def test_add_mol2(self): """ Test adding Mol2 file to ParmList """ parms = ParmList() parms.add_parm(get_fn('tripos9.mol2')) self.assertEqual(len(parms), 1) self.assertIsInstance(parms[0], Structure) self.assertIn(0, parms) self.assertNotIn(1, parms)
def test_add_charmm_psf_names(self): """ Test adding CHARMM PSF file names to ParmList """ parms = ParmList() parms.add_parm(get_fn('ala3_solv.psf')) parms.add_parm(get_fn('ala_ala_ala.psf')) parms.add_parm(get_fn('ala_ala_ala.psf.xplor')) parms.add_parm(get_fn('ala_ala_ala_autopsf.psf')) ala3, aaa, xaaa, aaaa = parms # Check proper instantiation for parm in parms: self.assertIsInstance(parm, CharmmPsfFile) # Check indexing self.assertIs(parms[0], ala3) self.assertIs(parms[1], aaa) self.assertIs(parms[2], xaaa) self.assertIs(parms[3], aaaa) # Test name indexing self.assertIs(parms[get_fn('ala3_solv.psf')], ala3) self.assertIs(parms[get_fn('ala_ala_ala.psf')], aaa) self.assertIs(parms[get_fn('ala_ala_ala.psf.xplor')], xaaa) self.assertIs(parms[get_fn('ala_ala_ala_autopsf.psf')], aaaa) # Check that the last parm added is active self.assertIs(parms.parm, parms[-1]) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, ala3) parms.set_new_active(get_fn('ala_ala_ala.psf')) self.assertIs(parms.parm, aaa)
def testAddCharmmPsfNames(self): """ Test adding CHARMM PSF file names to ParmList """ parms = ParmList() parms.add_parm(get_fn('ala3_solv.psf')) parms.add_parm(get_fn('ala_ala_ala.psf')) parms.add_parm(get_fn('ala_ala_ala.psf.xplor')) parms.add_parm(get_fn('ala_ala_ala_autopsf.psf')) ala3, aaa, xaaa, aaaa = parms # Check proper instantiation for parm in parms: self.assertIsInstance(parm, CharmmPsfFile) # Check indexing self.assertIs(parms[0], ala3) self.assertIs(parms[1], aaa) self.assertIs(parms[2], xaaa) self.assertIs(parms[3], aaaa) # Test name indexing self.assertIs(parms[get_fn('ala3_solv.psf')], ala3) self.assertIs(parms[get_fn('ala_ala_ala.psf')], aaa) self.assertIs(parms[get_fn('ala_ala_ala.psf.xplor')], xaaa) self.assertIs(parms[get_fn('ala_ala_ala_autopsf.psf')], aaaa) # Check that the last parm added is active self.assertIs(parms.parm, parms[-1]) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, ala3) parms.set_new_active(get_fn('ala_ala_ala.psf')) self.assertIs(parms.parm, aaa)
def test_add_charmm_psf(self): """ Test adding CHARMM PSF file to ParmList """ parms = ParmList() ala3 = CharmmPsfFile(get_fn('ala3_solv.psf')) aaa = CharmmPsfFile(get_fn('ala_ala_ala.psf')) xaaa = CharmmPsfFile(get_fn('ala_ala_ala.psf.xplor')) aaaa = CharmmPsfFile(get_fn('ala_ala_ala_autopsf.psf')) parms.add_parm(ala3) parms.add_parm(aaa) parms.add_parm(xaaa) parms.add_parm(aaaa) # Check indexing self.assertIs(parms[0], ala3) self.assertIs(parms[1], aaa) self.assertIs(parms[2], xaaa) self.assertIs(parms[3], aaaa) # Test name indexing self.assertIs(parms[get_fn('ala3_solv.psf')], ala3) self.assertIs(parms[get_fn('ala_ala_ala.psf')], aaa) self.assertIs(parms[get_fn('ala_ala_ala.psf.xplor')], xaaa) self.assertIs(parms[get_fn('ala_ala_ala_autopsf.psf')], aaaa) # Check that the last parm added is active self.assertIs(parms.parm, parms[-1]) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, ala3) parms.set_new_active(get_fn('ala_ala_ala.psf')) self.assertIs(parms.parm, aaa)
