(molB[:] - aresB, 20)
molC = molB.create_copy(chain_id='C')
aresC = molC.add_structure(pdb_file, chain_id='B', soft_check=True)
molC.add_representation(aresC, [1, 10])
molC.add_representation(molC[:] - aresC, 2)
root_hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb_movers = dof.create_rigid_body([molA, molB, molC], name="test RB")
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=root_hier,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=3,
monte_carlo_steps=10,
number_of_best_scoring_models=3,
global_output_directory='pdb_test/',
replica_exchange_object=rem)
rex.execute_macro()
for i in range(3):
self.assertTrue(os.path.isfile('pdb_test/pdbs/model.%i.pdb' % i))
mhtest = IMP.atom.read_pdb('pdb_test/pdbs/model.0.pdb', mdl)
self.assertEqual(len(IMP.core.get_leaves(mhtest)), 17)
shutil.rmtree("pdb_test/")
def test_gaussian_rb(self):
mdl = IMP.Model()
m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(
densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(em_rb)
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 1)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 1)
def test_rex_multistate(self):
"""Test you can do multi-state replica exchange"""
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
st1 = s.create_state()
m1 = st1.create_molecule("Prot1")
atomic_res = m1.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='A',
res_range=(55, 63),
offset=-54,
soft_check=True)
m1.add_representation(m1, resolutions=[1])
st2 = s.create_state()
m2 = st2.create_molecule("Prot1")
atomic_res2 = m2.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='A',
res_range=(55, 63),
offset=-54,
soft_check=True)
m2.add_representation(m2, resolutions=[1])
hier = s.build()
self.assertEqual(len(IMP.atom.get_by_type(hier, IMP.atom.STATE_TYPE)),
2)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.create_rigid_body(m1, nonrigid_parts=atomic_res)
dof.create_rigid_body(m2, nonrigid_parts=atomic_res2)
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=hier,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
def test_gaussian_rb(self):
mdl = IMP.Model()
s, m1, m2, m3 = self.init_topology_densities(mdl)
densities = [r.get_hierarchy() for r in m3.get_non_atomic_residues()]
gem_xtal = IMP.pmi.restraints.em.GaussianEMRestraint(densities,
self.get_input_file_name('prot_gmm.txt'),
target_is_rigid_body=True)
gem_xtal.get_restraint_set().set_was_used(True)
em_rb = gem_xtal.get_rigid_body()
em_rb.set_coordinates_are_optimized(False)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
movers, rb = dof.create_rigid_body(em_rb)
# Check assigning of names to existing rigid bodies
self.assertEqual(movers[0].get_name(), 'created rigid body')
movers, rb = dof.create_rigid_body(em_rb, name='foo')
self.assertEqual(movers[0].get_name(), 'foo')
self.assertTrue(em_rb in dof.get_rigid_bodies())
self.assertEqual(len(dof.get_rigid_bodies()), 2)
self.assertTrue(em_rb.get_coordinates_are_optimized())
self.assertEqual(len(dof.get_movers()), 2)
#psi = xlr.psi_dictionary["PSI"][0]
#psi.set_scale(0.04)
sf = IMP.core.RestraintsScoringFunction(IMP.pmi.tools.get_restraint_set(mdl))
print(sf.evaluate(False))
dof.get_nuisances_from_restraint(
xlr) # needed to sample the nuisance particles (noise params)
####################### SAMPLING #####################
# First shuffle the system
if not s.dry_run:
IMP.pmi.tools.shuffle_configuration(gdown1)
dof.optimize_flexible_beads(100)
print(dof.get_movers())
print(len(dof.get_movers()))
print(gdown1)
# Run replica exchange Monte Carlo sampling
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=root_hier, # pass the root hierarchy
crosslink_restraints=display_restraints, # will display like XLs
monte_carlo_temperature=1.0,
replica_exchange_minimum_temperature=1.0,
replica_exchange_maximum_temperature=2.5,
num_sample_rounds=1,
number_of_best_scoring_models=5,
monte_carlo_sample_objects=dof.get_movers(), # pass MC movers
global_output_directory='gdownrb_%d' % taskid,
output_objects=output_objects,
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)
start_time = process_time()
# In debug mode things are way too slow to actually run MC
if IMP.get_check_level() < IMP.USAGE_AND_INTERNAL:
