Covalent library preparation 2023

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Modify warhead to covalent adduct with SiH3 added.

Prepare “SMILES ID” file.

ssh n-1-17 (or another development node)

Source environment with RDkit 

source /mnt/nfs/ex9/work/ttummino/miniconda/etc/profile.d/conda.sh

conda activate base3.7

python ~ak87/PROGRAM/convert_smiles_to_covalent.py ald bbv-cov-ald.smi bbv-cov-ald-test.smi

This script enumerates all stereoisomers and converts SMILES to the covalent ones. Currently, only conversions for aldehydes and nitriles is supported. Usage:

  • First arg: ald or nitr for aldehyde or nitrile
  • Second arg: input smi file
  • Third arg: output file name
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