Test Featurizer

    num_mols = len(mols)

    atoms_per_mol = [mol.get_num_atoms() for mol in mols]

    # Get atoms by degree

    # Results should be sorted by (atom_degree, mol_index)

    atoms_by_deg = np.concatenate([x.atom_features for x in mols])

    degree_vector = np.concatenate([x.degree_list for x in mols], axis=0)

    # Mergesort is a "stable" sort, so the array maintains it's secondary sort of mol_index

    all_atoms = atoms_by_deg[degree_vector.argsort(kind='mergesort')]

    # Sort all atoms by degree.

from unittest import TestCase

import numpy as np

from deepchem.feat import ConvMolFeaturizer

from deepchem.feat.mol_graphs import ConvMol

from deepchem.molnet import load_bace_classification

class TestConvMol(TestCase):

  def get_molecules(self):

    tasks, all_dataset, transformers = load_bace_classification(

        featurizer="Raw")

    return all_dataset[0].X

  def test_mol_ordering(self):

    mols = self.get_molecules()

    featurizer = ConvMolFeaturizer()

    featurized_mols = featurizer.featurize(mols)

    for i in range(len(featurized_mols)):

      atom_features = featurized_mols[i].atom_features

      degree_list = np.expand_dims(featurized_mols[i].degree_list, axis=1)

      atom_features = np.concatenate([degree_list, atom_features], axis=1)

      featurized_mols[i].atom_features = atom_features

    conv_mol = ConvMol.agglomerate_mols(featurized_mols)

    for start, end in conv_mol.deg_slice.tolist():

      members = conv_mol.membership[start:end]

      sorted_members = np.array(sorted(members))

      members = np.array(members)

      self.assertTrue(np.all(sorted_members == members))

    conv_mol_atom_features = conv_mol.get_atom_features()

    adj_number = 0

    for start, end in conv_mol.deg_slice.tolist():

      deg_features = conv_mol_atom_features[start:end]

      adj_number_array = deg_features[:, 0]

      self.assertTrue(np.all(adj_number_array == adj_number))

      adj_number += 1