rdkit_utilities

Contained here are some helpful RDKit utilities for:

• generating conformers
  • ranking by MMFF electrostatic energy (for ELF conformer selection)
  • selecting to maximise diversity via RMS (for ELF conformer selection)
• finding symmetric atoms in a molecule
• finding the shell of neighbors around a central fragment, N bonds away

There are also convenience functions for:

• loading molecules from any input MolFromInput
• loading molecules from SMILES with keyword arguments for removeHs, etc.
• loading molecules and reordering by atom map number, analogous to the OpenFF toolkit Molecule.from_mapped_smiles
• generally reordering conformers
• optimizing molecules by specifying force field using a string name

Functions are in files such as rdchem, rdDistGeom, etc. to try to keep to RDKit's organisation convention. Similarly to RDKit, a Chem and AllChem are provided with group imports. Functions are written in PascalCase and keyword arguments in camelCase, also to keep to RDKit convention.

Copyright

Copyright (c) 2022, Lily Wang

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.5.