Commit 313d3a60 authored by nd-02110114's avatar nd-02110114
Browse files

👌 fix typo and update docstrings

parent c02779bd
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+13 −13
Original line number Diff line number Diff line
@@ -13,12 +13,12 @@ from deepchem.utils.graph_conv_utils import get_atom_type_one_hot, \
  get_bond_stereo_one_hot


def constrcut_atom_feature(atom: RDKitAtom, h_bond_infos: List[Tuple[int, str]],
def construct_atom_feature(atom: RDKitAtom, h_bond_infos: List[Tuple[int, str]],
                           sssr: List[Sequence]) -> List[float]:
  """Construct an atom feature from a RDKit atom object.

  Parameters
  ---------
  ----------
  atom: rdkit.Chem.rdchem.Atom
    RDKit atom object
  h_bond_infos: List[Tuple[int, str]]
@@ -32,7 +32,7 @@ def constrcut_atom_feature(atom: RDKitAtom, h_bond_infos: List[Tuple[int, str]],

  Returns
  -------
  List[Union[int, float]]
  List[float]
    A one-hot vector of the atom feature.
  """
  atom_type = get_atom_type_one_hot(atom)
@@ -59,7 +59,7 @@ def construct_bond_feature(bond: RDKitBond) -> List[float]:

  Returns
  -------
  List[int]
  List[float]
    A one-hot vector of the bond feature.
  """
  bond_type = get_bond_type_one_hot(bond)
@@ -72,10 +72,10 @@ def construct_bond_feature(bond: RDKitBond) -> List[float]:
class MolGraphConvFeaturizer(MolecularFeaturizer):
  """This class is a featurizer of gerneral graph convolution networks for molecules.

  The default node(atom) and edge(bond) representations are based on WeaveNet paper.
  If you want to use your own representations, you could use this class as a guide
  to define your original Featurizer. In many cases, it's enough to modify return values of
  `constrcut_atom_feature` or `constrcut_bond_feature`.
  The default node(atom) and edge(bond) representations are based on
  `WeaveNet paper <https://arxiv.org/abs/1603.00856>`_. If you want to use your own representations,
  you could use this class as a guide to define your original Featurizer. In many cases, it's enough
  to modify return values of `construct_atom_feature` or `construct_bond_feature`.

  The default node representation are constructed by concatenating the following values,
  and the feature length is 38.
@@ -126,8 +126,8 @@ class MolGraphConvFeaturizer(MolecularFeaturizer):

  def __init__(self, add_self_loop: bool = False):
    """
    Paramters
    ---------
    Parameters
    ----------
    add_self_loop: bool, default False
      Whether to add self-connected edges or not. If you want to use DGL,
      you sometimes need to add explict self-connected edges.
@@ -137,8 +137,8 @@ class MolGraphConvFeaturizer(MolecularFeaturizer):
  def _featurize(self, mol: RDKitMol) -> GraphData:
    """Calculate molecule graph features from RDKit mol object.

    Parametrs
    ---------
    Parameters
    ----------
    mol: rdkit.Chem.rdchem.Mol
      RDKit mol object.

@@ -166,7 +166,7 @@ class MolGraphConvFeaturizer(MolecularFeaturizer):
    # construct atom (node) feature
    atom_features = np.array(
        [
            constrcut_atom_feature(atom, h_bond_infos, sssr)
            construct_atom_feature(atom, h_bond_infos, sssr)
            for atom in mol.GetAtoms()
        ],
        dtype=np.float,
+4 −11
Original line number Diff line number Diff line
@@ -19,21 +19,14 @@ def test_gat_classification():
  featurizer = MolGraphConvFeaturizer()
  tasks, dataset, transformers, metric = get_dataset(
      'regression', featurizer=featurizer)
  n_tasks = len(tasks)

  # initialize models
  n_tasks = len(tasks)
  model = GATModel(
      in_node_dim=25,
      hidden_node_dim=64,
      heads=1,
      num_conv=3,
      predicator_hidden_feats=32,
      n_tasks=n_tasks,
      loss=losses.L2Loss(),
      batch_size=10,
      learning_rate=0.001)
      n_tasks=n_tasks, loss=losses.L2Loss(), batch_size=4, learning_rate=0.001)

  # overfit test
  model.fit(dataset, nb_epoch=100)
  scores = model.evaluate(dataset, [metric], transformers)
  assert scores['mean_absolute_error'] < 0.1
  # TODO: check this asseration is correct or not
  assert scores['mean_absolute_error'] < 1.0
+1 −1
Original line number Diff line number Diff line
@@ -302,7 +302,7 @@ def get_atom_formal_charge(atom: RDKitAtom) -> List[float]:
  List[float]
    A vector of the formal charge.
  """
  return [atom.GetFormalCharge()]
  return [float(atom.GetFormalCharge())]


def get_atom_partial_charge(atom: RDKitAtom) -> List[float]: