Problem Statement
Currently, standard embedding and optimization functions (such as RDKit’s MMFFOptimizeMolecule) occasionally produce non-physical geometries for certain small molecules. obabel can solve this, but it modifies metadata (changes atom name), which requires renaming.
Problem Case: Simple alkane chains are sometimes generated in a linear configuration (C-C-C bond angles near 180°) rather than the physically accurate tetrahedral geometry (approx. 109.5°).
Proposed Feature
- correct molecule to satisfy the basic geometry (no linear chain)
- metadata conservation: only change coordinates, not atom index, atom name, etc...
Problem Statement
Currently, standard embedding and optimization functions (such as RDKit’s MMFFOptimizeMolecule) occasionally produce non-physical geometries for certain small molecules. obabel can solve this, but it modifies metadata (changes atom name), which requires renaming.
Problem Case: Simple alkane chains are sometimes generated in a linear configuration (C-C-C bond angles near 180°) rather than the physically accurate tetrahedral geometry (approx. 109.5°).
Proposed Feature