Conformers are different configurations of a molecule (same formula and connections) obtained by rotating the single bonds.
This repository contains a simple workflow for minimum energy conformer search based on force field optimization methods (UFF and MMFF94) available from RDKit.
Workflow consists of the following steps:
- Import molecule from SMILES
- Generate conformers for given molecule
- Optimize conformers by force field optimization (UFF and MMFF94)
- Select the minimum energy conformer and write it into a SDF file
Requirements
- RDKit
Disclaimer/Warning from RDKit: Conformation generation is a difficult and subtle task. The original 2D->3D conversion provided with the RDKit was not intended to be a replacement for a “real” conformational analysis tool; it merely provides quick 3D structures for cases when they are required. We believe, however, that the newer ETKDG method[1] should be adequate for most purposes.
Note: It is recommended to use MMFF94 for organic-like molecules and UFF for metal contained molecules.
References
[1] Riniker, S.; Landrum, G. A. (2015). Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation J. Chem. Inf. Comp. Sci. 55:2562-74.