I have installed Spyder3.2.1 in the current version of Miniconda3 on my
Debian v-9.1.0 64 bit Linux platform. Spyder is performing well, but I am
having difficulty installing the RDKit.
I followed the directions in the RDKit_Docs_current.pdf"
How to install RDKit with Conda
Creating a new conda environment with the RDKit installed using these
packages requires one single command similar
to the following::
$ conda create -c rdkit -n my-rdkit-env rdkit
Finally, the new environment must be activated, so that the corresponding
python interpreter becomes available in the
same shell:
$ source activate my-rdkit-env
There were no warning or error messages during the installation, but when I
attempt running a simple Python script:
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 15 11:41:24 2017
@author: comp
"""
from __future__ import print_function
from rdkit import Chem
m = Chem.MolFromSmiles('Cc1ccccc1')
m
I get:
IPython 6.1.0 -- An enhanced Interactive Python.
runfile('/home/comp/Apps/Python/untitled0.py',
wdir='/home/comp/Apps/Python')
Traceback (most recent call last):
File "<ipython-input-1-3842c59475d8>", line 1, in <module>
runfile('/home/comp/Apps/Python/untitled0.py',
wdir='/home/comp/Apps/Python')
File
"/home/comp/Apps/miniconda3/lib/python3.6/site-packages/spyder/utils/site/sitecustomize.py",
line 688, in runfile
execfile(filename, namespace)
File
"/home/comp/Apps/miniconda3/lib/python3.6/site-packages/spyder/utils/site/sitecustomize.py",
line 101, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "/home/comp/Apps/Python/untitled0.py", line 10, in <module>
from rdkit import Chem
ModuleNotFoundError: No module named 'rdkit'
RDKit is installed in ~/miniconda3/envs/mr-rdkit-env
Unfortunately, I have no clue as to what the problem(s) may be, assistance
will be much appreciated.
Thanks in advance.
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