Unverified Commit b41f5f4e authored by Daiki Nishikawa's avatar Daiki Nishikawa Committed by GitHub
Browse files

Merge pull request #2088 from nd-02110114/fix-docs-rdkit 

Clarify rdkit type annotation
parents 37e61ee9 f7c12790

deepchem/dock/pose_generation.py

+10 −10
Original line number Diff line number Diff line
@@ -88,8 +88,8 @@ class VinaPoseGenerator(PoseGenerator): 
  is an environment variable you set) and invokes the executable

  to perform pose generation for you.



  Note

  ----

  Notes

  -----

  This class requires RDKit to be installed.

  """

deepchem/utils/conformers.py

+18 −18
Original line number Diff line number Diff line
@@ -66,13 +66,13 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object



    Returns

    -------

    mol: RDKit Mol

      A new RDKit Mol containing the chosen conformers, sorted by

    mol : rdkit.Chem.rdchem.Mol

      A new RDKit Mol object containing the chosen conformers, sorted by

      increasing energy.

    """

    return self.generate_conformers(mol)
@@ -86,13 +86,13 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object



    Returns

    -------

    mol: RDKit Mol

      A new RDKit Mol containing the chosen conformers, sorted by

    mol : rdkit.Chem.rdchem.Mol

      A new RDKit Mol object containing the chosen conformers, sorted by

      increasing energy.

    """
@@ -119,12 +119,12 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object



    Returns

    -------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object with embedded multiple conformers.

    """

    try:
@@ -147,7 +147,7 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object with embedded conformers.

    conf_id : int, optional

      ID of the conformer to associate with the force field.
@@ -156,7 +156,7 @@ class ConformerGenerator(object): 


    Returns

    -------

    ff: RDKit ForceField

    ff : rdkit.ForceField.rdForceField.ForceField

      RDKit force field instance for a molecule.

    """

    try:
@@ -183,7 +183,7 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object with embedded conformers.

    """

    for conf in mol.GetConformers():
@@ -196,7 +196,7 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object with embedded conformers.



    Returns
@@ -219,13 +219,13 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object



    Returns

    -------

    new_mol: RDKit Mol

      A new RDKit Mol containing the chosen conformers, sorted by

    new_mol : rdkit.Chem.rdchem.Mol

      A new rdkit.Chem.rdchem.Mol containing the chosen conformers, sorted by

      increasing energy.

    """

    try:
@@ -278,7 +278,7 @@ class ConformerGenerator(object): 


    Parameters

    ----------

    mol: RDKit Mol

    mol : rdkit.Chem.rdchem.Mol

      RDKit Mol object



    Returns

deepchem/utils/coordinate_box_utils.py

+22 −22
Original line number Diff line number Diff line
@@ -366,10 +366,10 @@ def get_face_boxes(coords: np.ndarray, pad: float = 5.0) -> List[CoordinateBox]: 
    x_min, x_max = int(np.floor(x_min)) - pad, int(np.ceil(x_max)) + pad

    x_bounds = (x_min, x_max)



    y_min, y_max = np.amin(points[:, 1]), np.amax(points[:, 1])

    y_min, y_max = np.amin(y_coords), np.amax(y_coords)

    y_min, y_max = int(np.floor(y_min)) - pad, int(np.ceil(y_max)) + pad

    y_bounds = (y_min, y_max)

    z_min, z_max = np.amin(points[:, 2]), np.amax(points[:, 2])

    z_min, z_max = np.amin(z_coords), np.amax(z_coords)

    z_min, z_max = int(np.floor(z_min)) - pad, int(np.ceil(z_max)) + pad

    z_bounds = (z_min, z_max)

    box = CoordinateBox(x_bounds, y_bounds, z_bounds)

deepchem/utils/fragment_utils.py

+10 −10
Original line number Diff line number Diff line 
"""A collection of utilities for dealing with Molecular Fragments"""

import itertools

import numpy as np

from typing import Any, List, Iterable, Optional, Sequence, Set, Tuple, Union

from typing import List, Optional, Sequence, Set, Tuple, Union



from deepchem.utils.typing import RDKitAtom, RDKitMol

from deepchem.utils.geometry_utils import compute_pairwise_distances
@@ -90,7 +90,7 @@ class MolecularFragment(object): 


    Parameters

    ----------

    atoms: Iterable[RDKit Atom]

    atoms: Iterable[rdkit.Chem.rdchem.Atom]