o = output.Output()
rmf = o.init_rmf("conformations.rmf3", [root_hier])
o.init_stat2("modeling.stat", log_objects)
o.write_rmf("conformations.rmf3")
o.init_pdb("conformations.pdb", root_hier)
for i in range(0, 10):
# print("Running job, frame number ", i)
mc.optimize(10)
def test_mc_super_rigid_body_disable(self):
"""test disable super rigid bodies, floppy bodies and rigid bodies"""
mdl = IMP.Model()
s, mols = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb1_mov, rb1 = dof.create_rigid_body(
mols[0], nonrigid_parts=mols[0].get_non_atomic_residues())
rb2_mov, rb2 = dof.create_rigid_body(
mols[1], nonrigid_parts=mols[1].get_non_atomic_residues())
rb3_mov, rb3 = dof.create_rigid_body(
mols[2], nonrigid_parts=mols[2].get_non_atomic_residues())
srb_mover = dof.create_super_rigid_body(mols,
chain_min_length=2,
chain_max_length=2)
### rbX = dof.create_rigid_body([mols[0],mols[1]]) should fail
# rb1:4, rb2:1, rb3:4, srbs:2
mvs = dof.get_movers()
self.assertEqual(len(mvs), 11)
#fixing all particles
particles = IMP.atom.Selection(s.hier).get_selected_particles()
xyzs, rbs = dof.disable_movers(particles)
self.assertEqual(len(xyzs), 6)
self.assertEqual(len(rbs), 3)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 0)
#enabling everything
dof.enable_all_movers()
mvs = dof.get_movers()
self.assertEqual(len(mvs), 11)
#fixing prot1
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), 1)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 6)
#fixing prot1 rb
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), 1)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 10)
#fixing prot1 fbs
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), 8)
#removing super rigid body
dof.enable_all_movers()
particles = IMP.atom.Selection(
s.hier, molecule="Prot1").get_selected_particles()
xyzs, rbs = dof.disable_movers(particles,
mover_types=[IMP.pmi.TransformMover])
self.assertEqual(len(xyzs), 0)
self.assertEqual(len(rbs), 0)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 10)
#removing rbmv, ballmovers and super rigid movers involving prot1
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,
IMP.core.BallMover,
IMP.pmi.TransformMover
])
self.assertEqual(len(xyzs), 3)
self.assertEqual(len(rbs), 1)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 6)
#removing rbmv, ballmovers and super rigid movers involving prot2
dof.enable_all_movers()
particles = IMP.atom.Selection(
s.hier, molecule="Prot2").get_selected_particles()
xyzs, rbs = dof.disable_movers(particles,
mover_types=[
IMP.core.RigidBodyMover,
IMP.core.BallMover,
IMP.pmi.TransformMover
])
self.assertEqual(len(xyzs), 0)
self.assertEqual(len(rbs), 1)
mvs = dof.get_movers()
self.assertEqual(len(mvs), 8)
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)
def test_atomic_xl(self):
""" test PMI setup of atomic XL restraint """
# fake data
tname = self.get_tmp_file_name("test.txt")
with open(tname, "w") as fh:
fh.write("prot1,res1,prot2,res2\nProt1,7,Prot1,39\n")
cldbkc = IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter()
cldbkc.set_protein1_key("prot1")
cldbkc.set_protein2_key("prot2")
cldbkc.set_residue1_key("res1")
cldbkc.set_residue2_key("res2")
cldb = IMP.pmi.io.crosslink.CrossLinkDataBase(cldbkc)
cldb.create_set_from_file(tname)
self.assertEqual(cldb.get_number_of_xlid(), 1)
# create two states, each with two copies of the protein
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
seqs = IMP.pmi.topology.Sequences(
self.get_input_file_name('multi_seq.fasta'),
name_map={'Protein_1': 'Prot1'})
# build state 1
st1 = s.create_state()
m1 = st1.create_molecule("Prot1", sequence=seqs["Prot1"], chain_id='A')
m1_res = m1.add_structure(self.get_input_file_name('multi.pdb'),
chain_id='A',
offset=-54,
model_num=0)
m1.add_representation(m1_res, resolutions=[0])
m1a = m1.create_copy(chain_id='G')
m1a_res = m1a.add_structure(self.get_input_file_name('multi.pdb'),
chain_id='G',
offset=-54)
m1a.add_representation(m1a_res, resolutions=[0])
# build state 2
st2 = s.create_state()
m2 = st2.create_molecule("Prot1", sequence=seqs["Prot1"], chain_id='A')
m2_res = m2.add_structure(self.get_input_file_name('multi.pdb'),
chain_id='A',
