Contained here are some helpful RDKit utilities for:
- generating conformers
- ranking by MMFF electrostatic energy (for ELF conformer selection)
- selecting to maximize 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 (c) 2022, Lily Wang
Project based on the Computational Molecular Science Python Cookiecutter version 1.5.