Пример #1
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def test_ring():
    """Test the Ring object from the ring module."""
    num_slots = 10
    # num_filled = 2
    num_geoms = 3
    num_atoms = 24
    # t_size = 7
    # num_muts = 3
    # num_swaps = 1
    pmem_dist = 2
    parser = Xyz(os.path.join(TEST_DIR, "caffeine.xyz"))
    parser.charge = 0
    parser.multip = 1
    ring = Ring(num_geoms, num_atoms, num_slots, pmem_dist, 0, 0.5, 0.5, parser)
    # check that ring has its attributes
    assert ring.parser.charge == 0
    assert ring.parser.multip == 1
    assert ring.num_slots == 10
    assert ring.num_filled == 0
    assert ring.num_geoms == 3
    assert ring.num_atoms == 24
    assert ring.pmem_dist == 2
    assert ring.fit_form == 0
    assert ring.coef_energy == 0.5
    assert ring.coef_rmsd == 0.5
    assert ring.pmems.shape == (10,)
    assert all([ring.pmems[i] is None for i in range(10)])
    # check that the zmatrix is the same as the
    # zmatrix that comes out of the openbabel gui
    czmat = CAFFEINE_ZMATRIX.split('\n')
    ring_czmat = ring.zmatrix.split('\n')
    assert len(czmat) == len(ring_czmat)
    for i, val in enumerate(czmat):
        assert val == ring_czmat[i]
Пример #2
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def test_ring_getitem():
    """Test the Ring.__getitem__ method."""
    parser = Xyz(os.path.join(TEST_DIR, "1,3-butadiene.xyz"))
    parser.charge = 0
    parser.multip = 1
    ring = Ring(3, 10, 15, 2, 0, 0.5, 0.5, parser)
    ring.fill(5, 0)
    for i in range(5):
        assert ring[i].birthday == 0
    assert ring[5] is None
    with assert_raises(KeyError):
        ring[1000]
        ring['one']
Пример #3
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def test_run_tournament():
    """Test run_tournament function from tournament module."""
    # ring init:
    # num_geoms, num_atoms, num_slots, pmem_dist, fit_form,
    # coef_energy, coef_rmsd, parser
    mol = Xyz(os.path.join(TEST_DIR, "1,3-butadiene.xyz"))
    mol.charge = 0
    mol.multip = 1
    ring = Ring(3, 10, 20, 2, 0, 0.5, 0.5, mol)
    ring.fill(3, 0)
    # tournament call:
    # t_size, num_muts, num_swaps, ring, current_mev
    # check that an empty ring error is raised when trying to
    # run a tournament size that is too big
    assert_raises(RingEmptyError, run_tournament, 7, 0, 0, ring, 0)
    run_tournament(2, 0, 0, ring, 0)
Пример #4
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def test_ring_setitem():
    """Test the Ring.__setitem__ method."""
    parser = Xyz(os.path.join(TEST_DIR, "1,3-butadiene.xyz"))
    parser.charge = 0
    parser.multip = 1
    ring = Ring(3, 10, 15, 2, 0, 0.5, 0.5, parser)
    with assert_raises(KeyError):
        ring[1000] = Pmem(1000, 3, 10, 1)
        ring['two'] = Pmem(2, 3, 10, 1)
        ring[1] = 'string'
    with assert_raises(AssertionError):
        ring[4] = Pmem(3, 3, 10, 1)
        ring[3] = Pmem(4, 2, 10, 1)
        ring[2] = Pmem(2, 3, 9, 1)
    ring.fill(1, 0)
    assert ring.num_filled == 1
    ring[0] = None
    assert ring.num_filled == 0
Пример #5
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def test_ring_fill():
    """Test the Ring.fill method."""
