def test_mc_super_rigid_body(self):
mdl = IMP.Model()
m1,m2,m3 = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
h1 = m1.get_hierarchy()
h2 = m1.get_hierarchy()
h3 = m1.get_hierarchy()
srb = dof.create_super_rigid_body([h1,h2,h3],chain_min_length=2,chain_max_length=2)
self.assertEqual(len(srb.get_movers()),2)
def test_mc_super_rigid_body(self):
mdl = IMP.Model()
m1, m2, m3 = self.init_topology3(mdl)
dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
h1 = m1.get_hierarchy()
h2 = m1.get_hierarchy()
h3 = m1.get_hierarchy()
srb = dof.create_super_rigid_body([h1, h2, h3],
chain_min_length=2,
chain_max_length=2)
self.assertEqual(len(srb.get_movers()), 2)
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_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)
# 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
kw = IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter()
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)
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_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)