import os from modeller import * import IMP import IMP.test import IMP.core import IMP.atom import IMP.modeller def assertSimilarModellerIMPScores(tst, modeller_model, imp_atoms): """Assert that Modeller and IMP give the same score and derivatives""" modeller_energy = selection(modeller_model).energy()[0] imp_score = imp_atoms.get_model().evaluate(True) tst.assertAlmostEqual(modeller_energy, imp_score, delta=0.001) for imp_atom, modeller_atom in zip(IMP.atom.get_leaves(imp_atoms), modeller_model.atoms): imp_deriv = IMP.core.XYZ(imp_atom).get_derivatives() tst.assertAlmostEqual(imp_deriv[0], modeller_atom.dvx, delta=1e-2, msg="x derivative for atom %s differs between " "Modeller (%f) and IMP (%f)" \ % (str(modeller_atom), modeller_atom.dvx, imp_deriv[0])) tst.assertAlmostEqual(imp_deriv[1], modeller_atom.dvy, delta=1e-2, msg="y derivative for atom %s differs between " "Modeller (%f) and IMP (%f)" \ % (str(modeller_atom), modeller_atom.dvy, imp_deriv[1])) tst.assertAlmostEqual(imp_deriv[2], modeller_atom.dvz, delta=1e-2, msg="z derivative for atom %s differs between " "Modeller (%f) and IMP (%f)" \ % (str(modeller_atom), modeller_atom.dvz, imp_deriv[2])) class Tests(IMP.test.TestCase): def remove_atom_types(self, hierarchy): """Remove atom types as assigned by Modeller so we can set our own""" atoms = IMP.atom.get_by_type(hierarchy, IMP.atom.ATOM_TYPE) k = IMP.atom.CHARMMAtom.get_charmm_type_key() for a in atoms: a.get_particle().remove_attribute(k) def test_read_static_restraints(self): """Check loading of Modeller static restraints""" e = environ() e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = model(e) modmodel.build_sequence('GGCC') m = IMP.Model() loader = IMP.modeller.ModelLoader(modmodel) protein = loader.load_atoms(m) at = modmodel.atoms restraints = [] # Typical distance restraints or stereochemical bonds: r = forms.gaussian(feature=features.distance(at[0], at[1]), mean=1.54, stdev=0.1, group=physical.xy_distance) restraints.append(r) r = forms.lower_bound(feature=features.distance(at[0], at[1]), mean=10.0, stdev=0.1, group=physical.xy_distance) restraints.append(r) r = forms.upper_bound(feature=features.distance(at[0], at[1]), mean=10.0, stdev=0.1, group=physical.xy_distance) restraints.append(r) # Typical stereochemical angle restraint: r = forms.gaussian(feature=features.angle(at[0], at[1], at[2]), mean=1.92, stdev=0.07, group=physical.xy_distance) restraints.append(r) # Typical stereochemical improper dihedral restraint: r = forms.gaussian(feature=features.dihedral(at[0], at[1], at[2], at[3]), mean=3.14, stdev=0.1, group=physical.xy_distance) restraints.append(r) # Typical stereochemical dihedral restraint: r = forms.cosine(feature=features.dihedral(at[0], at[1], at[2], at[3]), group=physical.xy_distance, phase=0.0, force=2.5, period=2) restraints.append(r) # Typical splined restraint: r = forms.spline(feature=features.distance(at[0], at[1]), open=True, low=1.0, high=5.0, delta=1.0, group=physical.xy_distance, lowderiv=0.0, highderiv=0.0, values=[100.0, 200.0, 300.0, 200.0, 100.0]) restraints.append(r) # Test forms.factor r = forms.factor(feature=features.angle(at[0], at[1], at[2]), factor=100.0, group=physical.xy_distance) restraints.append(r) # Test periodic splined restraint: r = forms.spline(feature=features.dihedral(at[0], at[1], at[2], at[3]), open=False, low=0.0, high=6.2832, delta=1.2566, group=physical.xy_distance, lowderiv=0.0, highderiv=0.0, values=[100.0, 200.0, 300.0, 400.0, 300.0]) restraints.append(r) # Test multiple binormal restraint r = forms.multi_binormal(features=(features.dihedral(*at[0:4]), features.dihedral(*at[4:8])), group=physical.xy_distance, weights=[0.2,0.8,0.3], means=[[0.1,0.2],[0.3,0.4],[0.5,0.6]], stdevs=[[0.1,0.2],[0.3,0.4],[0.1,0.3]], correls=[0.3,0.6,0.9]) restraints.append(r) for r in restraints: modmodel.restraints.clear() modmodel.restraints.add(r) rset = IMP.RestraintSet() m.add_restraint(rset) for rsr in loader.load_static_restraints(): rset.add_restraint(rsr) assertSimilarModellerIMPScores(self, modmodel, protein) rset.set_weight(0) def test_rsr_file_read(self): """Check reading of arbitrary Modeller restraint files""" e = environ() e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = model(e) modmodel.build_sequence('GGCC') open('test.rsr', 'w').write('MODELLER5 VERSION: MODELLER FORMAT\n' 'R 3 1 1 1 2 2 0 3' ' 2 1.5380 0.0364') modmodel.restraints.append('test.rsr') # Deprecated interface m = IMP.Model() loader = IMP.modeller.ModelLoader(modmodel) protein = loader.load_atoms(m) r = IMP.modeller.load_restraints_file('test.rsr', protein) self.assertIsInstance(r, list) for rsr in r: m.add_restraint(rsr) assertSimilarModellerIMPScores(self, modmodel, protein) # Need atoms before loading restraints m = IMP.Model() loader = IMP.modeller.ModelLoader(modmodel) self.assertRaises(ValueError, loader.load_static_restraints_file, 'test.rsr') # New interface protein = loader.load_atoms(m) for rsr in loader.load_static_restraints_file('test.rsr'): m.add_restraint(rsr) assertSimilarModellerIMPScores(self, modmodel, protein) os.unlink('test.rsr') def test_bond_restraints(self): """Check bond restraints against Modeller""" e = environ() e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = model(e) modmodel.build_sequence('G') modmodel.restraints.make(selection(modmodel), restraint_type='BOND', spline_on_site=False, residue_span_range=(0, 99999)) m = IMP.Model() loader = IMP.modeller.ModelLoader(modmodel) protein = loader.load_atoms(m) ff = IMP.atom.CHARMMParameters(IMP.atom.get_data_path('top.lib'), IMP.atom.get_data_path('par.lib')) topology = ff.create_topology(protein) topology.apply_default_patches() self.remove_atom_types(protein) topology.add_atom_types(protein) bonds = topology.add_bonds(protein) cont = IMP.container.ListSingletonContainer(m, "bonds") cont.add_particles(bonds) bss = IMP.atom.BondSingletonScore(IMP.core.Harmonic(0,1)) m.add_restraint(IMP.container.SingletonsRestraint(bss, cont)) assertSimilarModellerIMPScores(self, modmodel, protein) def test_improper_restraints(self): """Check improper restraints against Modeller""" e = environ() e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = model(e) modmodel.build_sequence('A') modmodel.restraints.make(selection(modmodel), restraint_type='IMPROPER', spline_on_site=False, residue_span_range=(0, 99999)) m = IMP.Model() loader = IMP.modeller.ModelLoader(modmodel) protein = loader.load_atoms(m) ff = IMP.atom.CHARMMParameters(IMP.atom.get_data_path('top.lib'), IMP.atom.get_data_path('par.lib')) topology = ff.create_topology(protein) topology.apply_default_patches() self.remove_atom_types(protein) topology.add_atom_types(protein) bonds = topology.add_impropers(protein) cont = IMP.container.ListSingletonContainer(m, "bonds") cont.add_particles(bonds) bss = IMP.atom.ImproperSingletonScore(IMP.core.Harmonic(0,1)) m.add_restraint(IMP.container.SingletonsRestraint(bss, cont)) assertSimilarModellerIMPScores(self, modmodel, protein) def test_angle_restraints(self): """Check angle restraints against Modeller""" e = environ() e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = model(e) modmodel.build_sequence('A') modmodel.restraints.make(selection(modmodel), restraint_type='ANGLE', spline_on_site=False, residue_span_range=(0, 99999)) m = IMP.Model() loader = IMP.modeller.ModelLoader(modmodel) protein = loader.load_atoms(m) ff = IMP.atom.CHARMMParameters(IMP.atom.get_data_path('top.lib'), IMP.atom.get_data_path('par.lib')) topology = ff.create_topology(protein) topology.apply_default_patches() self.remove_atom_types(protein) topology.add_atom_types(protein) bonds = topology.add_bonds(protein) angles = ff.create_angles(bonds) cont = IMP.container.ListSingletonContainer(m, "bonds") cont.add_particles(angles) bss = IMP.atom.AngleSingletonScore(IMP.core.Harmonic(0,1)) m.add_restraint(IMP.container.SingletonsRestraint(bss, cont)) assertSimilarModellerIMPScores(self, modmodel, protein) def test_dihedral_restraints(self): """Check dihedral restraints against Modeller""" e = environ() e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = model(e) modmodel.build_sequence('A') modmodel.restraints.make(selection(modmodel), restraint_type='DIHEDRAL', spline_on_site=False, residue_span_range=(0, 99999)) m = IMP.Model() loader = IMP.modeller.ModelLoader(modmodel) protein = loader.load_atoms(m) ff = IMP.atom.CHARMMParameters(IMP.atom.get_data_path('top.lib'), IMP.atom.get_data_path('par.lib')) topology = ff.create_topology(protein) topology.apply_default_patches() self.remove_atom_types(protein) topology.add_atom_types(protein) bonds = topology.add_bonds(protein) dihedrals = ff.create_dihedrals(bonds) cont = IMP.container.ListSingletonContainer(m, "bonds") cont.add_particles(dihedrals) bss = IMP.atom.DihedralSingletonScore() m.add_restraint(IMP.container.SingletonsRestraint(bss, cont)) assertSimilarModellerIMPScores(self, modmodel, protein) if __name__ == '__main__': IMP.test.main()