ArticleJournal of cheminformatics2026
strainedSMILES2xyz: a workflow for reliable 3D structures of strained molecules from SMILES.
Article in Journal of cheminformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Accurate 3D structure generation from SMILES is essential for data-driven chemistry but often fails for strained ring systems. We introduce strainedSMILES2xyz, a Python workflow that improves conformer generation by relaxing RDKit constraints, exploring stereoisomer variants, and correcting errors using force-field refinement. Benchmarking on strained and unstrained rings shows that it outperforms existing tools, generating correct geometries in nearly all cases. The workflow is available as a Python package and Jupyter notebook.Scientific ContributionThis work identifies a critical gap in automated SMILES-to-3D structure generation for strained molecules. Many established tools, including the widely used RDKit, frequently fail or produce incorrect geometries for these systems. By explicitly targeting these failure modes, the proposed approach enables reliable 3D structure generation for chemically relevant strained molecules within fully automated workflows.
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