pruner¶

Reduce conformer ensembles based on relative conformer energy and structural similarity.

Conformers without an energy property (e.g. from failed calculations) cannot be ranked; both pruners drop them and log a warning.

EnergyPruner¶

Removes conformers with high energy (energy - minimal_energy > threshold): Options:

• threshold: float = 20.0 : window above minimum energy in kcal/mol

RMSDPruner¶

Removes conformers that are structurally identical using rdMolAlign.GetBestRMS, accounting for symmetry by using all substructure matches. Energy and rotational prefilters decrease the computational cost by efficiently identifying dissimilar conformers as deviations of energy and rotational constants.

Options:

• threshold: float = 0.125 : RMSD in Å cutoff for considering conformers similar
• include_hs: bool = False : include hydrogens in RMSD calculations
• filter_energies: bool = True : use prefilter by energy difference
• energy_threshold: float = 0.1 : minimum energy in kcal/mol deviation to identify different conformers
• filter_rotations: bool = True : use prefilter by rotational constants
• rot_fraction_threshold: float = 0.03 : minimum rotational constant deviation to identify different conformers
• maxMatches: int = 10000 : maximum number of substructure matches for symmetry handling in rdMolAlign.GetBestRMS