Ejemplo n.º 1
0
 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)
Ejemplo n.º 2
0
 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)
Ejemplo n.º 3
0
 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)
Ejemplo n.º 4
0
 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)
Ejemplo n.º 5
0
 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()))
Ejemplo n.º 6
0
 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)
Ejemplo n.º 7
0
 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)
Ejemplo n.º 8
0
 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)
Ejemplo n.º 9
0
 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)
Ejemplo n.º 10
0
 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)
Ejemplo n.º 11
0
 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()))