      Each entry in this list should be a RDKit Atom.

    coords: np.ndarray

      Array of locations for atoms of shape `(N, 3)` where `N ==
@@ -135,7 +135,7 @@ def get_partial_charge(atom: Union[RDKitAtom, AtomShim]) -> float: 


  Parameters

  ----------

  atom: RDKit Atom or AtomShim

  atom: rdkit.Chem.rdchem.Atom or AtomShim

    Either a rdkit.Atom object or `AtomShim`



  Returns
@@ -209,7 +209,7 @@ def get_mol_subset( 
  ----------

  coords: np.ndarray

    Must be of shape (N, 3) and correspond to coordinates of mol.

  mol: RDKit Mol or MolecularFragment

  mol : rdkit.Chem.rdchem.Mol or MolecularFragment

    The molecule to strip

  atom_indices_to_keep: list

    List of the indices of the atoms to keep. Each index is a unique
@@ -252,7 +252,7 @@ def strip_hydrogens(coords: np.ndarray, mol: Union[RDKitMol, MolecularFragment] 
  ----------

  coords: np.ndarray

    The coords must be of shape (N, 3) and correspond to coordinates of mol.

  mol: RDKit Mol or MolecularFragment

  mol : rdkit.Chem.rdchem.Mol or MolecularFragment

    The molecule to strip



  Returns
@@ -288,7 +288,7 @@ def get_contact_atom_indices(fragments: List[Tuple[np.ndarray, RDKitMol]], 


  Parameters

  ----------

  fragments: List[Tuple[np.ndarray, RDKit Mol]]

  fragments: List[Tuple[np.ndarray, rdkit.Chem.rdchem.Mol]]

    As returned by `rdkit_utils.load_complex`, a list of tuples of

    `(coords, mol)` where `coords` is a `(N_atoms, 3)` array and `mol`

    is the rdkit molecule object.
@@ -335,7 +335,7 @@ def reduce_molecular_complex_to_contacts( 


  Parameters

  ----------

  fragments: List[Tuple[np.ndarray, RDKit Mol]]

  fragments: List[Tuple[np.ndarray, rdkit.Chem.rdchem.Mol]]

    As returned by `rdkit_utils.load_complex`, a list of tuples of

    `(coords, mol)` where `coords` is a `(N_atoms, 3)` array and `mol`

    is the rdkit molecule object.

deepchem/utils/pdbqt_utils.py

+9 −9
Original line number Diff line number Diff line
@@ -44,7 +44,7 @@ def convert_protein_to_pdbqt(mol: RDKitMol, outfile: str) -> None: 


  Parameters

  ----------

  mol: RDKit Mol

  mol : rdkit.Chem.rdchem.Mol

    Protein molecule

  outfile: str

    filename which already has a valid pdb representation of mol
@@ -75,7 +75,7 @@ def mol_to_graph(mol: RDKitMol): 


  Parameters

  ----------

  mol: RDKit Mol

  mol : rdkit.Chem.rdchem.Mol

    The molecule to convert into a graph.



  Returns
@@ -111,7 +111,7 @@ def get_rotatable_bonds(mol: RDKitMol) -> List[Tuple[int, int]]: 


  Parameters

  ----------

  mol: RDKit Mol

  mol : rdkit.Chem.rdchem.Mol

    Ligand molecule



  Returns
@@ -148,7 +148,7 @@ def convert_mol_to_pdbqt(mol: RDKitMol, outfile: str) -> None: 


  Parameters

  ----------

  mol: RDKit Mol

  mol : rdkit.Chem.rdchem.Mol

    The molecule whose value is stored in pdb format in outfile

  outfile: str

    Filename for a valid pdb file with the extention .pdbqt
@@ -245,8 +245,8 @@ def _create_component_map(mol: RDKitMol, 


  Parameters

  ----------

  mol: RDKit Mol

    molecule to find disconnected compontents in 

  mol : rdkit.Chem.rdchem.Mol

    The molecule to find disconnected components in

  components: List[List[int]]

    List of connected components
@@ -348,4 +348,4 @@ def _valid_bond(used_partitions: Set[int], bond: Tuple[int, int], 
    next_partition = part2

  else:

    next_partition = part1

  return not next_partition in used_partitions, next_partition
 
  return next_partition not in used_partitions, next_partition

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