offset=-54,
model_num=1)
m2.add_representation(m2_res, resolutions=[0])
m2a = m2.create_copy(chain_id='G')
m2a_res = m2a.add_structure(self.get_input_file_name('multi.pdb'),
chain_id='G',
offset=-54)
m2a.add_representation(m2a_res, resolutions=[0])
hier = s.build()
#IMP.atom.show_molecular_hierarchy(hier)
xl = IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint(
hier, cldb, nstates=[0, 1], atom_type="CA")
# check that you created 8 restraints:
# Each state: A1-B1, A1-B2, A2-B1, A2-B2
rs = xl.get_restraint_set()
rs.set_was_used(True)
self.assertEqual(rs.get_number_of_restraints(), 1)
xlrs = IMP.isd.AtomicCrossLinkMSRestraint.get_from(rs.get_restraint(0))
self.assertIsInstance(xlrs, IMP.isd.AtomicCrossLinkMSRestraint)
self.assertEqual(xlrs.get_number_of_contributions(), 8)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.get_nuisances_from_restraint(xl)
self.assertEqual(len(dof.get_movers()), 2)
def test_atomic_xl(self):
""" test PMI setup of atomic XL restraint """
# fake data
tname = self.get_tmp_file_name("test.txt")
with open(tname, "w") as fh:
fh.write("prot1,res1,prot2,res2\nProt1,7,Prot1,39\n")
cldbkc=IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter()
cldbkc.set_protein1_key("prot1")
cldbkc.set_protein2_key("prot2")
cldbkc.set_residue1_key("res1")
cldbkc.set_residue2_key("res2")
cldb = IMP.pmi.io.crosslink.CrossLinkDataBase(cldbkc)
cldb.create_set_from_file(tname)
self.assertEqual(cldb.get_number_of_xlid(),1)
# create two states, each with two copies of the protein
mdl = IMP.Model()
s = IMP.pmi.topology.System(mdl)
seqs = IMP.pmi.topology.Sequences(self.get_input_file_name('multi_seq.fasta'),
name_map={'Protein_1':'Prot1'})
# build state 1
st1 = s.create_state()
m1 = st1.create_molecule("Prot1",sequence=seqs["Prot1"],chain_id='A')
m1_res = m1.add_structure(self.get_input_file_name('multi.pdb'),
chain_id='A',offset=-54,
model_num=0)
m1.add_representation(m1_res,resolutions=[0])
m1a = m1.create_copy(chain_id='G')
m1a_res = m1a.add_structure(self.get_input_file_name('multi.pdb'),chain_id='G',offset=-54)
m1a.add_representation(m1a_res,resolutions=[0])
# build state 2
st2 = s.create_state()
m2 = st2.create_molecule("Prot1",sequence=seqs["Prot1"],chain_id='A')
m2_res = m2.add_structure(self.get_input_file_name('multi.pdb'),
chain_id='A',offset=-54,
model_num=1)
m2.add_representation(m2_res,resolutions=[0])
m2a = m2.create_copy(chain_id='G')
m2a_res = m2a.add_structure(self.get_input_file_name('multi.pdb'),chain_id='G',offset=-54)
m2a.add_representation(m2a_res,resolutions=[0])
hier = s.build()
#IMP.atom.show_molecular_hierarchy(hier)
xl = IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint(hier,
cldb,
nstates=[0,1],
atom_type="CA")
# check that you created 8 restraints:
# Each state: A1-B1, A1-B2, A2-B1, A2-B2
rs=xl.get_restraint_set()
self.assertEqual(rs.get_number_of_restraints(),1)
xlrs=IMP.isd.AtomicCrossLinkMSRestraint.get_from(rs.get_restraint(0))
self.assertIsInstance(xlrs,IMP.isd.AtomicCrossLinkMSRestraint)
self.assertEqual(xlrs.get_number_of_contributions(),8)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
dof.get_nuisances_from_restraint(xl)
self.assertEqual(len(dof.get_movers()),2)
psi.set_scale(0.05)
xl.set_psi_is_sampled(True)
xl.set_sigma_is_sampled(True)
sample_objects.append(xl)
output_objects.append(xl)
###################### SAMPLING #####################
# First shuffle the system
IMP.pmi.tools.shuffle_configuration(hier, max_translation=100)
# Quickly move all flexible beads into place
dof.optimize_flexible_beads(10)
# Run replica exchange Monte Carlo sampling
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=hier, # pass the root hierarchy
crosslink_restraints=[xl], # will display like XLs
monte_carlo_sample_objects=dof.get_movers() +
xl.get_movers(), # pass MC movers
global_output_directory='output/',
output_objects=output_objects,
monte_carlo_temperature=1.0,
replica_exchange_minimum_temperature=1.0,
replica_exchange_maximum_temperature=2.5,
monte_carlo_steps=10,
number_of_best_scoring_models=
0, # set >0 to store best PDB files (but this is slow to do online)
number_of_frames=10000) # increase number of frames to get better results!
