Unverified Commit d997acf3 authored by Bharath Ramsundar's avatar Bharath Ramsundar Committed by GitHub
Browse files

Merge pull request #2031 from nd-02110114/improve-mor-type 

Improve type of some utils function
parents ce379457 6621447b

deepchem/data/data_loader.py

+2 −2
Original line number Diff line number Diff line
@@ -17,7 +17,7 @@ from typing import List, Optional, Dict, Tuple, Any, Sequence, Union 
from deepchem.utils.typing import OneOrMany

from deepchem.utils.save import load_csv_files, load_json_files

from deepchem.utils.save import load_sdf_files

from deepchem.utils.genomics import encode_fasta_sequence

from deepchem.utils.genomics_utils import encode_bio_sequence

from deepchem.feat import UserDefinedFeaturizer, Featurizer

from deepchem.data import Dataset, DiskDataset, NumpyDataset, ImageDataset

import zipfile
@@ -725,7 +725,7 @@ class FASTALoader(DataLoader): 


    def shard_generator():

      for input_file in input_files:

        X = encode_fasta_sequence(input_file)

        X = encode_bio_sequence(input_file)

        ids = np.ones(len(X))

        # (X, y, w, ids)

        yield X, None, None, ids

deepchem/dock/binding_pocket.py

+2 −2
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ from deepchem.models import Model 
from deepchem.utils.rdkit_util import load_molecule

from deepchem.utils.coordinate_box_utils \

  import CoordinateBox, get_face_boxes, merge_overlapping_boxes

from deepchem.utils.fragment_util import get_contact_atom_indices

from deepchem.utils.fragment_utils import get_contact_atom_indices



logger = logging.getLogger(__name__)
@@ -90,7 +90,7 @@ class ConvexHullPocketFinder(BindingPocketFinder): 


    Parameters

    ----------

    scoring_model: `dc.models.Model`, optional

    scoring_model: Model, optional (default None)

      If specified, use this model to prune pockets.

    pad: float, optional (default 5.0)

      The number of angstroms to pad around a binding pocket's atoms

deepchem/dock/docking.py

+15 −10
Original line number Diff line number Diff line
@@ -3,15 +3,17 @@ Docks Molecular Complexes 
"""

import logging

import tempfile

from typing import cast, Optional, Tuple

from typing import cast, Generator, Optional, Tuple, Union

import numpy as np



from deepchem.utils.typing import RDKitMol

from deepchem.models import Model

from deepchem.feat import ComplexFeaturizer

from deepchem.data import NumpyDataset

from deepchem.dock import PoseGenerator



logger = logging.getLogger(__name__)

POSED_COMPLEX = Tuple[RDKitMol, RDKitMol]





class Docker(object):
@@ -36,11 +38,11 @@ class Docker(object): 


    Parameters

    ----------

    pose_generator: `PoseGenerator`

    pose_generator: PoseGenerator

      The pose generator to use for this model

    featurizer: `ComplexFeaturizer`, optional (default None)

    featurizer: ComplexFeaturizer, optional (default None)

      Featurizer associated with `scoring_model`

    scoring_model: `Model`, optional (default None)

    scoring_model: Model, optional (default None)

      Should make predictions on molecular complex.

    """

    if ((featurizer is not None and scoring_model is None) or
@@ -60,7 +62,9 @@ class Docker(object): 
           num_modes: int = 9,

           num_pockets: Optional[int] = None,

           out_dir: Optional[str] = None,

           use_pose_generator_scores: bool = False):

           use_pose_generator_scores: bool = False

          ) -> Union[Generator[POSED_COMPLEX, None, None], Generator[Tuple[

              POSED_COMPLEX, float], None, None]]:

    """Generic docking function.



    This docking function uses this object's featurizer, pose
@@ -69,13 +73,13 @@ class Docker(object): 


    Parameters

    ----------

    molecular_complex: Tuple[str]

    molecular_complex: Tuple[str, str]

      A representation of a molecular complex. This tuple is

      (protein_file, ligand_file).

