Python core.System类代码示例

    def test_from_batch(self):
        mols = self._make_molecules()

        system = System()
        with system.batch() as batch:
            [batch.append(mol) for mol in mols]
        self._assert_init(system)

 def test_reorder_molecules(self):
     mols = self._make_molecules()
     system = System(mols)
     system.bonds = np.array([[0, 1], [3, 5]])
     # Reordering
     system.reorder_molecules([1, 0, 2, 3])
     assert_eqbonds(system.bonds, [[0, 2], [3, 4]])

    def test_remove_atoms(self):
        # This will remove the first and last molecules
        mols = self._make_molecules()
        system = System(mols)
        system.remove_atoms([0, 1, 11])

        assert_eqbonds(system.bonds, [[0, 1], [0, 2], [3, 4], [3, 5]])
        assert_npequal(system.type_array, np.array(["O", "H", "H", "O", "H", "H"], dtype="object"))

def test_bond_orders():
    # Get a molecule with some bonds
    wat = _make_water()
    wat_o = wat.copy()
    # 0,1 0,2
    assert_npequal(wat.bond_orders, np.array([0, 0]))

    # Remove a bond
    wat.bonds = np.array([[0, 1]])
    assert_npequal(wat.bond_orders, np.array([0]))

    wat.bond_orders = np.array([2])

    # Try with a system
    s = System()

    s.add(wat_o)
    s.add(wat)

    assert_npequal(s.bond_orders, np.array([0, 0, 2]))
    s.reorder_molecules([1, 0])
    # Bonds get sorted accordingly
    assert_npequal(s.bond_orders, np.array([2, 0, 0]))

    s.bonds = np.array([[0, 1], [0, 2], [3, 4], [3, 5]])
    assert_npequal(s.bond_orders, np.array([2, 0, 0, 0]))

def test_write_gromacs():
    water = Molecule(
        [
            Atom("O", [0.0, 0.0, 0.0], export={"grotype": "OW"}),
            Atom("H", [0.1, 0.0, 0.0], export={"grotype": "HW1"}),
            Atom("H", [-0.03333, 0.09428, 0.0], export={"grotype": "HW2"}),
        ],
        export={"groname": "SOL"},
    )

    sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
    for i in range(200):
        sys.add(water.copy())

    df = datafile("/tmp/dummy.gro", mode="w")
    df.write("system", sys)

    with assert_raises(Exception):
        df = datafile("/tmp/dummy.gro")
        df.write("system", sys)

    df = datafile("/tmp/dummy.gro")
    sread = df.read("system")

    assert all(sread.type_array == sys.type_array)

def test_bond_orders():
    # Get a molecule with some bonds
    wat = _make_water()
    wat_o = wat.copy()
    # 0,1 0,2
    assert_npequal(wat.bond_orders, np.array([1, 1]))

    # Remove a bond
    wat.bonds = np.array([[0, 1]])
    assert_npequal(wat.bond_orders, np.array([1]))

    wat.bond_orders = np.array([2])

    # Try with a system
    s = System.empty(2, 6)

    s.add(wat_o)
    s.add(wat)

    assert_npequal(s.bond_orders , np.array([1, 1, 2]))
    s.reorder_molecules([1, 0]) # We don't actually sort bonds again
    assert_npequal(s.bond_orders , np.array([1, 1, 2]))

    s.bonds = np.array([[0, 1], [0, 2], [3, 4], [3, 5]])
    assert_npequal(s.bond_orders, np.array([1, 1, 2, 1]))

def test_merge_system():
    # take a protein
    from chemlab.io import datafile
    from chemlab.graphics import display_system

    from chemlab.db import ChemlabDB

    water = ChemlabDB().get("molecule", "example.water")

    prot = datafile("tests/data/3ZJE.pdb").read("system")