rex.execute_macro()
def test_mc_super_rigid_body_disable(self):
"""test disable super rigid bodies, floppy bodies and rigid bodies"""
mdl = IMP.Model()
s,mols = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
rb1_mov,rb1 = dof.create_rigid_body(mols[0],
nonrigid_parts = mols[0].get_non_atomic_residues())
rb2_mov,rb2 = dof.create_rigid_body(mols[1],
nonrigid_parts = mols[1].get_non_atomic_residues())
rb3_mov,rb3 = dof.create_rigid_body(mols[2],
nonrigid_parts = mols[2].get_non_atomic_residues())
srb_mover = dof.create_super_rigid_body(mols,chain_min_length=2,
chain_max_length=2)
### rbX = dof.create_rigid_body([mols[0],mols[1]]) should fail
# rb1:4, rb2:1, rb3:4, srbs:2
mvs = dof.get_movers()
self.assertEqual(len(mvs),11)
#fixing all particles
particles=IMP.atom.Selection(s.hier).get_selected_particles()
xyzs,rbs=dof.disable_movers(particles)
self.assertEqual(len(xyzs),6)
self.assertEqual(len(rbs),3)
mvs = dof.get_movers()
self.assertEqual(len(mvs),0)
#enabling everything
dof.enable_all_movers()
mvs = dof.get_movers()
self.assertEqual(len(mvs),11)
#fixing prot1
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),1)
mvs = dof.get_movers()
self.assertEqual(len(mvs),6)
#fixing prot1 rb
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),1)
mvs = dof.get_movers()
self.assertEqual(len(mvs),10)
#fixing prot1 fbs
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),8)
#removing super rigid body
dof.enable_all_movers()
particles=IMP.atom.Selection(s.hier,molecule="Prot1").get_selected_particles()
xyzs,rbs=dof.disable_movers(particles,mover_types=[IMP.pmi.TransformMover])
self.assertEqual(len(xyzs),0)
self.assertEqual(len(rbs),0)
mvs = dof.get_movers()
self.assertEqual(len(mvs),10)
#removing rbmv, ballmovers and super rigid movers involving prot1
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,IMP.core.BallMover,IMP.pmi.TransformMover])
self.assertEqual(len(xyzs),3)
self.assertEqual(len(rbs),1)
mvs = dof.get_movers()
self.assertEqual(len(mvs),6)
#removing rbmv, ballmovers and super rigid movers involving prot2
dof.enable_all_movers()
particles=IMP.atom.Selection(s.hier,molecule="Prot2").get_selected_particles()
xyzs,rbs=dof.disable_movers(particles,mover_types=[IMP.core.RigidBodyMover,IMP.core.BallMover,IMP.pmi.TransformMover])
self.assertEqual(len(xyzs),0)
self.assertEqual(len(rbs),1)
mvs = dof.get_movers()
self.assertEqual(len(mvs),8)
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')
output_objects.append(mr)
# For visualization purposes
mr.create_membrane_density()
###########################
# External barrier
###########################
eb = IMP.pmi.restraints.basic.ExternalBarrier(hierarchies=hier, radius=50)
eb.add_to_model()
##############################
# Shuffle
##############################
IMP.pmi.tools.shuffle_configuration(hier, max_translation=300)
print(dof.get_movers())
##############################
# Sampling
##############################
frames = 10 if IMP.get_is_quick_test() else 2000
rex = IMP.pmi.macros.ReplicaExchange0(
model,
root_hier=hier,
crosslink_restraints=rmf_restraints,
monte_carlo_sample_objects=dof.get_movers(),
replica_exchange_maximum_temperature=3.0,
global_output_directory="output/",
output_objects=output_objects,
monte_carlo_steps=10,
### Excluded volume - one for each state (they don't interact)
evr1 = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects = (m1A,m1B,m1C))
evr1.add_to_model()
output_objects.append(evr1)
evr2 = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(included_objects = (m2A,m2C))
evr2.add_to_model()
output_objects.append(evr2)
###################### SAMPLING #####################