    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
@@ -96,6 +100,7 @@ class Docker(object): 


    Returns

    -------

    Generator[Tuple[`posed_complex`, `score`]] or Generator[`posed_complex`]

      A generator. If `use_pose_generator_scores==True` or

      `self.scoring_model` is set, then will yield tuples

      `(posed_complex, score)`. Else will yield `posed_complex`.

deepchem/dock/pose_generation.py

+18 −14
Original line number Diff line number Diff line
@@ -9,16 +9,17 @@ import tarfile 
import numpy as np

from subprocess import call

from subprocess import check_output

from typing import Optional, Tuple

from typing import List, Optional, Tuple, Union



from deepchem.dock.binding_pocket import BindingPocketFinder

from deepchem.utils import download_url, get_data_dir

from deepchem.utils.mol_xyz_util import get_molecule_range

from deepchem.utils.geometry_utils import compute_centroid

from deepchem.utils.typing import RDKitMol

from deepchem.utils.geometry_utils import compute_centroid, compute_protein_range

from deepchem.utils.rdkit_util import load_molecule, write_molecule

from deepchem.utils.vina_utils import load_docked_ligands, write_vina_conf



logger = logging.getLogger(__name__)

DOCKED_POSES = List[Tuple[RDKitMol, RDKitMol]]





class PoseGenerator(object):
@@ -52,7 +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
@@ -102,7 +103,7 @@ class VinaPoseGenerator(PoseGenerator): 
    sixty_four_bits: bool, optional (default True)

      Specifies whether this is a 64-bit machine. Needed to download

      the correct executable.

    pocket_finder: object, optional (default None)

    pocket_finder: BindingPocketFinder, optional (default None)

      If specified should be an instance of

      `dc.dock.BindingPocketFinder`.

    """
@@ -156,20 +157,22 @@ class VinaPoseGenerator(PoseGenerator): 
                     num_modes: int = 9,

                     num_pockets: Optional[int] = None,

                     out_dir: Optional[str] = None,

                     generate_scores: bool = False):

                     generate_scores: bool = False

                    ) -> Union[Tuple[DOCKED_POSES, List[float]], DOCKED_POSES]:

    """Generates the docked complex and outputs files for docked complex.



    TODO: How can this work on Windows? We need to install a .msi file and invoke it correctly from Python for this to work.

    TODO: How can this work on Windows? We need to install a .msi file and

    invoke it correctly from Python for this to work.



    Parameters

    ----------

    molecular_complexes: Tuple[str]

    molecular_complexes: Tuple[str, str]

      A representation of a molecular complex. This tuple is

      (protein_file, ligand_file).

    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
@@ -190,10 +193,11 @@ class VinaPoseGenerator(PoseGenerator): 


    Returns

    -------

    Tuple of `(docked_poses, scores)`. `docked_poses` is a list of

    docked molecular complexes. Each entry in this list contains a

    `(protein_mol, ligand_mol)` pair of RDKit molecules. `scores` is a

    list of binding free energies predicted by Vina.

    Tuple[`docked_poses`, `scores`] or `docked_poses`

      Tuple of `(docked_poses, scores)` or `docked_poses`. `docked_poses`

      is a list of docked molecular complexes. Each entry in this list

      contains a `(protein_mol, ligand_mol)` pair of RDKit molecules.

      `scores` is a list of binding free energies predicted by Vina.



    Raises

    ------
@@ -232,7 +236,7 @@ class VinaPoseGenerator(PoseGenerator): 
      if self.pocket_finder is None:

        logger.info("Pockets not specified. Will use whole protein to dock")

        protein_centroid = compute_centroid(protein_mol[0])

        protein_range = get_molecule_range(protein_mol[0])

        protein_range = compute_protein_range(protein_mol[0])

        box_dims = protein_range + 5.0

        centroids, dimensions = [protein_centroid], [box_dims]

      else:

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

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