def _parse_fragment_tree(self, el):
fragments = []
for el_fragments in el.findall('fragments'):
for el_f in el_fragments:
fragments.append(self._parse_fragment_tree(el_f))
atoms = []
for el_atoms in el.findall('atoms'):
for el_a in el_atoms:
atom_classes = {"dummy": im.dummy,
"unknown": im.unknown,
"element": im.element}
descr = atom_classes[el_a.get('type')](el_a.get('name'))
atoms.append((el_a.get('label'),
im.atom(descr, int(el_a.get('nsites', '1')))))
bonds = []
for el_bonds in el.findall('bonds'):
for el_b in el_bonds:
a1, a2 = el_b.get('atoms').split()
bonds.append((a1, a2, el_b.get('order')))
label = el.get('label')
species = el.get('species')
polymer_type = el.get('polymer_type', None)
if polymer_type is None:
return label, im.fragment(species, fragments, atoms, bonds)
else:
assert len(atoms) == 0
return label, im.polymer(species, fragments, bonds, polymer_type)
def test_equality(self):
same_mol = make_water_fragment()
changed_bond_order = M.fragment("water", (),
(("H1", M.atom(M.element("H"))),
("H2", M.atom(M.element("H"))),
("O", M.atom(M.element("O")))),
(("O", "H2", "single"),
("O", "H1", "single")))
changed_atom_order = M.fragment("water", (),
(("O", M.atom(M.element("O"))),
("H1", M.atom(M.element("H"))),
("H2", M.atom(M.element("H")))),
(("O", "H1", "single"),
("O", "H2", "single")))
self.assertEqual(self.mol, self.mol)
self.assertEqual(self.mol, same_mol)
self.assertEqual(self.mol, changed_bond_order)
self.assertNotEqual(self.mol, changed_atom_order)
def test_bonds(self):
carbon = M.atom(M.element("C"))
# Bond specified by only one atom
self.assertRaises(ValueError,
lambda: M.fragment('m', (),
(('C1', carbon), ('C2', carbon)),
(('C1', ),)))
# Bond specified by two atoms but no bond order
self.assertRaises(ValueError,
lambda: M.fragment('m', (),
(('C1', carbon), ('C2', carbon)),
(('C1', 'C2'),)))
# Bond specified by two identical atoms
self.assertRaises(ValueError,
lambda: M.fragment('m', (),
(('C1', carbon), ('C2', carbon)),
(('C1', 'C1', ''),)))
# Bond specified by an atom name that is undefined
self.assertRaises(ValueError,
lambda: M.fragment('m', (),
(('C1', carbon), ('C2', carbon)),
(('C1', 'C3', ''),)))
# Bond specified at the wrong fragment level
f = M.fragment('x', (), (('C1', carbon), ('C2', carbon)), ())
self.assertRaises(ValueError,
lambda: M.fragment('m', (('x', f),),
(('C3', carbon),),
(('x.C1', 'x.C2', ''),)))
def _make_molecule(self):
C = M.element('C')
H = M.element('H')
N = M.element('N')
O = M.element('O')
peptide_group = M.fragment('peptide',
(),
(('CA', M.atom(C)),
('HA', M.atom(H)),
('H', M.atom(H)),
('N', M.atom(N)),
('C', M.atom(C)),
('O', M.atom(O))),
(('N', 'H', "single"),
('N', 'CA', "single"),
('CA', 'HA', "single"),
('CA', 'C', "single"),
('C', 'O', "double")))
ala_sidechain = M.fragment('ala_sidechain',
(),
(('CB', M.atom(C)),
('HB1', M.atom(H)),
('HB2', M.atom(H)),
('HB3', M.atom(H))),
(('CB', 'HB1', "single"),
('CB', 'HB2', "single"),
('CB', 'HB3', "single"),))
ala = M.fragment('alanine',
(('peptide', peptide_group),
('sidechain', ala_sidechain)),
(),
(('peptide.CA', 'sidechain.CB', "single"),))
return M.polymer('alanine_dipeptide',
(('ALA1', ala),
('ALA2', ala)),
(('ALA1.peptide.C', 'ALA2.peptide.N', "single"),),
'polypeptide')
def test_universe(self):
mol = M.fragment("water", (),
(("H1", M.atom(M.element("H"), 8)),
("H2", M.atom(M.element("H"), 8)),
("O", M.atom(M.element("O"), 2))),
(("H1", "O", "single"), ("H2", "O", "single")))
self.assertRaises(TypeError,
lambda: M.universe(0, [(mol, 'water', 10)]))
self.assertRaises(ValueError,
lambda: M.universe('strange', [(mol, 'water', 10)]))
self.assertRaises(ValueError,
lambda: M.universe('strange', [(mol, 10)]))
self.assertRaises(TypeError,
lambda: M.universe('infinite', mol))
self.assertRaises(ValueError,
lambda: M.universe('infinite', [("water", 10)]))
self.assertRaises(TypeError,
lambda: M.universe('infinite', [mol]))
self.assertRaises(ValueError,
lambda: M.universe('infinite', [(10, mol)]))
self.assertRaises(ValueError,
lambda: M.universe('infinite', [(mol, 'water', 10)],
[(IN.zeros((3,3), N.float64),
IN.zeros((3,), N.float64))]))
def __init__(self, mode='r'):
self.file = h5py.File(self.filename, mode)
def close(self):
self.file.close()
def __enter__(self):
return self.file
def __exit__(self, type, value, traceback):
self.close()
return False
water = M.fragment("water", (),
(("H1", M.atom(M.element("H"), 1)),
("H2", M.atom(M.element("H"), 1)),
("O", M.atom(M.element("O"), 1))),
(("H1", "O", "single"), ("H2", "O", "single")))
class WriteReadTest(unittest.TestCase):
def setUp(self):
TestHDF5File.initialize()
def tearDown(self):
TestHDF5File.cleanup()
def test_infinite(self):
universe = M.universe('infinite', [(water, 'water', 5)])
nsites = universe.number_of_sites
conf1 = M.Configuration(universe,
def make_water_fragment(nsites=1):
return M.fragment("water", (),
(("H1", M.atom(M.element("H"), nsites)),
("H2", M.atom(M.element("H"), nsites)),
("O", M.atom(M.element("O"), nsites))),
(("H1", "O", "single"), ("H2", "O", "single")))
def test_fragment(self):
carbon = M.atom(M.element("C"))
# Illegal fragments
self.assertRaises(TypeError,
lambda: M.fragment('m', None, (("C", carbon),), ()))
self.assertRaises(TypeError,
lambda: M.fragment('m', [1, 2], (("C", carbon),), ()))
self.assertRaises(TypeError,
lambda: M.fragment('m', (("C", carbon),), (), ()))
# Illegal atoms
self.assertRaises(TypeError,
lambda: M.fragment('m', (), None, ()))
self.assertRaises(TypeError,
lambda: M.fragment('m', (), [1, 2], ()))
self.assertRaises(TypeError,
lambda: M.fragment('m', (), (carbon,), ()))
self.assertRaises(ValueError,
lambda: M.fragment('m', (),
(("C", carbon),
("C", carbon)),
()))
# Illegal bond lists
self.assertRaises(TypeError,
lambda: M.fragment('m', (), (("C", carbon),), None))
self.assertRaises(TypeError,
lambda: M.fragment('m', (), (("C", carbon),),
[1, 2, 3]))
self.assertRaises(TypeError,
lambda: M.fragment('m', (), (("C", carbon),),
(('X', 'X'))))
self.assertRaises(TypeError,
lambda: M.fragment('m', (), (("C", carbon),),
(['X', 'X', 'single'])))