Commit 28002034 authored by nd-02110114's avatar nd-02110114
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parent f1ded1be

deepchem/feat/__init__.py

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@@ -26,7 +26,7 @@ from deepchem.feat.molecule_featurizers import CoulombMatrixEig 
from deepchem.feat.molecule_featurizers import RawFeaturizer

from deepchem.feat.molecule_featurizers import RDKitDescriptors

from deepchem.feat.molecule_featurizers import SmilesToImage

from deepchem.feat.molecule_featurizers import SmilesToSeq

from deepchem.feat.molecule_featurizers import SmilesToSeq, create_char_to_idx



# material featurizers

from deepchem.feat.material_featurizers import ElementPropertyFingerprint

deepchem/feat/base_classes.py

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@@ -232,9 +232,9 @@ class MolecularFeaturizer(Featurizer): 
    """

    try:

      from rdkit import Chem

      from rdkit.Chem.rdchem import Mol

      from rdkit.Chem import rdmolfiles

      from rdkit.Chem import rdmolops

      from rdkit.Chem.rdchem import Mol

    except ModuleNotFoundError:

      raise ValueError("This class requires RDKit to be installed.")

deepchem/feat/binding_pocket_features.py

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@@ -101,5 +101,6 @@ class BindingPocketFeaturizer(Featurizer): 
        if residue not in res_map:

          logger.info("Warning: Non-standard residue in PDB file")

          continue

        atomtype = atom_name.split("-")[1]

        all_features[pocket_num, res_map[residue]] += 1

    return all_features

deepchem/feat/molecule_featurizers/__init__.py

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@@ -6,6 +6,6 @@ from deepchem.feat.molecule_featurizers.coulomb_matrices import CoulombMatrixEig 
from deepchem.feat.molecule_featurizers.raw_featurizer import RawFeaturizer

from deepchem.feat.molecule_featurizers.rdkit_descriptors import RDKitDescriptors

from deepchem.feat.molecule_featurizers.smiles_to_image import SmilesToImage

from deepchem.feat.molecule_featurizers.smiles_to_seq import SmilesToSeq

from deepchem.feat.molecule_featurizers.smiles_to_seq import SmilesToSeq, create_char_to_idx

from deepchem.feat.molecule_featurizers.mol_graph_conv_featurizer import MolGraphConvFeaturizer

deepchem/feat/tests/test_one_hot.py

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import unittest

from deepchem.feat import OneHotFeaturizer





class TestOneHotFeaturizer(unittest.TestCase):

  """Tests for the one-hot featurizer."""



  def test_featurize(self):

    from rdkit import Chem

    smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O", "CC(=O)N1CN(C(C)=O)C(O)C1O"]

    mols = [Chem.MolFromSmiles(smile) for smile in smiles]

    featurizer = OneHotFeaturizer()

    one_hots = featurizer.featurize(mols)

    untransformed = featurizer.untransform(one_hots)

    assert len(smiles) == len(untransformed)

    for i in range(len(smiles)):

      assert smiles[i] == untransformed[i]

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