def test_calculate_rmsd_3(self):
distogram_1 = Distogram("test_1")
distogram_1.add(Distance(1, 5, (0.25, 0.45, 0.05, 0.05, 0.2), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.add(Distance(2, 3, (0.15, 0.15, 0.60, 0.1, 0.0), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.add(Distance(1, 4, (0.05, 0.2, 0.0, 0.6, 0.15), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.add(Distance(3, 5, (0.4, 0.1, 0.35, 0.05, 0.1), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.sequence = conkit.core.Sequence("test_seq", "AAAAA")
distogram_2 = Distogram("test_2")
distogram_2.add(Distance(1, 5, (0.45, 0.05, 0.25, 0.25), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.add(Distance(2, 3, (0.1, 0.15, 0.15, 0.6), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.add(Distance(1, 4, (0.75, 0.20, 0.05, 0.0), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.add(Distance(3, 5, (0.05, 0.1, 0.35, 0.5), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.add(Distance(1, 6, (0.5, 0.1, 0.35, 0.05), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.sequence = conkit.core.Sequence("test_seq", "AAAAA")
with self.assertRaises(ValueError):
Distogram.calculate_rmsd(distogram_1, distogram_2, seq_len=5, calculate_wrmsd=True)
def test_calculate_rmsd_2(self):
distogram_1 = Distogram("test_1")
distogram_1.add(Distance(1, 5, (0.25, 0.45, 0.05, 0.05, 0.2), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.add(Distance(2, 3, (0.15, 0.15, 0.60, 0.1, 0.0), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.add(Distance(1, 4, (0.05, 0.2, 0.0, 0.6, 0.15), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.add(Distance(3, 5, (0.4, 0.1, 0.35, 0.05, 0.1), ((0, 4), (4, 6), (6, 8), (8, 10), (10, np.inf))))
distogram_1.sequence = conkit.core.Sequence("test_seq", "AAAAA")
distogram_2 = Distogram("test_2")
distogram_2.add(Distance(1, 5, (0.45, 0.05, 0.25, 0.25), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.add(Distance(2, 3, (0.1, 0.15, 0.15, 0.6), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.add(Distance(1, 4, (0.75, 0.20, 0.05, 0.0), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.add(Distance(3, 5, (0.05, 0.1, 0.35, 0.5), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
distogram_2.sequence = conkit.core.Sequence("test_seq", "AAAAA")
output = Distogram.calculate_rmsd(distogram_1, distogram_2, seq_len=5, calculate_wrmsd=True)
expected = [4.09, 2.324, 3.937, 5.422, 3.85]
self.assertListEqual(expected, [round(x, 3) for x in output])
def get_rmsd(distogram_1, distogram_2, calculate_wrmsd=True):
"""Calculate the RMSD between two different distograms
Parameters
----------
distogram_1 : :obj:`~conkit.core.distogram.Distogram`
Distogram 1
distogram_2 : :obj:`~conkit.core.distogram.Distogram`
Distogram 2
calculate_wrmsd: bool
If True then the WRMSD is calculated using the confidence scores from distogram 1
Returns
-------
tuple
Two lists with the raw/smoothed RMSD values at each residue position
"""
rmsd_raw = Distogram.calculate_rmsd(distogram_1,
distogram_2,
calculate_wrmsd=calculate_wrmsd)
rmsd_smooth = convolution_smooth_values(np.nan_to_num(rmsd_raw), 10)
return rmsd_raw, rmsd_smooth
