def test_len_check_pairs():
trj = md.load(get_fn('tip3p_test.trr'), top=get_fn('tip3p_test.gro'))
first = make_comtrj(trj[0])
first_direct = pairing.pairing._generate_direct_correlation(first,
cutoff=0.3)
check = pairing.check_pairs(trj, 0.3, first_direct)
assert len(check) == trj.n_frames
def test_check_pairs():
ref = np.asarray([[1, 0, 0, 0, 0], [0, 1, 0, 0, 0], [0, 0, 1, 0, 0],
[0, 0, 0, 1, 0], [0, 0, 0, 0, 1]])
trj = md.load(get_fn('tip3p_test.trr'), top=get_fn('tip3p_test.gro'))
first = make_comtrj(trj[0])
first_direct = pairing.pairing._generate_direct_correlation(first,
cutoff=0.3)
check = pairing.check_pairs(trj, 0.3, first_direct)
assert (check[20] == ref).all()
def test_cluster_analysis():
trj = md.load(get_fn('sevick1988.gro'))
direct = pairing.pairing._generate_direct_correlation(trj, cutoff=0.8)
indirect = pairing.pairing._generate_indirect_connectivity(direct)
reduction = pairing.pairing._generate_clusters(indirect)
assert pairing.analyze_clusters(reduction) == (2.5, 1.5)
def test_indirect_matrix_reduction():
trj = md.load(get_fn('sevick1988.gro'))
direct = pairing.pairing._generate_direct_correlation(trj, cutoff=0.8)
indirect = pairing.pairing._generate_indirect_connectivity(direct)
c_R = np.asarray([[0, 1], [0, 1], [0, 1], [1, 0], [0, 1]])
assert (c_R == pairing.pairing._generate_clusters(indirect)).all()
def test_generate_direct_correlation():
trj = md.load(get_fn('sevick1988.gro'))
ref = np.asarray([[1, 0, 0, 0, 1], [0, 1, 1, 0, 0], [0, 1, 1, 0, 1],
[0, 0, 0, 1, 0], [1, 0, 1, 0, 1]],
dtype=np.int32)
gen = pairing.pairing._generate_direct_correlation(trj, cutoff=0.8)
assert (ref == gen).all()
def test_len_indirect():
trj = md.load(get_fn('tip3p_test.trr'), top=get_fn('tip3p_test.gro'))
direct = pairing.calc_direct(trj, cutoff=0.3)
indirect = pairing.calc_indirect(direct)
assert len(indirect) == trj.n_frames
def test_40_atoms():
trj = md.load(get_fn('sevick1988.gro'))
direct = pairing.pairing._generate_direct_correlation(trj, cutoff=0.8)
indirect = pairing.pairing._generate_indirect_connectivity(direct)
assert indirect.dtype == np.int32