RDKit is an open source cheminformatics toolkit made available under the permissive Berkeley Software Distribution (BSD) license.
By using RDKit can be generated 3D conformations for molecules using distance geometry. The algorithm followed is:
- The molecule’s distance bounds matrix is calculated based on the connection table and a set of rules.
- The bounds matrix is smoothed using a triangle-bounds smoothing algorithm.
- A random distance matrix that satisfies the bounds matrix is generated.
- This distance matrix is embedded in 3D dimensions (producing coordinates for each atom).
- The resulting coordinates are cleaned up somewhat using a crude force field and the bounds matrix.
Finally, the 3D conformation(s) can be optimized by using the Molecular Mechanic Force Field (MMFF94) or Universal Force Field (UFF).