def test_add_amber_parm_names(self): """ Test adding Amber prmtop file names to ParmList """ parms = ParmList() parms.add_parm(get_fn('tip4p.parm7')) parms.add_parm(get_fn('ala_ala_ala.parm7')) parms.add_parm(get_fn('nma.parm7')) amber, chamber, amoeba = parms self.assertEqual(len(parms), 3) # Check that they are the correct type self.assertIs(type(parms[0]), AmberParm) self.assertIs(type(parms[1]), ChamberParm) self.assertIs(type(parms[2]), AmoebaParm) self.assertRaises(IndexError, lambda: parms[3]) # Test name indexing self.assertIs(parms[get_fn('tip4p.parm7')], amber) self.assertIs(parms[get_fn('ala_ala_ala.parm7')], chamber) self.assertIs(parms[get_fn('nma.parm7')], amoeba) self.assertRaises(IndexError, lambda: parms['noparm']) # Check that the last added parm is active self.assertIs(parms.parm, amoeba) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, amber) parms.set_new_active(get_fn('ala_ala_ala.parm7')) self.assertIs(parms.parm, chamber) self.assertRaises(IndexError, lambda: parms.set_new_active(3)) self.assertIs(parms.parm, chamber)
def testAddCharmmPsf(self): """ Test adding CHARMM PSF file to ParmList """ parms = ParmList() ala3 = CharmmPsfFile(get_fn('ala3_solv.psf')) aaa = CharmmPsfFile(get_fn('ala_ala_ala.psf')) xaaa = CharmmPsfFile(get_fn('ala_ala_ala.psf.xplor')) aaaa = CharmmPsfFile(get_fn('ala_ala_ala_autopsf.psf')) parms.add_parm(ala3) parms.add_parm(aaa) parms.add_parm(xaaa) parms.add_parm(aaaa) # Check indexing self.assertIs(parms[0], ala3) self.assertIs(parms[1], aaa) self.assertIs(parms[2], xaaa) self.assertIs(parms[3], aaaa) # Test name indexing self.assertIs(parms[get_fn('ala3_solv.psf')], ala3) self.assertIs(parms[get_fn('ala_ala_ala.psf')], aaa) self.assertIs(parms[get_fn('ala_ala_ala.psf.xplor')], xaaa) self.assertIs(parms[get_fn('ala_ala_ala_autopsf.psf')], aaaa) # Check that the last parm added is active self.assertIs(parms.parm, parms[-1]) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, ala3) parms.set_new_active(get_fn('ala_ala_ala.psf')) self.assertIs(parms.parm, aaa)
def testAddAmberParmNames(self): """ Test adding Amber prmtop file names to ParmList """ parms = ParmList() parms.add_parm(get_fn('tip4p.parm7')) parms.add_parm(get_fn('ala_ala_ala.parm7')) parms.add_parm(get_fn('nma.parm7')) amber, chamber, amoeba = parms self.assertEqual(len(parms), 3) # Check that they are the correct type self.assertIs(type(parms[0]), AmberParm) self.assertIs(type(parms[1]), ChamberParm) self.assertIs(type(parms[2]), AmoebaParm) self.assertRaises(IndexError, lambda: parms[3]) # Test name indexing self.assertIs(parms[get_fn('tip4p.parm7')], amber) self.assertIs(parms[get_fn('ala_ala_ala.parm7')], chamber) self.assertIs(parms[get_fn('nma.parm7')], amoeba) self.assertRaises(IndexError, lambda: parms['noparm']) # Check that the last added parm is active self.assertIs(parms.parm, amoeba) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, amber) parms.set_new_active(get_fn('ala_ala_ala.parm7')) self.assertIs(parms.parm, chamber) self.assertRaises(IndexError, lambda: parms.set_new_active(3)) self.assertIs(parms.parm, chamber)
def testAddAmberParm(self): """ Test adding AmberParm-derived instances to ParmList """ parms = ParmList() amber = AmberParm(get_fn('tip4p.parm7')) chamber = ChamberParm(get_fn('ala_ala_ala.parm7')) amoeba = AmoebaParm(get_fn('nma.parm7')) parms.add_parm(amber) parms.add_parm(chamber) parms.add_parm(amoeba) self.assertEqual(len(parms), 3) # Test int indexing self.assertIs(parms[0], amber) self.assertIs(parms[1], chamber) self.assertIs(parms[2], amoeba) self.assertRaises(IndexError, lambda: parms[3]) # Test name indexing self.assertIs(parms[get_fn('tip4p.parm7')], amber) self.assertIs(parms[get_fn('ala_ala_ala.parm7')], chamber) self.assertIs(parms[get_fn('nma.parm7')], amoeba) self.assertRaises(IndexError, lambda: parms['noparm']) # Check that the last added parm is active self.assertIs(parms.parm, amoeba) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, amber) parms.set_new_active(get_fn('ala_ala_ala.parm7')) self.assertIs(parms.parm, chamber) self.assertRaises(IndexError, lambda: parms.set_new_active(3)) self.assertIs(parms.parm, chamber)