# randomize particles a bit
IMP.pmi.tools.shuffle_configuration(root_hier,
max_translation=20)
# Shift state 2
# Even though the two states don't interact,
# it'll be easier to look at the RMF if we separate them
trans = IMP.algebra.Transformation3D([50,0,0])
for fb in IMP.core.get_leaves(m2A.get_hierarchy())+IMP.core.get_leaves(m2C.get_hierarchy()):
IMP.core.transform(IMP.core.XYZ(fb),trans)
# Run replica exchange Monte Carlo sampling
rex=IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=root_hier, # pass the root hierarchy
crosslink_restraints=rmf_restraints, # will display as springs
monte_carlo_sample_objects=dof.get_movers(), # pass MC movers
global_output_directory='ambiguity_output/',
output_objects=output_objects,
monte_carlo_steps=10,
number_of_frames=1) # increase number of frames to get better results!
rex.execute_macro()
def test_restraint_probability_beads(self):
"""Test restraint works for all-bead systems"""
for i in range(2):
m = IMP.Model()
if i==0:
rbeads=self.init_representation_beads(m)
xlbeads,cldb=self.setup_crosslinks_beads(rbeads,"single_category")
else:
rbeads,dof=self.init_representation_beads_pmi2(m)
xlbeads,cldb=self.setup_crosslinks_beads(root_hier=rbeads,mode="single_category")
self.assertEqual(len(dof.get_movers()),60)
dof.get_nuisances_from_restraint(xlbeads)
self.assertEqual(len(dof.get_movers()),62)
for xl in xlbeads.xl_list:
chain1 = xl[cldb.protein1_key]
chain2 = xl[cldb.protein2_key]
res1 = xl[cldb.residue1_key]
res2 = xl[cldb.residue2_key]
ids = xl[cldb.unique_id_key]
# randomize coordinates and check that the probability is OK
print("testing PMI version "+str(i+1))
for j in range(100):
if i==0:
rbeads.shuffle_configuration(max_translation=10)
else:
IMP.pmi.tools.shuffle_configuration(rbeads,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)
if i==0:
rex0 = IMP.pmi.macros.ReplicaExchange0(m,
rbeads,
monte_carlo_sample_objects=[rbeads],
number_of_frames=2,
test_mode=True,
replica_exchange_object = rem)
rex0.execute_macro()
else:
rex = IMP.pmi.macros.ReplicaExchange0(m,
root_hier=rbeads,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object = rem)
rex.execute_macro()
for output in ['excluded.None.xl.db',
'included.None.xl.db', 'missing.None.xl.db']:
os.unlink(output)
def test_restraint_probability_complex(self):
"""Test restraint gets correct probabilities"""
m = IMP.Model()
rcomplex, dof = self.init_representation_complex_pmi2(m)
xlc, cldb = self.setup_crosslinks_complex(root_hier=rcomplex,
mode="single_category")
self.assertEqual(len(dof.get_movers()), 42)
dof.get_nuisances_from_restraint(xlc)
self.assertEqual(len(dof.get_movers()), 44)
# check all internals didn't change since last time
o = IMP.pmi.output.Output()
o.write_test("expensive_test_new_cross_link_ms_restraint.dat", [xlc])
passed = o.test(
self.get_input_file_name(
"expensive_test_new_cross_link_ms_restraint.dat"), [xlc])
self.assertEqual(passed, True)
rs = xlc.get_restraint()
# check the probability of cross-links
restraints = []
for xl in xlc.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]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist = IMP.core.get_distance(d0, d1)
test_prob = get_probability([d0], [d1], [sig1], [sig2], [psi],
21.0, 0.0)
restraints.append(xl["Restraint"])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score = rs.unprotected_evaluate(None)
test_log_wrapper_score = log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score,
test_log_wrapper_score,
delta=0.00001)
rex = IMP.pmi.macros.ReplicaExchange0(
m,
root_hier=rcomplex,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
for output in [
'excluded.None.xl.db',
