test_featurizer.py 文件源码

def test_Group_Mindist_All_Three_Groups_threshold(self):
        threshold = .7
        group0 = [0, 20, 30, 0]
        group1 = [1, 21, 31, 1]
        group2 = [2, 22, 32, 2]
        self.feat.add_group_mindist(group_definitions=[group0, group1, group2], threshold=threshold)
        D = self.feat.transform(self.traj)

        # Now the references, computed separately for each combination of groups
        dist_list_01 = np.array(list(product(np.unique(group0), np.unique(group1))))
        dist_list_02 = np.array(list(product(np.unique(group0), np.unique(group2))))
        dist_list_12 = np.array(list(product(np.unique(group1), np.unique(group2))))
        Dref_01 = mdtraj.compute_distances(self.traj, dist_list_01).min(1)
        Dref_02 = mdtraj.compute_distances(self.traj, dist_list_02).min(1)
        Dref_12 = mdtraj.compute_distances(self.traj, dist_list_12).min(1)
        Dref = np.vstack((Dref_01, Dref_02, Dref_12)).T

        Dbinary = np.zeros_like(Dref)
        I = np.argwhere(Dref <= threshold)
        Dbinary[I[:, 0], I[:, 1]] = 1

        assert np.allclose(D, Dbinary)
        assert len(self.feat.describe())==self.feat.dimension()