ZINC22:Fine Tranching with RDKit using Heavy Atom Count and LogP: Difference between revisions

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Written by Jennifer Young on April 14, 2020  
Written by Jennifer Young on April 14, 2020  


=Introduction=
=Introduction https://github.com/docking-org/ZINC21-Tools=
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).  The scripts are located in
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).   
    /nfs/home/jyoung/code/fine_tranche_hlogp_scripts
 
See github repo https://github.com/docking-org/ZINC21-Tools


=How to run=
=How to run=


==Create and/or source a conda environment for RDKit==
==(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.
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.
     bash  
     bash  
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     source /mnt/nfs/home/devtest/anaconda3/bin/activate my-rdkit-env
     source /mnt/nfs/home/devtest/anaconda3/bin/activate my-rdkit-env


==Run Python script with the desired arguments==
==If you need to create a conda environment, follow the instructions at https://rdkit.org/docs/Install.html==
The smiles file and batch size are command line arguments.  If you choose a batch size of 10,000, the output file will be written to after each batch of 10,000 molecules is processed.
Read the section : How to install RDKit with Conda. Once you do
    python /nfs/home/jyoung/code/fine_tranche_hlogp_scripts/rdkit_hlogp_batch.py <smiles_file> <batch_size>
    conda activate my-rdkit-env
 
    conda install -c conda-forge tqdm


==Sample Bash script for running on many smiles files==
You are ready to run the Python script.
If your smiles file is large, split into chunks of 1 million (or whatever your desired size).
    split -l 1000000 <your_smiles>


Then run
==Run Python script with the desired arguments==
    /nfs/home/jyoung/code/fine_tranche_hlogp_scripts/runall.sh
The input smiles file should have the following 2 columns
*smiles
*ID


Change the x?? to the desired pattern and change the batch size to the desired value.
    python rdkit_hlogp_batch_mp.py <smiles>


    #!/usr/bin/env bash
The output file will be a file with the name <smiles_file>_hlogp and will have the following 3 columns
    for i in x??;
* original smiles
    do
* original ID
      source /mnt/nfs/home/devtest/anaconda3/bin/activate my-rdkit-env
* HxxPyyy HxxMyyy
      python /nfs/home/jyoung/code/fine_tranche_hlogp_scripts/rdkit_hlogp_batch.py $i 10000
    done

Revision as of 22:29, 17 April 2020

Written by Jennifer Young on April 14, 2020

Introduction https://github.com/docking-org/ZINC21-Tools

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. 

    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

  • smiles
  • ID
   python rdkit_hlogp_batch_mp.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
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