    # Take a box of water
    NWAT = 50000
    bsize = 20.0
    pos = np.random.random((NWAT, 3)) * bsize
    wat = water.copy()

    s = System.empty(NWAT, NWAT*3, box_vectors=np.eye(3)*bsize)
    for i in range(NWAT):
        wat.move_to(pos[i])
        s.add(wat)

    prot.r_array += 10
    s = merge_systems(s, prot, 0.5)

    display_system(s, 'ball-and-stick')

def test_attributes():
    coords = [np.random.rand(10, 3) for i in range(10)]
    t = np.arange(0, 10, 0.1)
    traj = Trajectory(coords, t)
    system = System.from_arrays(r_array=coords[0])
    
    system.update(traj.at(1))    
    npeq_(system.r_array, coords[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_local():
    db = ChemlabDB()
    bz = db.get("molecule", "example.norbornene")

    pre_string = bz.tojson()
    db = LocalDB("/tmp/testdb/")
    db.store("molecule", 'norbornene', bz, nowarn=True)
    
    post_string = db.get('molecule', 'norbornene').tojson()
    assert pre_string == post_string
    
    # Do the same thing for a system of 3 norbornenes
    s = System([bz.copy() for i in range(3)])
    pre_string = s.tojson()
    db.store("system", 'norbornene-3', s, nowarn=True)
    post_string = db.get('system', 'norbornene-3').tojson()
    
    assert pre_string == post_string

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_local():
    db = ChemlabDB()
    bz = db.get("molecule", "example.norbornene")
    pre_dict = bz.to_dict()

    db = LocalDB("/tmp/testdb/")
    db.store("molecule", 'norbornene', bz, nowarn=True)
    
    post_dict = db.get('molecule', 'norbornene').to_dict()
    
    npeq_(pre_dict['r_array'], post_dict['r_array'])
    
    # Do the same thing for a system of 3 norbornenes
    s = System([bz.copy() for i in range(3)])
    pre_dict = s.to_dict()
    db.store("system", 'norbornene-3', s, nowarn=True)
    post_dict = db.get('system', 'norbornene-3').to_dict()
    
    npeq_(pre_dict['r_array'], post_dict['r_array'])

def test_display():
    d = Display('povray')
    s = System.from_arrays(type_array=['O', 'H', 'H'],
                           r_array=[[0.0, 0.0, 0.0], [0.15, 0.0, 0.0], [0.0, 0.15, 0.0]])
    d.system(s)
    
    s.r_array = s.r_array + 0.3
    d.system(s, alpha=0.5)
    
    d.render()

 def test_from_arrays(self):
     mols = self._make_molecules()
     system = System.from_arrays(
         r_array=np.concatenate([m.r_array for m in mols]),
         type_array=np.concatenate([m.type_array for m in mols]),
         bonds=np.concatenate([m.bonds + 3 * i for i, m in enumerate(mols)
                               ]),
         maps={
             ('atom', 'molecule'): [0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3],
             ('bond', 'molecule'): [0, 0, 1, 1, 2, 2, 3, 3]
         })
     self._assert_init(system)

    def test_atom_type(self):
        self.s = System.from_arrays(
            type_array=["Cl", "Cl", "O", "H", "H", "O", "H", "H", "O", "H", "H", "Na", "Na"],
            maps={("atom", "molecule"): [0, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 6]},
        )

        idx = self.s.where(atom_type="O")
        assert_npequal(
            idx["atom"], [False, False, True, False, False, True, False, False, True, False, False, False, False]
        )
        assert_npequal(idx["molecule"], [False, False, True, True, True, False, False])

        self.s = System.from_arrays(
            type_array=["Cl", "Cl", "O", "H", "H", "O", "H", "H", "O", "H", "H", "Na", "Na"],
            maps={("atom", "molecule"): [0, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 6]},
        )

        idx = self.s.where(atom_type=["Na", "Cl"])
        assert_npequal(
            idx["atom"], [True, True, False, False, False, False, False, False, False, False, False, True, True]
        )