ZINC22:Fine Tranching with RDKit using Heavy Atom Count and LogP
Written by Jennifer Young on April 14, 2020. Updated by Khanh Tang on March 14, 2022
These scripts perform fine tranching with RDKit to compute the heavy atom count and logP for each molecule and put it in a bucket of the form HxxPyyy for positive valued logp (i.e. 0 < logp) and HxxMyyy for negative valued logp (i.e. logp < 0).
See github repo https://github.com/docking-org/ZINC21-Tools
How to run
(If you are using our cluster) Source conda environment for RDKit
If you are using our cluster, there is already a conda environment with RDKit available and you just need to source it using the following command. You need to use bash.
source /mnt/nfs/home/devtest/anaconda3/bin/activate my-rdkit-env
If you need to create a conda environment, follow the instructions at https://rdkit.org/docs/Install.html
Read the section : How to install RDKit with Conda. Once you do
conda activate my-rdkit-env
conda install -c conda-forge tqdm
You are ready to run the Python script.
Run Python script with the desired arguments
The input smiles file should have the following 2 columns
python rdkit_hlogp_batch_mp_2.py <smiles>
The output file will be a file with the name <smiles_file>_hlogp and will have the following 3 columns
- original smiles
- original ID
- HxxPyyy HxxMyyy