    parser = Xyz(os.path.join(TEST_DIR, "1,3-butadiene.xyz"))
    parser.charge = 0
    parser.multip = 1
    ring = Ring(3, 10, 15, 2, 0, 0.5, 0.5, parser)
    # try to put more pmems in than there are slots
    assert_raises(RingOverflowError, ring.fill, 200, 0)
    assert ring.num_filled == 0
    ring.fill(1, 0)
    assert ring.num_filled == 1
    # same test twice except getitem syntax can be used
    assert ring.pmems[0].birthday == 0
    assert ring[0].birthday == 0
    ring.fill(5, 1)
    assert ring.num_filled == 6
    assert ring[1].birthday == 1
    # test adding without contiguous segment present
    ring[9] = Pmem(9, 3, 10, 2)
    ring.fill(5, 3)
    assert ring.num_filled == 12
    assert ring[11] is not None
    assert ring[12] is None
    assert ring[8].birthday == 3
Пример #6
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def test_ring_update():
    """Test the Ring.update method."""
    # parent_index, child, current_mev
    parser = Xyz(os.path.join(TEST_DIR, "1,3-butadiene.xyz"))
    parser.charge = 0
    parser.multip = 1
    ring = Ring(3, 10, 15, 2, 0, 0.5, 0.5, parser)
    # ring is empty, try adding random pmems
    # testing backflow
    ring.update(0, [[1, 2, 3, 4, 5, 6, 7], [1, 2, 3, 4, 2, 1, 1],
                    [7, 6, 5, 4, 3, 2, 1]], 0)
    # possible places the update took place
    slots = [0, 1, 2, 13, 14]
    not_slots = [3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
    assert sum(ring[i] is not None for i in slots) == 1
    assert all(ring[i] is None for i in not_slots)
    ring[0] = None
    ring[1] = None
    ring[2] = None
    ring[13] = None
    ring[14] = None
    # test case where pmem_dist is zero
    ring.pmem_dist = 0
    ring.update(0, [[1, 2, 3, 4, 5, 6, 7], [1, 2, 3, 4, 2, 1, 1],
                    [7, 6, 5, 4, 3, 2, 1]], 0)
    assert ring[0] is not None
    assert sum(ring[i] is not None for i in range(ring.num_slots)) == 1
    # test overflow
    ring[0] = None
    ring.pmem_dist = 4
    ring.update(13, [[1, 2, 3, 4, 5, 6, 7], [1, 2, 3, 4, 2, 1, 1],
                     [7, 6, 5, 4, 3, 2, 1]], 0)
    slots = [13, 14, 0, 1, 2, 9, 10, 11, 12]
    assert (sum(ring[i] is not None for i in slots)) == 1
    not_slots = [3, 4, 5, 6, 7, 8]
    assert all(ring[i] is None for i in not_slots)
    # test no overflow or backflow (now, pmem dist is 4)
    for slot in slots:
        ring[slot] = None
    ring.update(7, [[1, 2, 3, 4, 5, 6, 7], [1, 2, 3, 4, 2, 1, 1],
                    [7, 6, 5, 4, 3, 2, 1]], 0)
    slots = [7, 8, 9, 10, 11, 3, 4, 5, 6]
    assert (sum(ring[i] is not None for i in slots)) == 1
    not_slots = [0, 1, 2, 12, 13, 14]
    assert all(ring[i] is None for i in not_slots)
    for slot in slots:
        ring[slot] = None
    # now check that slot is not updated if child has worse fitness
    ring.pmem_dist = 0
    # fitness = 230.09933808553276
    ring[0] = Pmem(0, 3, 10, 0, [[239, 278, 5, 248, 40, 67, 299],
                                 [36, 123, 295, 111, 322, 267, 170],
                                 [61, 130, 26, 139, 290, 238, 331]])
    ring.set_fitness(0)
    # fitness = 77.4576053229711
    ring.update(0, [[132, 272, 40, 226, 44, 154, 339],
                    [182, 119, 106, 157, 194, 244, 168],
                    [95, 81, 202, 261, 197, 166, 161]], 1)
    assert ring[0].dihedrals == [[239, 278, 5, 248, 40, 67, 299],
                                 [36, 123, 295, 111, 322, 267, 170],
                                 [61, 130, 26, 139, 290, 238, 331]]
    assert ring.num_filled == 1
    assert ring[0].birthday == 0