/RDKit-tools

basics of rdkit

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RDKit tools

This repository containins tools built using RDKit to make life easier for cheminformatics.

Scripts and their use:

  1. add-column-to-sdf-files-in-a-directory.py: Can add a property to all SDF files in a folder with it's respective file name for easy backtracing. Requires RDKit.
  2. excel-to-sdf-conversion.py: Can convert an excel (.xlsx) file into an SDF file. Requires RDKit.
  3. random-sdf-selector.py: Can select a given number of molecules from an SDF file randomly for unbiased sampling. Requires RDKit.
  4. synthetic_accessibility_scorer_SYBA.py: Can calculate the synthetic accessibility scores for an SDF file. Requires RDKit and SYBA.
  5. e3fp.multiprocessor.ipynb: Can calculate the E3FP fingerprints for molecules in an SDF file. Requires RDKit and E3FP.
  6. plip-tools: Can generate pymol sessions for protein-ligand complexes in a folder (.pdb and .mae) formats.
  7. graph-featurizer: Functions to create graph objects as numpy arrays for molecules (.csv and .sdf) formats. Requires RDKit and networkx.