diff --git a/prody/dynamics/anmd.py b/prody/dynamics/anmd.py index 83fb1470c..7d1a3e49a 100755 --- a/prody/dynamics/anmd.py +++ b/prody/dynamics/anmd.py @@ -41,8 +41,7 @@ __all__ = ['runANMD'] -def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=2, - tolerance=10.0, solvent='imp', force_field=None): +def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=2, tolerance=10.0): """Runs the ANMD hybrid simulation method ([CM22]_), which generates conformations along single modes and minimises them. The first non-zero mode is scaled to *max_rmsd* and the remaining modes are scaled accordingly using their eigenvalues. @@ -63,16 +62,6 @@ def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=2, in kilojoule_per_mole. Default is 10 :type tolerance: float - :arg solvent: Solvent model to be used. If it is set to 'imp' (default), - implicit solvent model will be used, whereas 'exp' stands for explicit solvent model. - Warning: In the case of nucleotide chains, explicit solvent model is automatically set. - :type solvent: str - - :arg force_field: Implicit solvent force field is ('amber99sbildn.xml', 'amber99_obc.xml'). - Explicit solvent force field is ('amber14-all.xml', 'amber14/tip3pfb.xml'). - Experimental feature: Forcefields already implemented in OpenMM can be used. - :type force_field: tuple of strings - .. [CM22] Mary Hongying Cheng, James M Krieger, Anupam Banerjee, Yufei Xiang, Burak Kaynak, Yi Shi, Moshe Arditi, Ivet Bahar. Impact of new variants on SARS-CoV-2 infectivity and neutralization: @@ -99,19 +88,6 @@ def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=2, if not isinstance(tolerance, Number): raise TypeError('tolerance should be a float') - - if not isinstance(solvent, str): - raise TypeError('solvent should be a string') - if solvent not in ['imp', 'exp']: - raise ValueError('solvent should be "imp" or "exp"') - - if not isinstance(force_field, (type(None), tuple)): - raise TypeError('force_field should be None or a tuple') - if force_field is not None: - if len(force_field) != 2: - raise ValueError('force_field tuple should have 2 elements') - if not isinstance(force_field[0], str) or not isinstance(force_field[1], str): - raise TypeError('force_field tuple entries should be strings') pdb_name=atoms.getTitle().replace(' ', '_') @@ -164,7 +140,7 @@ def runANMD(atoms, num_modes=2, max_rmsd=2., num_steps=2, sc_rmsd=((1/eval_i)**0.5/(1/eval_0)**0.5)*max_rmsd traj_aa=traverseMode(anm_ex[i], atoms_all, n_steps=num_steps, rmsd=sc_rmsd) traj_aa.setAtoms(atoms_all) - + target_ensemble = Ensemble('mode {0} ensemble'.format(ip1)) target_ensemble.setAtoms(atoms_all) target_ensemble.setCoords(atoms_all) diff --git a/prody/tests/dynamics/test_anmd.py b/prody/tests/dynamics/test_anmd.py index 65fa76d02..f6b8dbc4a 100644 --- a/prody/tests/dynamics/test_anmd.py +++ b/prody/tests/dynamics/test_anmd.py @@ -49,26 +49,6 @@ def testAnmdToleranceWrongType(self): if prody.PY3K: self.assertRaises(TypeError, self.runANMD, self.ATOMS, tolerance='nogood') - def testAnmdSolventWrongType(self): - """Test response to wrong type *solvent* argument.""" - if prody.PY3K: - self.assertRaises(TypeError, self.runANMD, self.ATOMS, solvent=1) - - def testAnmdSolventWrongValue(self): - """Test response to wrong value *solvent* argument.""" - if prody.PY3K: - self.assertRaises(ValueError, self.runANMD, self.ATOMS, solvent='nogood') - - def testAnmdFFWrongType(self): - """Test response to wrong type *force_field* argument.""" - if prody.PY3K: - self.assertRaises(TypeError, self.runANMD, self.ATOMS, force_field=1) - - def testAnmdFFWrongValue(self): - """Test response to wrong value *force_field* argument.""" - if prody.PY3K: - self.assertRaises(ValueError, self.runANMD, self.ATOMS, force_field='nogood') - class TestAnmdResults(TestANMD): def testResults(self):