コード例 #1
0
    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)
コード例 #2
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ファイル: test_dof.py プロジェクト: j-ma-bu-l-l-ock/imp
    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)
コード例 #3
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    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)
コード例 #4
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ファイル: test_dof.py プロジェクト: salilab/imp
    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)
コード例 #5
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ファイル: test_tools.py プロジェクト: j-ma-bu-l-l-ock/imp
    def test_shuffle(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])
        hier = s.build()

        dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
        dof.create_rigid_body(mol, nonrigid_parts=mol.get_non_atomic_residues())
        rbs = dof.get_rigid_bodies()
        IMP.pmi.tools.shuffle_configuration(hier)
コード例 #6
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ファイル: test_tools.py プロジェクト: jmabullock/imp
    def test_shuffle(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])
        hier = s.build()

        dof = IMP.pmi.dof.DegreesOfFreedom(mdl)
        dof.create_rigid_body(mol,
                              nonrigid_parts=mol.get_non_atomic_residues())
        rbs = dof.get_rigid_bodies()
        IMP.pmi.tools.shuffle_configuration(hier)
コード例 #7
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            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  |||||")

# Write a single-frame RMF to view the system
out = IMP.pmi.output.Output()
out.init_rmf("symmetry_test1.rmf3", hierarchies=[root_hier])
out.write_rmf("symmetry_test1.rmf3")