def test_simple(self):
""" Tests converting standard Gromacs system into Amber prmtop """
top = load_file(get_fn(os.path.join('03.AlaGlu', 'topol.top')))
self.assertEqual(top.combining_rule, 'lorentz')
parm = amber.AmberParm.from_structure(top)
parm.write_parm(get_fn('ala_glu.parm7', written=True))
parm = load_file(get_fn('ala_glu.parm7', written=True))
self.assertIsInstance(parm, amber.AmberParm)
self.assertEqual(len(top.atoms), len(parm.atoms))
self.assertEqual(len(top.bonds), len(parm.bonds))
self.assertEqual(len(top.angles), len(parm.angles))
self.assertEqual(len(top.residues), len(parm.residues))
for a1, a2 in zip(top.atoms, parm.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.type, a2.type)
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertAlmostEqual(a1.mass, a2.mass)
self.assertIs(type(a1), type(a2))
self.assertAlmostEqual(a1.charge, a2.charge)
self.assertEqual(set([a.idx for a in a1.bond_partners]),
set([a.idx for a in a2.bond_partners]))
self.assertEqual(set([a.idx for a in a1.angle_partners]),
set([a.idx for a in a2.angle_partners]))
self.assertEqual(set([a.idx for a in a1.dihedral_partners]),
set([a.idx for a in a2.dihedral_partners]))
# Make sure that assign_nbidx_from_types compresses maximally. First
# add a new, equivalent L-J type. Then call assign_nbidx_from_types
# again, which should recompress
before_nbidx = [a.nb_idx for a in parm.atoms]
addLJType(parm, '@1').execute()
after_nbidx = [a.nb_idx for a in parm.atoms]
self.assertEqual(before_nbidx[1:], after_nbidx[1:])
self.assertEqual(after_nbidx[0], max(before_nbidx) + 1)
parm.atoms.assign_nbidx_from_types()
# Should recompress
self.assertEqual(before_nbidx, [a.nb_idx for a in parm.atoms])
def test_simple(self):
""" Tests converting standard Gromacs system into Amber prmtop """
top = load_file(get_fn(os.path.join('03.AlaGlu', 'topol.top')))
self.assertEqual(top.combining_rule, 'lorentz')
parm = amber.AmberParm.from_structure(top)
parm.write_parm(get_fn('ala_glu.parm7', written=True))
parm = load_file(get_fn('ala_glu.parm7', written=True))
self.assertIsInstance(parm, amber.AmberParm)
self.assertEqual(len(top.atoms), len(parm.atoms))
self.assertEqual(len(top.bonds), len(parm.bonds))
self.assertEqual(len(top.angles), len(parm.angles))
self.assertEqual(len(top.residues), len(parm.residues))
for a1, a2 in zip(top.atoms, parm.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.type, a2.type)
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertAlmostEqual(a1.mass, a2.mass)
self.assertIs(type(a1), type(a2))
self.assertAlmostEqual(a1.charge, a2.charge)
self.assertEqual(set([a.idx for a in a1.bond_partners]),
set([a.idx for a in a2.bond_partners]))
self.assertEqual(set([a.idx for a in a1.angle_partners]),
set([a.idx for a in a2.angle_partners]))
self.assertEqual(set([a.idx for a in a1.dihedral_partners]),
set([a.idx for a in a2.dihedral_partners]))
# Make sure that assign_nbidx_from_types compresses maximally. First
# add a new, equivalent L-J type. Then call assign_nbidx_from_types
# again, which should recompress
before_nbidx = [a.nb_idx for a in parm.atoms]
addLJType(parm, '@1').execute()
after_nbidx = [a.nb_idx for a in parm.atoms]
self.assertEqual(before_nbidx[1:], after_nbidx[1:])
self.assertEqual(after_nbidx[0], max(before_nbidx)+1)
parm.atoms.assign_nbidx_from_types()
# Should recompress
self.assertEqual(before_nbidx, [a.nb_idx for a in parm.atoms])