Synple utils

Utility functions and helper functions for python scripts focus on cheminformatics.

Setup

Setup python package:

make env

If make doesn't work, manually set upt the environment:

conda env create -f ./environment.yaml -p ./env
./env/bin/python -m pip install -e .

Then, activate the environment:

source activate ./env

Available modules

synutils.featurisers

This module contains functions to featurise molecules. Currently, it supports the following featurisers:

• fingerprint featurizers:
  • morgan
  • morgan_count
  • rdkit
  • rdkit_count
  • topological_torsion
  • topological_torsion_count
• physichem featurisers:
  • rdkit_2d
• combined featurisers:
  • morgan_rdkit_2d
  • morgan_count_rdkit_2d

synutils.dimension_pickers

This module contains functions to pick dimensions from featurised molecules. Currently, it supports the following dimension pickers:

• pca
• ica
• umap

Cheminoformatics useful tutorials

TeachOpenCADD Talktorials: Nice serise of tutorials for cheminformatics.

Cheminformatics useful external links

openbabel: Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

obabel -icdx input.cdx -osmi -O output.smi