def test_nnang_spread_10mols45():
#initialize dummy snapshot
trj = op.join(data_path, 'DFAG.gro')
ats = 29
molno = 1
t = 0
cutoff = 1.
ainds = np.arange(0, 3)
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
#reset all snapshot properties
snap.nclusts = 1
snap.box = np.array([30, 30, 30])
snap.clusterIDs = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
snap.pos = np.array([[0., 0., 0., 1., 0., 0., 2., 0., 0.],
[0., 1., 0., 1., 1., 0., 2., 1., 0.],
[0., 2., 0., 1., 2., 0., 2., 2., 0.],
[0., 3., 0., 1., 3., 0., 2., 3., 0.],
[0., 4., 0., 1., 4., 0., 2., 4., 0.],
[
1 - np.sin(np.pi / 4), 5., 0. - np.cos(np.pi / 4),
1., 5., 0., 1. + np.sin(np.pi / 4), 5.,
np.cos(np.pi / 4)
], [0., 6., 0., 1., 6., 0., 2., 6., 0.],
[0., 7., 0., 1., 7., 0., 2., 7., 0.],
[0., 8., 0., 1., 8., 0., 2., 8., 0.],
[0., 9., 0., 1., 9., 0., 2., 9., 0.]])
snap.setClusterID(cutoff)
angMat = snap.nnangSpread(ainds)
expangMat = np.array([[10, 0.17453292519943295, 0.34632803675275337]])
npt.assert_array_almost_equal(angMat, expangMat)
def test_contactXTC_clustering_contact():
"""
Make sure we cluster correctly for contact cluster from xtc/gro
"""
trj = op.join(data_path, 'contact_test.gro')
ats = 5
molno = 2
t = 0
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
snap.setClusterID(1.0)
assert (snap.nclusts == 1)
def test_nnang_spread_1mol():
"""
For one molecule, the output should be an empty matrix
"""
trj = op.join(data_path, 'DFAG.gro')
ats = 29
molno = 1
t = 0
cutoff = 0.5
ainds = np.arange(9, 20)
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
snap.setClusterID(cutoff)
angMat = snap.nnangSpread(ainds)
expangMat = np.array([])
#pdb.set_trace()
npt.assert_array_almost_equal(angMat, expangMat)
def test_contactXTC_init_optical():
"""
Test initializing an optical cluster from xtc/gro
"""
trj = op.join(data_path, 'optical_test.gro')
ats = 5
molno = 2
t = 0
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
pos = np.array(
[[0., 0., 0., 0.5, 0., 0., 0.75, 0.443, 0., 1., 0., 0., 1.5, 0., 0.],
[
0., 0., 0.5, 0.5, 0., 0.5, 0.75, 0.443, 0.5, 1., 0., 0.5, 1.5, 0.,
0.5
]])
npt.assert_array_equal(snap.pos, pos)
def test_contactXTC_init_contact():
"""
Test initializing a contact cluster from xtc/gro
"""
trj = op.join(data_path, 'contact_test.gro')
ats = 5
molno = 2
t = 0
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
pos = np.array([[
0., 0., 0., 0.354, 0.354, 0.0, 0.604, 0.8, 0.0, 0.854, 0.354, 0.0,
1.207, 0.0, 0.0
],
[
0.0, -0.8, 0.0, 0.354, -1.154, 0.0, 0.604, -1.6, 0.0,
0.854, -1.154, 0.0, 1.207, -0.8, 0.0
]])
npt.assert_array_equal(snap.pos, pos)
def test_ang_spread_2mols_rotate_long90():
#initialize dummy snapshot
trj = op.join(data_path, 'DFAG.gro')
ats = 29
molno = 1
t = 0
cutoff = 20. * 20.
ainds = np.arange(0, 3)
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
snap.setClusterID(cutoff)
#reset all snapshot properties
snap.nclusts = 1
snap.box = np.array([20, 20, 20])
snap.clusterIDs = [0, 0]
snap.pos = np.array([[0., 0., 0., 1., 0., 0., 2., 0., 0.],
[1., 10., 1., 1., 10., 0., 1., 10., -1.]])
angMat = snap.angSpread(cutoff, ainds)
expangMat = np.array([[2, 1.1107, 0.]])
npt.assert_array_almost_equal(angMat, expangMat, decimal=4)
def test_ang_spread_2mols_no_rotate_short():
"""
two molecules parallel to one another should have an angle spread of 0
the mean projection should depend on how far apart they are (because it
depends on the direction of the principal gyration tensor)
"""
#initialize dummy snapshot
trj = op.join(data_path, 'DFAG.gro')
ats = 29
molno = 1
t = 0
cutoff = 2.
ainds = np.arange(0, 3)
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
snap.setClusterID(cutoff)
#reset all snapshot properties
snap.nclusts = 1
snap.box = np.array([20, 20, 20])
snap.clusterIDs = [0, 0]
snap.pos = np.array([[0., 0., 0., 1., 0., 0., 2., 0., 0.],
[0., 1., 0., 1., 1., 0., 2., 1., 0.]])
angMat = snap.angSpread(cutoff, ainds)
expangMat = np.array([[2, 0., 1.]])
npt.assert_array_almost_equal(angMat, expangMat)
def test_nnang_spread_2mols_no_rotate_short():
"""
two molecules parallel to one another should make an angle of 0 and
by definition stddev should be 0
"""
#initialize dummy snapshot
trj = op.join(data_path, 'DFAG.gro')
ats = 29
molno = 1
t = 0
cutoff = 2.
ainds = np.arange(0, 3)
snap = cl.ContactClusterSnapshotXTC(t, trj, ats, molno)
#reset all snapshot properties
snap.nclusts = 1
snap.box = np.array([20, 20, 20])
snap.clusterIDs = [0, 0]
snap.pos = np.array([[0., 0., 0., 1., 0., 0., 2., 0., 0.],
[0., 1., 0., 1., 1., 0., 2., 1., 0.]])
snap.setClusterID(cutoff)
angMat = snap.nnangSpread(ainds)
expangMat = np.array([[2, 0., 0.]])
npt.assert_array_almost_equal(angMat, expangMat)