'expensive_test_new_cross_link_ms_restraint.dat',
'included.None.xl.db', 'missing.None.xl.db'
]:
os.unlink(output)
included_objects=(m1A, m1B, m1C))
evr1.add_to_model()
output_objects.append(evr1)
evr2 = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(
included_objects=(m2A, m2C))
evr2.add_to_model()
output_objects.append(evr2)
###################### SAMPLING #####################
# randomize particles a bit
IMP.pmi.tools.shuffle_configuration(root_hier, max_translation=20)
# Shift state 2
# Even though the two states don't interact,
# it'll be easier to look at the RMF if we separate them
trans = IMP.algebra.Transformation3D([50, 0, 0])
for fb in IMP.core.get_leaves(m2A.get_hierarchy()) + IMP.core.get_leaves(
m2C.get_hierarchy()):
IMP.core.transform(IMP.core.XYZ(fb), trans)
# Run replica exchange Monte Carlo sampling
rex = IMP.pmi.macros.ReplicaExchange0(
mdl,
root_hier=root_hier, # pass the root hierarchy
monte_carlo_sample_objects=dof.get_movers(), # pass MC movers
global_output_directory='ambiguity_output/',
output_objects=output_objects,
monte_carlo_steps=10,
number_of_frames=1) # increase number of frames to get better results!
rex.execute_macro()
output_objects.append(mr)
# For visualization purposes
mr.create_membrane_density()
###########################
# External barrier
###########################
eb = IMP.pmi.restraints.basic.ExternalBarrier(hierarchies=hier, radius=50)
eb.add_to_model()
##############################
# Shuffle
##############################
IMP.pmi.tools.shuffle_configuration(hier, max_translation=300)
print(dof.get_movers())
##############################
# Sampling
##############################
frames = 10 if IMP.get_is_quick_test() else 2000
rex = IMP.pmi.macros.ReplicaExchange0(model,
root_hier=hier,
crosslink_restraints=rmf_restraints,
monte_carlo_sample_objects=dof.get_movers(),
replica_exchange_maximum_temperature=3.0,
global_output_directory="output/",
output_objects=output_objects,
monte_carlo_steps=10,
number_of_frames=frames,
def test_restraint_probability_complex(self):
"""Test restraint gets correct probabilities"""
for i in range(2):
m = IMP.Model()
print("Testing PMI version",i+1)
if i==0:
rcomplex = self.init_representation_complex(m)
xlc,cldb = self.setup_crosslinks_complex(rcomplex,"single_category")
else:
rcomplex,dof=self.init_representation_complex_pmi2(m)
xlc,cldb = self.setup_crosslinks_complex(root_hier=rcomplex,
mode="single_category")
self.assertEqual(len(dof.get_movers()),42)
dof.get_nuisances_from_restraint(xlc)
self.assertEqual(len(dof.get_movers()),44)
# check all internals didn't change since last time
o=IMP.pmi.output.Output()
o.write_test("expensive_test_new_cross_link_ms_restraint.dat", [xlc])
passed=o.test(self.get_input_file_name("expensive_test_new_cross_link_ms_restraint.dat"),
[xlc])
self.assertEqual(passed, True)
rs = xlc.get_restraint()
# check the probability of cross-links
restraints=[]
for xl in xlc.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]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
sig1 = xl["Particle_sigma1"]
sig2 = xl["Particle_sigma2"]
psi = xl["Particle_psi"]
d0 = IMP.core.XYZ(p0)
d1 = IMP.core.XYZ(p1)
dist=IMP.core.get_distance(d0, d1)
test_prob=get_probability([d0],[d1],[sig1],[sig2],[psi],21.0,0.0)
restraints.append(xl["Restraint"])
# check that the probability is the same for
# each cross-link
self.assertAlmostEqual(prob, test_prob, delta=0.00001)
# check the log_wrapper
log_wrapper_score=rs.unprotected_evaluate(None)
test_log_wrapper_score=log_evaluate(restraints)
self.assertAlmostEqual(log_wrapper_score, test_log_wrapper_score, delta=0.00001)
if i==0:
