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_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(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 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_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 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 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_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()))