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_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_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_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)
reader = IMP.pmi.topology.TopologyReader(tf.name,
pdb_dir = '.',
fasta_dir = '.',
gmm_dir = 'gmm')
bs = IMP.pmi.macros.BuildSystem(mdl)
bs.add_state(reader) # note you can call this multiple times to create a multi-state system
#IMP.pmi.plotting.topology.draw_component_composition(bs)
hier, dof = bs.execute_macro(max_rb_trans=4.0, max_rb_rot=0.3, max_bead_trans=4.0, max_srb_trans=4.0,max_srb_rot=0.3)
particles=IMP.atom.Selection(hier,molecule="TssK",residue_indexes=range(1,315+1)).get_selected_particles()
fixedxyz,fixedrbs=dof.disable_movers(particles,[IMP.core.RigidBodyMover])
for xyz in fixedxyz:
IMP.core.XYZ(xyz).set_coordinates_are_optimized(False)
for rb in fixedrbs:
IMP.core.RigidBody(rb).set_coordinates_are_optimized(False)
particles=IMP.atom.Selection(hier,molecule="TssF",copy_index=0).get_selected_particles()
for p in particles:
rad=IMP.core.XYZR(p).get_radius()
IMP.core.XYZR(p).set_radius(rad*0.75)
p.set_value(IMP.FloatKey(4),296)
p.set_value(IMP.FloatKey(5),216)
p.set_value(IMP.FloatKey(6),262)
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)
fixed_particles=[]
for prot in [
"Rpb1","Rpb2","Rpb3","Rpb4","Rpb5","Rpb6","Rpb7","Rpb8","Rpb9","Rpb10","Rpb11","Rpb12",
"Med6","Med8","Med11","Med17","Med18","Med20","Med22",
"Med4","Med7","Med9","Med10","Med14","Med19","Med21","Med31",
"Spt15","Toa1","Toa2","Sua7","Tfg1","Tfg2","Tfa1","Tfa2",
"Rad3","Tfb1","Tfb2","Tfb4","Tfb5","Ssl1","Ssl2",
"NDNA","TDNA"
]:
fixed_particles+=IMP.atom.Selection(representation,molecule=prot).get_selected_particles()
fixed_particles+=IMP.atom.Selection(representation, molecule="Tfb3", residue_indexes=range(8,145)).get_selected_particles()
# Fix corresponding movers using dof
fixed_beads,fixed_rbs=dof.disable_movers(fixed_particles,
[IMP.core.RigidBodyMover,
IMP.pmi.TransformMover])
# Shuffling for random initial conformations
IMP.pmi.tools.shuffle_configuration(representation,
excluded_rigid_bodies=fixed_rbs,
max_translation=20,
verbose=False,
cutoff=5.0,
niterations=100)
# Add default mover parameters to simulation
outputobjects = [] # reporter objects (for stat files)
sampleobjects = [] # sampling objects