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Python System.from_arrays方法代码示例

本文整理汇总了Python中chemlab.core.System.from_arrays方法的典型用法代码示例。如果您正苦于以下问题：Python System.from_arrays方法的具体用法？Python System.from_arrays怎么用？Python System.from_arrays使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类chemlab.core.System的用法示例。


在下文中一共展示了System.from_arrays方法的11个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: test_attributes

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
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])
开发者ID:BrendonYim，项目名称:chemlab，代码行数:10，代码来源:test_trajectory.py

示例2: test_bonds

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
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')
开发者ID:cordor，项目名称:chemlab，代码行数:46，代码来源:test_core.py

示例3: test_display

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
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()
开发者ID:hainm，项目名称:chemlab，代码行数:12，代码来源:test_notebook.py

示例4: test_from_arrays

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
 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)
开发者ID:chemlab，项目名称:chemlab，代码行数:14，代码来源:test_core.py

示例5: test_atom_type

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
    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]
        )
开发者ID:mcanthony，项目名称:chemlab，代码行数:23，代码来源:test_core.py

示例6: test_from_arrays

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
    def test_from_arrays(self):
        mols = self._make_molecules()
        r_array = np.concatenate([m.r_array for m in mols])
        type_array = np.concatenate([m.type_array for m in mols])
        mol_indices = [0, 3, 6, 9]
        bonds = np.concatenate([m.bonds + 3*i for i, m in enumerate(mols)])

        system = System.from_arrays(r_array=r_array,
                                    type_array=type_array,
                                    mol_indices=mol_indices,
                                    bonds=bonds)

        self._assert_init(system)
开发者ID:cordor，项目名称:chemlab，代码行数:15，代码来源:test_core.py

示例7: test_atom_type

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
    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(type_array='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(type_array=['Na', 'Cl'])
        assert_npequal(idx['atom'],
                       [True, True, False, False, False, False, False, False,
                        False, False, False, True, True])
开发者ID:chemlab，项目名称:chemlab，代码行数:26，代码来源:test_core.py

示例8: test_query

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
def test_query():
    type_array = ['Cl', 'Cl', 'O', 'H', 'H', 'O', 'H', 'H', 'Na', 'Na']
    mol_indices = [0, 1, 2, 5, 8, 9]
    s = System.from_arrays(type_array = type_array, mol_indices=mol_indices)
    array_eq_(s.where(type_in=['Na', 'Cl']), 
              [True, True, False, False, False, False, False, False, True, True])
    
    array_eq_(s.where(type='Cl'), 
              [True, True, False, False, False, False, False, False, False, False])
    
    # We move the Cl away
    cl = s.where(type='Cl')
    s.r_array[cl.nonzero()[0]] = [1, 0, 0]
    s.box_vectors = np.diag([3, 3, 3])
    
    array_eq_(s.where(type_in=['H', 'O'], within_of=(0.2, [8, 9])),
             [False, False, True, True, True, True, True, True, False, False])

    array_eq_(s.where(type_in=['H', 'O'], within_of=(0.2, 8)),
             [False, False, True, True, True, True, True, True, False, False])

    array_eq_(s.where(type_in=['H', 'O'], within_of=(0.2, [8])),
             [False, False, True, True, True, True, True, True, False, False])
开发者ID:hainm，项目名称:chemlab，代码行数:25，代码来源:test_query.py

示例9: test_query

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
def test_query():
    type_array = ['Cl', 'Cl', 'O', 'H', 'H', 'O', 'H', 'H', 'Na', 'Na']
    maps = {('atom', 'molecule'): [0, 1, 2, 2, 2, 3, 3, 3, 4, 5]}
    s = System.from_arrays(type_array = type_array, maps=maps)
    
    assert_npequal(s.where(type_array=['Na', 'Cl'])['atom'], 
              [True, True, False, False, False, False, False, False, True, True])
    
    assert_npequal(s.where(type_array='Cl')['atom'], 
              [True, True, False, False, False, False, False, False, False, False])
    
    # We move the Cl away
    cl = s.where(type_array='Cl')['atom']
    s.r_array[cl.nonzero()[0]] = [1, 0, 0]
    s.box_vectors = np.diag([3, 3, 3])
    
    assert_npequal(s.where(type_array=['H', 'O'], within_of=(0.2, [8, 9]))['atom'],
             [False, False, True, True, True, True, True, True, False, False])

    assert_npequal(s.where(type_array=['H', 'O'], within_of=(0.2, 8))['atom'],
             [False, False, True, True, True, True, True, True, False, False])

    assert_npequal(s.where(type_array=['H', 'O'], within_of=(0.2, [8]))['atom'],
             [False, False, True, True, True, True, True, True, False, False])
开发者ID:chemlab，项目名称:chemlab，代码行数:26，代码来源:test_core.py

示例10: setup

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
 def setup(self):
     self.s = System.from_arrays(
         type_array=['O', 'H', 'H', 'O', 'H', 'H', 'O', 'H', 'H'],
         maps={('atom', 'molecule'): [0, 0, 0, 1, 1, 1, 2, 2, 2]})
开发者ID:chemlab，项目名称:chemlab，代码行数:6，代码来源:test_core.py

示例11: setup

# 需要导入模块: from chemlab.core import System [as 别名]
# 或者: from chemlab.core.System import from_arrays [as 别名]
 def setup(self):
     self.s = System.from_arrays(
         type_array=["O", "H", "H", "O", "H", "H", "O", "H", "H"],
         maps={("atom", "molecule"): [0, 0, 0, 1, 1, 1, 2, 2, 2]},
     )
开发者ID:mcanthony，项目名称:chemlab，代码行数:7，代码来源:test_core.py


注：本文中的chemlab.core.System.from_arrays方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。