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HARMONSMILE: Harmonize SMILES Strings for Cheminformatics and Machine Learning

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 18 May 2026Embargo end date: 09 Jul 2025Publisher:Zenodo
Authors: Contreras-Torres, Flavio F.;
Code repository: https://github.com/NanoBiostructuresRG/harmonsmile/tree/v0.1.3

doi: 10.5281/zenodo.20295241 , 10.5281/zenodo.20287617 , 10.5281/zenodo.21287306 , 10.5281/zenodo.21273234 , 10.5281/zenodo.21270800 , 10.5281/zenodo.20275498 , 10.5281/zenodo.20275499 , 10.5281/zenodo.20307688 , 10.5281/zenodo.20321584 , 10.5281/zenodo.21232677 , 10.5281/zenodo.20319503 , 10.5281/zenodo.20330338 , 10.5281/zenodo.20567264

HARMONSMILE: Harmonize SMILES Strings for Cheminformatics and Machine Learning

Abstract

v0.1.3 (2026-05-19) HARMONSMILE is a toolkit for harmonizing SMILES strings to a consistent convention: canonical + isomeric + Kekulized, as used by RDKit. It automates the preparation of SMILES for cheminformatics workflows and machine learning applications within the computational drug discovery pipeline, enabling standardized comparison across PubChem, ChEMBL, and independent molecular databases.

If you use this software, please cite it as below.

Related Organizations
Keywords

PubChem, SMILES standardization, ChEMBL, cheminformatics, molecular datasets, RDKit, COCONUT, SMILES, drug discovery

  • BIP!
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    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    		 0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    		 Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    		 Average
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average