On a clean conda environment created with
conda create -n env_name python==3.11 on Linux, and then
pip install graphein
graphein
I get the following:
[04/05/24 12:07:30] WARNING To use the Graphein submodule graphein.protein.features.sequence.embeddings, you need to embeddings.py:34
install: torch
To do so, use the following command: pip install torch
WARNING To use the Graphein submodule graphein.protein.features.sequence.embeddings, you need to embeddings.py:45
install: biovec
To do so, use the following command: pip install biovec
Alternatively, you can install graphein with the extras:
pip install graphein[extras]
WARNING To use the Graphein submodule graphein.protein.visualisation, you need to install: visualisation.py:36
pytorch3d
pytorch3d cannot be installed via pip
WARNING To use the Graphein submodule graphein.protein.meshes, you need to install: pytorch3d meshes.py:30
To do so, use the following command: pip install pytorch3d
Traceback (most recent call last):
File "/home/cam/.local/bin/graphein", line 5, in <module>
from graphein.cli import main
File "/home/cam/.local/lib/python3.10/site-packages/graphein/cli.py", line 10, in <module>
from graphein.utils.config_parser import parse_config
File "/home/cam/.local/lib/python3.10/site-packages/graphein/utils/config_parser.py", line 11, in <module>
from graphein.molecule.config import MoleculeGraphConfig
File "/home/cam/.local/lib/python3.10/site-packages/graphein/molecule/__init__.py", line 1, in <module>
from .atoms import *
File "/home/cam/.local/lib/python3.10/site-packages/graphein/molecule/atoms.py", line 98, in <module>
Chem.rdchem.HybridizationType.SP,
NameError: name 'Chem' is not defined
Appears that the try: except: wrapper around the import statement isn't doing what it's meant to? Nothing mentioning rdkit was picked up in the pip install as far as I can tell.
Thanks for flagging. I think pip install rdkit will do the trick for now. Looks like there are some imports that need to be caught and some better logging too.
On a clean conda environment created with
conda create -n env_name python==3.11
on Linux, and thenI get the following:
Appears that the
try: except:
wrapper around the import statement isn't doing what it's meant to? Nothing mentioningrdkit
was picked up in thepip install
as far as I can tell.Note: this occurs when using
python==3.10
as well.