odifentse
commented
2 weeks ago Dear Dr Covell,
Thank you so much for contacting me regarding the notebooks.
I was hoping that the requirements file would contain all the packages to run the code so that you do not have to encounter installation errors. I must have overlooked this one.
Query 1: Installing rdkit
In order to fix this error, may you please install rdkit. You can do so by executing any one of the following codes (I used the first one):
- conda install conda-forge::rdkit
- conda install conda-forge/label/cf201901::rdkit
- conda install conda-forge/label/cf202003::rdkit
- conda install conda-forge/label/gcc7::rdkit
- conda install conda-forge/label/rdkit_rc::rdkit
Additional information regarding this installation can be found at the Anaconda rdkit link here: https://anaconda.org/conda-forge/rdkit
Query 2: File path
The file path should be the exact folder/location where you saved your input files.
- For example, you can create a folder called "FBDD" in your local folder, where you save the input and output files for this project.
- Then you can call this path in your code. This could read 'C:\Users\david\FBDD\Chembl_C09.sdf'
For instance, my path is '/Users/odilehasa/Hypertension/Final_Experiments/Data/Chembl_C09.sdf', which indicates that I saved the file (Chembl_C09.sdf) in my local drive (indicated by /Users/odilehasa), under the folder "Data", which is in the folder "Final_Experiments", which is inside the "Hypertension" folder.
Your computer's operating system also influences the syntax, specifically the backslash, C and colon. For example:
- Mac computer path is: '/Users/odilehasa/Hypertension/Final_Experiments/Data/Chembl_C09.sdf'
- Windows computer path would be: 'C:\Users\odilehasa\Hypertension\Final_Experiments\Data\Chembl_C09.sdf'
Have a look at this link which better explains how to get your path: https://www.geeksforgeeks.org/find-path-to-the-given-file-using-python/
I hope this helps.
I thanks the authors for making their Jupyter notebooks available through open source. Following the specified steps, beginning with Phase 0; importing relevant libraries, I am getting the same error as your example
ModuleNotFoundError Traceback (most recent call last) Cell In[1], line 3 1 # import all relevant libraries ----> 3 from rdkit.Chem import AllChem 4 from rdkit import Chem 5 from rdkit.Chem import BRICS
ModuleNotFoundError: No module named 'rdkit'
If possible could you provide the steps for installing rdkit?
In addition, I do not know the proper syntax for setting $PATH to include the input and output directories. I have placed the github directories in my local folder.
Thanks in advance, David Covell, Ph.D.