Commit 5231d757 authored by nd-02110114's avatar nd-02110114
Browse files

♻️ refactor docs

parent bec9a6b4

deepchem/dock/docking.py

+1 −1
Original line number Diff line number Diff line
@@ -79,7 +79,7 @@ class Docker(object): 
    centroid: np.ndarray, optional (default None)

      The centroid to dock against. Is computed if not specified.

    box_dims: np.ndarray, optional (default None)

      Of shape `(3,)` holding the size of the box to dock. If not

      A numpy array of shape `(3,)` holding the size of the box to dock. If not

      specified is set to size of molecular complex plus 5 angstroms.

    exhaustiveness: int, optional (default 10)

      Tells pose generator how exhaustive it should be with pose

deepchem/dock/pose_generation.py

+2 −2
Original line number Diff line number Diff line
@@ -53,7 +53,7 @@ class PoseGenerator(object): 
    centroid: np.ndarray, optional (default None)

      The centroid to dock against. Is computed if not specified.

    box_dims: np.ndarray, optional (default None)

      Of shape `(3,)` holding the size of the box to dock. If not

      A numpy array of shape `(3,)` holding the size of the box to dock. If not

      specified is set to size of molecular complex plus 5 angstroms.

    exhaustiveness: int, optional (default 10)

      Tells pose generator how exhaustive it should be with pose
@@ -172,7 +172,7 @@ class VinaPoseGenerator(PoseGenerator): 
    centroid: np.ndarray, optional

      The centroid to dock against. Is computed if not specified.

    box_dims: np.ndarray, optional

      Of shape `(3,)` holding the size of the box to dock. If not

      A numpy array of shape `(3,)` holding the size of the box to dock. If not

      specified is set to size of molecular complex plus 5 angstroms.

    exhaustiveness: int, optional (default 10)

      Tells Autodock Vina how exhaustive it should be with pose

deepchem/dock/pose_scoring.py

+12 −12
Original line number Diff line number Diff line
@@ -10,9 +10,9 @@ def pairwise_distances(coords1: np.ndarray, coords2: np.ndarray) -> np.ndarray: 
  Parameters

  ----------

  coords1: np.ndarray

    Of shape `(N, 3)`

    A numpy array of shape `(N, 3)`

  coords2: np.ndarray

    Of shape `(M, 3)`

    A numpy array of shape `(M, 3)`



  Returns

  -------
@@ -28,7 +28,7 @@ def cutoff_filter(d: np.ndarray, x: np.ndarray, cutoff=8.0) -> np.ndarray: 
  Parameters

  ----------

  d: np.ndarray

    Pairwise distances matrix. Of shape `(N, M)`

    Pairwise distances matrix. A numpy array of shape `(N, M)`

  x: np.ndarray

    Matrix of shape `(N, M)`

  cutoff: float, optional (default 8)
@@ -48,7 +48,7 @@ def vina_nonlinearity(c: np.ndarray, w: float, Nrot: int) -> np.ndarray: 
  Parameters

  ----------

  c: np.ndarray

    Of shape `(N, M)`

    A numpy array of shape `(N, M)`

  w: float

    Weighting term

  Nrot: int
@@ -69,7 +69,7 @@ def vina_repulsion(d: np.ndarray) -> np.ndarray: 
  Parameters

  ----------

  d: np.ndarray

    Of shape `(N, M)`.

    A numpy array of shape `(N, M)`.



  Returns

  -------
@@ -87,7 +87,7 @@ def vina_hydrophobic(d: np.ndarray) -> np.ndarray: 
  Parameters

  ----------

  d: np.ndarray

    Of shape `(N, M)`.

    A numpy array of shape `(N, M)`.



  Returns

  -------
@@ -113,7 +113,7 @@ def vina_hbond(d: np.ndarray) -> np.ndarray: 
  Parameters

  ----------

  d: np.ndarray

    Of shape `(N, M)`.

    A numpy array of shape `(N, M)`.



  Returns

  -------
@@ -140,7 +140,7 @@ def vina_gaussian_first(d: np.ndarray) -> np.ndarray: 
  Parameters

  ----------

  d: np.ndarray

    Of shape `(N, M)`.

    A numpy array of shape `(N, M)`.



  Returns

  -------
@@ -165,7 +165,7 @@ def vina_gaussian_second(d: np.ndarray) -> np.ndarray: 
  Parameters

  ----------

  d: np.ndarray

    Of shape `(N, M)`.

    A numpy array of shape `(N, M)`.



