def test_modeller_restraints(self):
"""Check using Modeller restraints in IMP"""
e = modeller.environ()
e.edat.dynamic_sphere = False
e.libs.topology.read("${LIB}/top_heav.lib")
e.libs.parameters.read("${LIB}/par.lib")
modmodel = modeller.model(e)
modmodel.build_sequence("GGCC")
feat = modeller.features.distance(modmodel.atoms[0], modmodel.atoms[-1])
r = modeller.forms.gaussian(feature=feat, mean=10.0, stdev=1.0, group=modeller.physical.xy_distance)
modmodel.restraints.add(r)
m = IMP.kernel.Model()
protein = IMP.modeller.ModelLoader(modmodel).load_atoms(m)
atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE)
m.add_restraint(IMP.modeller.ModellerRestraints(m, modmodel, atoms))
assertSimilarModellerIMPScores(self, modmodel, protein)
self.assertAlmostEqual(m.evaluate(False), 5.7837, delta=1e-3)
def test_imp_restraints(self):
"""Check using IMP restraints in Modeller"""
e = modeller.environ()
e.edat.dynamic_sphere = False
e.libs.topology.read('${LIB}/top_heav.lib')
e.libs.parameters.read('${LIB}/par.lib')
modmodel = modeller.model(e)
modmodel.build_sequence('GGCC')
m = IMP.Model()
protein = IMP.modeller.ModelLoader(modmodel).load_atoms(m)
atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE)
r = IMP.core.DistanceRestraint(m, IMP.core.Harmonic(10.0, 1.0),
atoms[0], atoms[-1])
sf = IMP.core.RestraintsScoringFunction([r])
t = modmodel.env.edat.energy_terms
t.append(IMP.modeller.IMPRestraints(atoms, sf))
assertSimilarModellerIMPScores(self, sf, modmodel, protein)
self.assertAlmostEqual(sf.evaluate(False), 9.80, delta=1e-2)
def test_imp_restraints(self):
"""Check using IMP restraints in Modeller"""
e = modeller.environ()
e.edat.dynamic_sphere = False
e.libs.topology.read('${LIB}/top_heav.lib')
e.libs.parameters.read('${LIB}/par.lib')
modmodel = modeller.model(e)
modmodel.build_sequence('GGCC')
m = IMP.Model()
protein = IMP.modeller.ModelLoader(modmodel).load_atoms(m)
atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE)
r = IMP.core.DistanceRestraint(m, IMP.core.Harmonic(10.0, 1.0),
atoms[0], atoms[-1])
sf = IMP.core.RestraintsScoringFunction([r])
t = modmodel.env.edat.energy_terms
t.append(IMP.modeller.IMPRestraints(atoms, sf))
assertSimilarModellerIMPScores(self, sf, modmodel, protein)
self.assertAlmostEqual(sf.evaluate(False), 9.80, delta=1e-2)
def test_modeller_restraints(self):
"""Check using Modeller restraints in IMP"""
e = modeller.environ()
e.edat.dynamic_sphere = False
e.libs.topology.read('${LIB}/top_heav.lib')
e.libs.parameters.read('${LIB}/par.lib')
modmodel = modeller.model(e)
modmodel.build_sequence('GGCC')
feat = modeller.features.distance(modmodel.atoms[0],
modmodel.atoms[-1])
r = modeller.forms.gaussian(feature=feat,
mean=10.0,
stdev=1.0,
group=modeller.physical.xy_distance)
modmodel.restraints.add(r)
m = IMP.kernel.Model()
protein = IMP.modeller.ModelLoader(modmodel).load_atoms(m)
atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE)
m.add_restraint(IMP.modeller.ModellerRestraints(m, modmodel, atoms))
assertSimilarModellerIMPScores(self, modmodel, protein)
self.assertAlmostEqual(m.evaluate(False), 5.7837, delta=1e-3)