hsiaoyi0504 / awesome-cheminformatics Goto Github PK

https://github.com/dataprofessor/code/tree/master/python

https://fiehnlab.ucdavis.edu/staff/kind/chemoinformatics

https://github.com/mcs07/MolVS

https://sourceforge.net/projects/pharmit/

https://github.com/mkusner/grammarVAE

I'm in ipython, working through my first tutorial -Graph Convolutions For Tox21. When I get to the line to import deepchem as dc, it expands and does a lot of things, and gives me what looks like an error on importing numpy as np. However, if I type import numpy as np, it works fine. if I backup to the previous line, import deepchem.utils.rdkit_util as rdkit_util, and try that by itself, I get the same error that it has no attribute 'utils'. if it try import deepchem.utils I get the same error. So, it appears that deepchem.utils doesn't exist somehow, which is weird because the master lists it as existing. Am I doing something wrong, and How do I fix this ?
Thanks

----> 1 import deepchem as dc

/home/daniels/repo/deepchem/deepchem/init.py in ()
6 from future import unicode_literals
7
----> 8 import deepchem.data
9 import deepchem.feat
10 import deepchem.hyper

/home/daniels/repo/deepchem/deepchem/data/init.py in ()
15 from deepchem.data.datasets import densify_features
16 from deepchem.data.supports import *
---> 17 from deepchem.data.data_loader import DataLoader
18 from deepchem.data.data_loader import CSVLoader
19 from deepchem.data.data_loader import UserCSVLoader

/home/daniels/repo/deepchem/deepchem/data/data_loader.py in ()
20 from deepchem.utils.save import load_csv_files
21 from deepchem.utils.save import load_sdf_files
---> 22 from deepchem.feat import UserDefinedFeaturizer
23 from deepchem.data import DiskDataset
24

/home/daniels/repo/deepchem/deepchem/feat/init.py in ()
19 from deepchem.feat.coulomb_matrices import CoulombMatrix
20 from deepchem.feat.coulomb_matrices import CoulombMatrixEig
---> 21 from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer
22 from deepchem.feat.nnscore_utils import hydrogenate_and_compute_partial_charges
23 from deepchem.feat.binding_pocket_features import BindingPocketFeaturizer

/home/daniels/repo/deepchem/deepchem/feat/rdkit_grid_featurizer.py in ()
14 from rdkit import Chem
15 from rdkit.Chem import AllChem
---> 16 import deepchem.utils.rdkit_util as rdkit_util
17
18 import numpy as np

AttributeError: 'module' object has no attribute 'utils'

In [23]:

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad354/7186501

https://chem.libretexts.org/Courses/University_of_Arkansas_Little_Rock/ChemInformatics_(2017)%3A_Chem_4399%2F%2F5399

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0309-4

https://pytorch-geometric.readthedocs.io/en/latest/

https://github.com/swansonk14/chemprop

https://github.com/isayev/ReLeaSE

https://github.com/barupal/ChemRICH

http://chembl.blogspot.com/2017/07/using-autoencoders-for-molecule.html

http://prody.csb.pitt.edu/

https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00286

Not sure if this is exactly in scope, but Tim Cernak's group just published a great set of tutorials for programming applied to medicinal chemistry:

• the paper: https://pubs.acs.org/doi/full/10.1021/acs.jchemed.3c00357
• the GitHub repo: https://github.com/cernaklab/jchemed-chemoinformatics

https://github.com/wengong-jin/chemprop

https://github.com/Mishima-syk/py4chemoinformatics

https://github.com/tsudalab/ChemTS

https://github.com/bp-kelley/descriptastorus

https://github.com/volkamerlab/TeachOpenCADD

https://dasher.wustl.edu/chem430/

https://bitbucket.org/fiehnlab/fiehnlab-cts/src/master/

Source code of Chemical Translation Service of Fiehn Laboratory of UC Davis.

https://github.com/maxhodak/keras-molecules

https://chem.libretexts.org/Courses/Intercollegiate_Courses/Cheminformatics_OLCC_(2019)

https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0232-0

Molecular descriptor

https://github.com/mordred-descriptor/mordred

http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/index.html

https://git.durrantlab.pitt.edu/jdurrant/gypsum_dl

https://github.com/kamikaze0923/jtvae

https://ambermd.org/AmberTools.php

https://github.com/hachmannlab/chemml

http://ambit.sourceforge.net/

https://iwatobipen.wordpress.com/

https://github.com/Et9797/rdkit-obabel-confgen

https://github.com/HIPS/molecule-autoencoder