Cheminformatics Agent v1.0.0

Overview

Advanced cheminformatics toolkit for 3D molecular analysis and drug development workflows. Extends Chemistry Query (which handles 2D lookup/properties/visualization) with predictive and structural capabilities that require 3D reasoning.

Chemistry Query = "What is this molecule?" (2D, lookup, descriptors) Cheminformatics = "What can this molecule become?" (3D, conformers, pharmacophores, fragments, stereoisomers)

Scripts

scripts/conformer_gen.py

3D conformer ensemble generation using ETKDG with MMFF/UFF optimization.

--smiles <SMILES> --action <generate|ensemble|best> [--num_confs N] [--optimize mmff|uff|none] [--energy_window F] [--prune_rms F] [--output file.sdf]