  Returns

  -------
@@ -188,9 +188,9 @@ def weighted_linear_sum(w: np.ndarray, x: np.ndarray) -> np.ndarray: 
  Parameters

  ----------

  w: np.ndarray

    Of shape `(N,)`

    A numpy array of shape `(N,)`

  x: np.ndarray

    Of shape `(N,)`

    A numpy array of shape `(N,)`



  Returns

  -------
@@ -211,7 +211,7 @@ def vina_energy_term(coords1: np.ndarray, coords2: np.ndarray, 
  coords2: np.ndarray

    Molecular coordinates of shape `(M, 3)`

  weights: np.ndarray

    Of shape `(5,)`

    A numpy array of shape `(5,)`

  wrot: float

    The scaling factor for nonlinearity

  Nrot: int

deepchem/utils/coordinate_box_utils.py

+9 −9
Original line number Diff line number Diff line
@@ -98,7 +98,7 @@ class CoordinateBox(object): 


    Parameters

    ----------

    other: `CoordinateBox`

    other: CoordinateBox

      Compare this coordinate box to the other one.



    Returns
@@ -175,7 +175,7 @@ class CoordinateBox(object): 


    Parameters

    ----------

    other: `CoordinateBox`

    other: CoordinateBox

      The box to check is contained in this box.



    Returns
@@ -236,14 +236,14 @@ def intersection(box1: CoordinateBox, box2: CoordinateBox) -> CoordinateBox: 


  Parameters

  ----------

  box1: `CoordinateBox`

  box1: CoordinateBox

    First `CoordinateBox`

  box2: `CoordinateBox`

  box2: CoordinateBox

    Another `CoordinateBox` to intersect first one with.



  Returns

  -------

  `CoordinateBox`

  CoordinateBox

    A `CoordinateBox` containing the intersection. If the intersection is empty,

    returns the box with 0 bounds.

  """
@@ -260,14 +260,14 @@ def union(box1: CoordinateBox, box2: CoordinateBox) -> CoordinateBox: 


  Parameters

  ----------

  box1: `CoordinateBox`

  box1: CoordinateBox

    First box to merge in

  box2: `CoordinateBox`

  box2: CoordinateBox

    Second box to merge into this box



  Returns

  -------

  `CoordinateBox`

  CoordinateBox

    Smallest `CoordinateBox` that contains both `box1` and `box2`

  """

  x_min = min(box1.x_range[0], box2.x_range[0])
@@ -332,7 +332,7 @@ def get_face_boxes(coords: np.ndarray, pad: float = 5.0) -> List[CoordinateBox]: 
  Parameters

  ----------

  coords: np.ndarray

    Of shape `(N, 3)`. The coordinates of a molecule.

    A numpy array of shape `(N, 3)`. The coordinates of a molecule.

  pad: float, optional (default 5.0)

    The number of angstroms to pad.

deepchem/utils/genomics_utils.py

+5 −5
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ def seq_one_hot_encode(sequences: Union[np.ndarray, Iterator[Iterable[str]]], 


  Parameters

  ----------

  sequences: np.ndarray or Iterator[`Bio.SeqRecord`]

  sequences: np.ndarray or Iterator[Bio.SeqRecord]

    Iterable object of genetic sequences

  letters: str, optional (default "ATCGN")

    String with the set of possible letters in the sequences.
@@ -27,7 +27,7 @@ def seq_one_hot_encode(sequences: Union[np.ndarray, Iterator[Iterable[str]]], 
  Returns

  -------

  np.ndarray

    Shape `(N_sequences, N_letters, sequence_length, 1)`.

    A numpy array of shape `(N_sequences, N_letters, sequence_length, 1)`.

  """



  # The label encoder is given characters for ACGTN
@@ -68,7 +68,7 @@ def _seq_to_encoded(seq: Union[str, Iterable[str]], 


  Parameters

  ----------

  seq: str or `Bio.SeqRecord`

  seq: str or Bio.SeqRecord

    a genetic sequence

  letter_encoder: Dict[str, int]

    The keys are letters and the values are unique int values (like 0, 1, 2...).
@@ -80,7 +80,7 @@ def _seq_to_encoded(seq: Union[str, Iterable[str]], 
  Returns

  -------

  encoded_seq: np.ndarray

    Shape `(N_letters, sequence_length)`.

    A numpy array of shape `(N_letters, sequence_length)`.

  """

  encoded_seq = np.zeros((alphabet_length, sequence_length))

  seq_ints = [letter_encoder[s] for s in seq]
@@ -107,7 +107,7 @@ def encode_bio_sequence(fname: str, 
  Returns

  -------

  np.ndarray

    Shape `(N_sequences, N_letters, sequence_length, 1)`.

    A numpy array of shape `(N_sequences, N_letters, sequence_length, 1)`.



  Note

  ----

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