rex0 = IMP.pmi.macros.ReplicaExchange0(m,
rcomplex,
monte_carlo_sample_objects=[rcomplex],
number_of_frames=2,
test_mode=True,
replica_exchange_object = rem)
rex0.execute_macro()
else:
rex = IMP.pmi.macros.ReplicaExchange0(m,
root_hier=rcomplex,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object = rem)
rex.execute_macro()
for output in ['excluded.None.xl.db',
'expensive_test_new_cross_link_ms_restraint.dat',
'included.None.xl.db', 'missing.None.xl.db']:
os.unlink(output)
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)
def test_restraint_probability_beads(self):
"""Test restraint works for all-bead systems"""
m = IMP.Model()
rbeads, dof = self.init_representation_beads_pmi2(m)
xlbeads, cldb = self.setup_crosslinks_beads(root_hier=rbeads,
mode="single_category")
self.assertEqual(len(dof.get_movers()), 60)
dof.get_nuisances_from_restraint(xlbeads)
self.assertEqual(len(dof.get_movers()), 62)
for xl in xlbeads.xl_list:
chain1 = xl[cldb.protein1_key]
chain2 = xl[cldb.protein2_key]
res1 = xl[cldb.residue1_key]
res2 = xl[cldb.residue2_key]
ids = xl[cldb.unique_id_key]
# randomize coordinates and check that the probability is OK
for j in range(100):
IMP.pmi.tools.shuffle_configuration(rbeads, 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)
rex = IMP.pmi.macros.ReplicaExchange0(
m,
root_hier=rbeads,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=2,
test_mode=True,
replica_exchange_object=rem)
rex.execute_macro()
for output in [
'excluded.None.xl.db', 'included.None.xl.db',
'missing.None.xl.db'
]:
os.unlink(output)
def init_with_copies(self,mdl):
s = IMP.pmi.topology.System(mdl)
st1 = s.create_state()
seqs = IMP.pmi.topology.Sequences(self.get_input_file_name('seqs.fasta'),
name_map={'Protein_1':'Prot1',
'Protein_2':'Prot2',
'Protein_3':'Prot3'})
m1 = st1.create_molecule("Prot1",chain_id='A',sequence=seqs["Prot1"])
a1 = m1.add_structure(self.get_input_file_name('prot.pdb'),
chain_id='A',res_range=(55,64),offset=-54)
m1.add_representation(a1,resolutions=[1])
m1.add_representation(m1[:]-a1,resolutions=[1])
m2 = m1.create_clone('B')
hier = s.build()
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
mv1,rb1 = dof.create_rigid_body(m1,nonrigid_parts = m1.get_non_atomic_residues(),
max_trans=0.000001)
mv2,rb2 = dof.create_rigid_body(m2,nonrigid_parts = m2.get_non_atomic_residues(),
max_trans=0.000001)
trans = IMP.algebra.Transformation3D(IMP.algebra.Vector3D(100,0,0))
IMP.core.transform(rb2,trans)
ps0 = IMP.atom.Selection(hier,molecule='Prot1',copy_index=0).get_selected_particles()
ps1 = IMP.atom.Selection(hier,molecule='Prot1',copy_index=1).get_selected_particles()
with IMP.allow_deprecated():
rex = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=hier,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=1,
number_of_best_scoring_models=0,
global_output_directory = \
self.get_input_file_name("pmi2_copies_0/"))
rex.execute_macro()
coords0A = [IMP.core.XYZ(p).get_coordinates() for p in ps0]
coords1A = [IMP.core.XYZ(p).get_coordinates() for p in ps1]
# swap the objects
IMP.core.transform(rb2,trans.get_inverse())
IMP.core.transform(rb1,trans)
with IMP.allow_deprecated():
rex2 = IMP.pmi.macros.ReplicaExchange0(mdl,
root_hier=hier,
monte_carlo_sample_objects=dof.get_movers(),
number_of_frames=1,
number_of_best_scoring_models=0,
global_output_directory = \
self.get_input_file_name("pmi2_copies_1/"),
replica_exchange_object = rex.get_replica_exchange_object())
rex2.execute_macro()
coords0B = [IMP.core.XYZ(p).get_coordinates() for p in ps0]
coords1B = [IMP.core.XYZ(p).get_coordinates() for p in ps1]
rmsd = IMP.algebra.get_rmsd(coords0A+coords1A,coords1B+coords0B)
return rmsd