def test_bonds(): # TODO: deprecate this shit from chemlab.io import datafile bz = datafile("tests/data/benzene.mol").read('molecule') na = Molecule([Atom('O', [0.0, 0.0, 0.0]), Atom('H', [0.0, 0.0, 0.0]), Atom('H', [0.0, 0.0, 0.0]), ]) # Adding bonds s = System() with s.batch() as b: b.append(bz) assert_npequal(s.bonds, bz.bonds) assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2]) assert_npequal(s.bond_orders, bz.bond_orders) s.add(bz) assert_npequal(s.type_array, ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C']) eq_(s.dimensions['atom'], 12) assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7))) # Reordering s.bonds = np.array([[0, 1], [6, 8]]) s.reorder_molecules([1, 0]) assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]])) # Selection ss = subsystem_from_molecules(s, [1]) assert_npequal(ss.bonds, np.array([[0, 1]]))
def test_bonds(): # TODO: deprecate this shit from chemlab.io import datafile bz = datafile("tests/data/benzene.mol").read('molecule') na = Molecule([ Atom('O', [0.0, 0.0, 0.0]), Atom('H', [0.0, 0.0, 0.0]), Atom('H', [0.0, 0.0, 0.0]), ]) # Adding bonds s = System() with s.batch() as b: b.append(bz) assert_npequal(s.bonds, bz.bonds) assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2]) assert_npequal(s.bond_orders, bz.bond_orders) s.add(bz) assert_npequal( s.type_array, ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C']) eq_(s.dimensions['atom'], 12) assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7))) # Reordering s.bonds = np.array([[0, 1], [6, 8]]) s.reorder_molecules([1, 0]) assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]])) # Selection ss = subsystem_from_molecules(s, [1]) assert_npequal(ss.bonds, np.array([[0, 1]]))
def test_bonds(): from chemlab.io import datafile bz = datafile("tests/data/benzene.mol").read('molecule') na = Molecule([Atom('Na', [0.0, 0.0, 0.0])]) # Adding bonds s = System.empty(2, 2 * bz.n_atoms) s.add(bz) assert_npequal(s.bonds, bz.bonds) assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2]) assert_npequal(s.bond_orders, bz.bond_orders) s.add(bz) assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 6))) #assert_npequal(s.bond_orders) # Reordering orig = np.array([[0, 1], [6, 8]]) s.bonds = orig s.reorder_molecules([1, 0]) assert_npequal(s.bonds, np.array([[6, 7], [0, 2]])) # This doesn't change the bond_ordering # Selection ss = subsystem_from_molecules(s, [1]) assert_npequal(ss.bonds, np.array([[0, 1]])) import inspect ss2 = System.from_arrays(**dict(inspect.getmembers(ss))) ss2.r_array += 10.0 ms = merge_systems(ss, ss2) assert_npequal(ms.bonds, np.array([[0, 1], [6, 7]])) assert_npequal(ms.bond_orders, np.array([1, 1])) # From_arrays s = System.from_arrays(mol_indices=[0], bonds=bz.bonds, **bz.__dict__) assert_npequal(s.bonds, bz.bonds) assert_npequal(s.bond_orders, bz.bond_orders) # Get molecule entry # Test the bonds when they're 0 s.bonds = np.array([]) assert_equals(s.get_derived_molecule_array('formula'), 'C6')
def test_bonds(): from chemlab.io import datafile bz = datafile("tests/data/benzene.mol").read('molecule') na = Molecule([Atom('Na', [0.0, 0.0, 0.0])]) # Adding bonds s = System.empty(2, 2*bz.n_atoms) s.add(bz) assert_npequal(s.bonds, bz.bonds) assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2]) assert_npequal(s.bond_orders, bz.bond_orders) s.add(bz) assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 6))) #assert_npequal(s.bond_orders) # Reordering orig = np.array([[0, 1], [6, 8]]) s.bonds = orig s.reorder_molecules([1, 0]) assert_npequal(s.bonds, np.array([[6, 7], [0, 2]])) # This doesn't change the bond_ordering # Selection ss = subsystem_from_molecules(s, [1]) assert_npequal(ss.bonds, np.array([[0, 1]])) import inspect ss2 = System.from_arrays(**dict(inspect.getmembers(ss))) ss2.r_array += 10.0 ms = merge_systems(ss, ss2) assert_npequal(ms.bonds, np.array([[0, 1], [6, 7]])) assert_npequal(ms.bond_orders, np.array([1, 1])) # From_arrays s = System.from_arrays(mol_indices=[0], bonds=bz.bonds, **bz.__dict__) assert_npequal(s.bonds, bz.bonds) assert_npequal(s.bond_orders, bz.bond_orders) # Get molecule entry # Test the bonds when they're 0 s.bonds = np.array([]) assert_equals(s.get_derived_molecule_array('formula'), 'C6')
def test_system(): wat = Molecule([Atom("O", [-4.99, 2.49, 0.0]), Atom("H", [-4.02, 2.49, 0.0]), Atom("H", [-5.32, 1.98, 1.0])], export={'hello': 1.0}) wat.r_array *= 0.1 # Initialization from empty s = System.empty(4, 4*3) mols = [] for i in xrange(s.n_mol): wat.r_array += 0.1 s.add(wat) m = wat.copy() mols.append(wat.copy()) # Printing just to test if there aren't any exception print "Init from Empty" print "*" * 72 _print_sysinfo(s) print "Init Normal" print "*" * 72 s = System(mols) _print_sysinfo(s) # 3 water molecules r_array = np.random.random((9, 3)) type_array = ['O', 'H', 'H', 'O', 'H', 'H', 'O', 'H', 'H'] mol_indices = [0, 3, 6] mol_n_atoms = [3, 3, 3] s2 = System.from_arrays(r_array=r_array, type_array=type_array, mol_indices=mol_indices, mol_n_atoms=mol_n_atoms) print 'bonds', s2._mol_bonds sub2 = subsystem_from_molecules(s2, np.array([0, 2])) assert sub2.n_mol == 2 sub = subsystem_from_atoms(s2, np.array([True, True, False, False, False, False, False, False, False])) assert sub.n_mol == 1
def test_subsystem_from_molecules(self): mols = self._make_molecules() system = System(mols) subsystem = subsystem_from_molecules(system, np.array([0, 2])) assert_equals(subsystem.n_mol, 2)