Commit 0d8033ad authored by nd-02110114's avatar nd-02110114
Browse files

🐛 fix docs

parent 1aaea1d2

deepchem/dock/pose_generation.py

+0 −1
Original line number Diff line number Diff line
@@ -9,7 +9,6 @@ import os 
import tempfile

import tarfile

from subprocess import call

from deepchem.utils.rdkit_util import add_hydrogens_to_mol

from subprocess import check_output

from deepchem.utils import rdkit_util

from deepchem.utils import mol_xyz_util

deepchem/utils/rdkit_util.py

+3 −3
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ import numpy as np 
from io import StringIO

from copy import deepcopy

from collections import Counter

from deepchem.utils import pdbqt_utils

from deepchem.utils.pdbqt_utils import pdbqt_to_pdb

from deepchem.utils.pdbqt_utils import convert_mol_to_pdbqt

from deepchem.utils.pdbqt_utils import convert_protein_to_pdbqt

from deepchem.utils.geometry_utils import angle_between
@@ -328,9 +328,9 @@ def write_molecule(mol, outfile, is_protein=False): 
    writer.write(mol)

    writer.close()

    if is_protein:

      pdbqt_utils.convert_protein_to_pdbqt(mol, outfile)

      convert_protein_to_pdbqt(mol, outfile)

    else:

      pdbqt_utils.convert_mol_to_pdbqt(mol, outfile)

      convert_mol_to_pdbqt(mol, outfile)

  elif ".pdb" in outfile:

    writer = Chem.PDBWriter(outfile)

    writer.write(mol)

docs/conf.py

+3 −2
Original line number Diff line number Diff line
@@ -77,6 +77,7 @@ html_logo = '_static/logo.png' 


import inspect

from os.path import relpath, dirname

import deepchem



for name in ['sphinx.ext.linkcode', 'numpydoc.linkcode']:

  try:
@@ -141,10 +142,10 @@ def linkcode_resolve(domain, info): 
      fn, start=os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))



  if 'dev' in deepchem.__version__:

    return "https://github.com/numpy/numpy/blob/master/numpy/%s%s" % (

    return "https://github.com/deepchem/deepchem/blob/master/deepchem/%s%s" % (

        fn, linespec)

  else:

    return "https://github.com/numpy/numpy/blob/v%s/numpy/%s%s" % (

    return "https://github.com/deepchem/deepchem/blob/v%s/deepchem/%s%s" % (

        deepchem.__version__, fn, linespec)

docs/requirements.rst

+65 −64
Original line number Diff line number Diff line
@@ -22,69 +22,70 @@ Soft requirements 


DeepChem has a number of "soft" requirements.



+--------------------------------+---------------+----------------------------------------+

| Package name                   | version       | Modules that use this packages         |

+================================+===============+========================================+

| `BioPython`_                   | 1.77          |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| Package name                   | Version       | Location where this package is imported           |

|                                |               | (dc: deepchem)                                    |

+================================+===============+===================================================+

| `BioPython`_                   | 1.77          | :code:`dc.utlis.genomics`                         |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `OpenAI Gym`_                  | Not Testing   |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `OpenAI Gym`_                  | Not Testing   | :code:`dc.rl`                                     |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `matminer`_                    | 1.77          |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `matminer`_                    | 1.77          | :code:`dc.feat.materials_featurizers`             |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `MDTraj`_                      | 1.9.4         |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `MDTraj`_                      | 1.9.4         | :code:`dc.utils.pdbqt_utils`                      |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `NetworkX`_                    | 2.2           |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `NetworkX`_                    | 2.2           | :code:`dc.utils.rdkit_utils`                      |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `OpenMM`_                      | 7.4.2         |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `OpenMM`_                      | 7.4.2         | :code:`dc.utils.rdkit_utils`                      |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `PDBFixer`_                    | 1.6           |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `PDBFixer`_                    | 1.6           | :code:`dc.utils.rdkit_utils`                      |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `Pillow`_                      | 7.1.2         |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `Pillow`_                      | 7.1.2         | :code:`dc.data.data_loader`,                      |

|                                |               | :code:`dc.trans.transformers`                     |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `pyGPGO`_                      | 0.4.0.dev1    | :code:`dc.hyper.gaussian_process`                 |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `pyGPGO`_                      | 0.4.0.dev1    |                                        |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `Pymatgen`_                    | 2020.7.3      | :code:`dc.feat.materials_featurizers`             |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `Pymatgen`_                    | 2020.7.3      |                                        |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `PyTorch`_                     | Not Testing   | :code:`dc.data.datasets`                          |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `PyTorch`_                     |               |                                        |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `RDKit`_                       | 2020.03.4     | Many modules                                      |

|                                |               | (we recommend you to instal)                      |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `RDKit`_                       | 2020.03.4     |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `Tensorflow Probability`_      | 0.10          | :code:`dc.rl`                                     |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `Tensorflow Probability`_      | 0.10          |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `XGBoost`_                     | 0.90          | :code:`dc.models.xgboost_models`                  |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+----------------------------------------+

| `XGBoost`_                     | 0.90          |                                        |

+--------------------------------+---------------+---------------------------------------------------+

| `Weights & Biases`_            | Not Testing   | :code:`dc.models.keras_model`,                    |

|                                |               | :code:`dc.models.callbacks`                       |

|                                |               |                                                   |

|                                |               |                                        |

+--------------------------------+---------------+----------------------------------------+

| `Weights & Biases`_            | Not Testing   |                                        |

|                                |               |                                        |

|                                |               |                                        |

+--------------------------------+---------------+----------------------------------------+

+--------------------------------+---------------+---------------------------------------------------+

          

.. _`joblib`: https://pypi.python.org/pypi/joblib

.. _`NumPy`: https://numpy.org/

CRA Git | Maintained and supported by SUSTech CRA and CCSE