embedder

Embedding strategies for TS-constrained conformer generation.

Constructor parameters:

  • remove_all_conformers: bool = True : Removes all prior conformers, i.e., the .xyz structure.
  • useRandomCoords: bool = True : Use random coordinates for the embedding.
  • ETversion: int = 2 : Used for the RDKit embedding parameters.
  • pruneRmsThresh: float = -1 : RMSD threshold for pruning directly after embedding. (default: remove identical conformers with RMSD = 0)

CmapEmbedder

Uses a coordinate map for the distance geometry-based embedding. The atomic positions of frozen_atoms are fixed to the TS coordinates.

BoundsMatrixEmbedder

Uses a distance-bounds matrix derived from the TS geometry:

  1. Fixes distances among reacting atoms and between reacting atoms and their neighbors (via frozen_atoms), matching TS distances.
  2. Performs triangle smoothing (DoTriangleSmoothing) with gradually increased tolerance until success