def test_add_amber_parm(self): """ Test adding AmberParm-derived instances to ParmList """ parms = ParmList() amber = AmberParm(get_fn('tip4p.parm7')) chamber = ChamberParm(get_fn('ala_ala_ala.parm7')) amoeba = AmoebaParm(get_fn('nma.parm7')) parms.add_parm(amber) parms.add_parm(chamber) parms.add_parm(amoeba) self.assertEqual(len(parms), 3) # Test int indexing self.assertIs(parms[0], amber) self.assertIs(parms[1], chamber) self.assertIs(parms[2], amoeba) self.assertRaises(IndexError, lambda: parms[3]) # Test name indexing self.assertIs(parms[get_fn('tip4p.parm7')], amber) self.assertIs(parms[get_fn('ala_ala_ala.parm7')], chamber) self.assertIs(parms[get_fn('nma.parm7')], amoeba) self.assertRaises(IndexError, lambda: parms['noparm']) # Check that the last added parm is active self.assertIs(parms.parm, amoeba) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, amber) parms.set_new_active(get_fn('ala_ala_ala.parm7')) self.assertIs(parms.parm, chamber) self.assertRaises(IndexError, lambda: parms.set_new_active(3)) self.assertIs(parms.parm, chamber) self.assertRaises(exc.DuplicateParm, lambda: parms.add_parm(get_fn('ala_ala_ala.parm7'))) self.assertRaises( exc.DuplicateParm, lambda: parms.add_parm(load_file(get_fn('ala_ala_ala.parm7')))) self.assertRaises( exc.ParmError, lambda: parms.add_parm( os.path.join(get_fn('pptest1'), 'pptest1.h'))) self.assertRaises(exc.ParmError, lambda: parms.add_parm(get_fn('amino12.lib'))) self.assertRaises(exc.ParmError, lambda: parms.add_parm(object()))
def test_add_amber_parm(self): """ Test adding AmberParm-derived instances to ParmList """ parms = ParmList() amber = AmberParm(get_fn('tip4p.parm7')) chamber = ChamberParm(get_fn('ala_ala_ala.parm7')) amoeba = AmoebaParm(get_fn('nma.parm7')) parms.add_parm(amber) parms.add_parm(chamber) parms.add_parm(amoeba) self.assertEqual(len(parms), 3) # Test int indexing self.assertIs(parms[0], amber) self.assertIs(parms[1], chamber) self.assertIs(parms[2], amoeba) self.assertRaises(IndexError, lambda: parms[3]) # Test name indexing self.assertIs(parms[get_fn('tip4p.parm7')], amber) self.assertIs(parms[get_fn('ala_ala_ala.parm7')], chamber) self.assertIs(parms[get_fn('nma.parm7')], amoeba) self.assertRaises(IndexError, lambda: parms['noparm']) # Check that the last added parm is active self.assertIs(parms.parm, amoeba) # Set a new active topology parms.set_new_active(0) self.assertIs(parms.parm, amber) parms.set_new_active(get_fn('ala_ala_ala.parm7')) self.assertIs(parms.parm, chamber) self.assertRaises(IndexError, lambda: parms.set_new_active(3)) self.assertIs(parms.parm, chamber) self.assertRaises(exc.DuplicateParm, lambda: parms.add_parm(get_fn('ala_ala_ala.parm7'))) self.assertRaises(exc.DuplicateParm, lambda: parms.add_parm(load_file(get_fn('ala_ala_ala.parm7')))) self.assertRaises(exc.ParmError, lambda: parms.add_parm(os.path.join(get_fn('pptest1'), 'pptest1.h'))) self.assertRaises(exc.ParmError, lambda: parms.add_parm(get_fn('amino12.lib'))) self.assertRaises(exc.ParmError, lambda: parms.add_parm(object()))