Repositories list

• DECIMER.ai

  Public
  This repository contains the code for https://decimer.ai

  PHP

  •

  MIT License

  •13•25•4•0•Updated Nov 3, 2025Nov 3, 2025

• cheminformatics-microservice

  Public
  This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

  dockerchemistrycheminformatics+ 5reactjsrdkitopenbabelmicroservices-architecturechemistry-development-kit

  JavaScript

  •

  MIT License

  •9•58•4•1•Updated Nov 3, 2025Nov 3, 2025

• coconut

  Public
  COCONUT (COlleCtion of Open Natural prodUcTs): A comprehensive platform facilitating natural product research by providing data, tools, and services for deposition, curation, and reuse.

  cheminformaticsnatural-products

  PHP

  •4•39•72•4•Updated Oct 30, 2025Oct 30, 2025

• cdk

  Public
  The Chemistry Development Kit

  Java

  •

  GNU Lesser General Public License v2.1

  •171•0•0•0•Updated Oct 2, 2025Oct 2, 2025

• SugarRemoval

  Public
  The Sugar Removal Utility - An algorithmic approach for in silico removal of circular and linear sugars from molecular structures.

  Java

  •

  MIT License

  •2•0•0•0•Updated Oct 2, 2025Oct 2, 2025

• MORTAR

  Public

  Steinbeck-Lab/MORTAR’s past year of commit activity
  MOlecule fRagmenTAtion fRamework

  Java

  •

  MIT License

  •4•0•0•0•Updated Oct 2, 2025Oct 2, 2025

• nmrium

  Public
  React component to display and process nuclear magnetic resonance (NMR) spectra.

  TypeScript

  •

  MIT License

  •31•0•0•0•Updated Jun 17, 2025Jun 17, 2025

• toolminutes

  Public
  JavaScript

  •9•0•0•0•Updated May 5, 2025May 5, 2025

• .github

  Public
  0•0•0•0•Updated Mar 17, 2025Mar 17, 2025

• ErtlFunctionalGroupsFinder

  Public
  Open reimplementation of the Ertl algorithm for functional group identification based on the Chemistry Development Kit (CDK)

  Java

  •

  GNU Lesser General Public License v2.1

  •6•0•0•0•Updated Feb 24, 2025Feb 24, 2025

• RanDepict

  Public
  This repository contains RanDepict, an easy-to-use utility to generate a big variety of chemical structure depictions (random depiction styles and image augmentations) based on RDKit, CDK, Indigo and PIKAChU.

  Python

  •

  MIT License

  •10•0•0•1•Updated Feb 21, 2025Feb 21, 2025

• cheminf-jena-logos

  Public
  This repository contains logos for the tools and projects created and maintained by the Steinbeck group at Friedrich-Schiller University, Jena.

  MIT License

  •1•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• DECIMER-Image_Transformer

  Public
  DECIMER Image Transformer is a deep-learning-based tool designed for automated recognition of chemical structure images. Leveraging transformer architectures, the model converts chemical images into SMILES strings, enabling the digitization of chemical data from scanned documents, literature, and patents.

  Python

  •

  MIT License

  •73•1•0•1•Updated Nov 21, 2024Nov 21, 2024

• DECIMER-Image-Classifier

  Public
  PureBasic

  •6•0•0•0•Updated Nov 1, 2024Nov 1, 2024

• ChemIcal-DatasEt-comparatoR

  Public
  ChemIcal DatasEt comparatoR (CIDER) is a Python package and ready-to-use Jupyter Notebook workflow which primarily utilizes RDKit to compare two or more chemical structure datasets (SD files) in different aspects, e.g. size, overlap, molecular descriptor distributions, chemical space clustering, etc., most of which can be visually inspected.

  Jupyter Notebook

  •

  Other

  •4•9•2•1•Updated Sep 18, 2024Sep 18, 2024

• AutoNMR-An-Automated-Tool-for-NMR-Chemical-Shift-Calculations-using-NWChem

  Public
  AutoNMR is a novel Python package designed to streamline and automate the workflow of NMR chemical shift calculations using NWChem.

  Python

  •1•0•0•0•Updated Aug 20, 2024Aug 20, 2024

• ART2a-Clustering-for-Java

  Public
  Implementation of the ART2a fingerprint clustering algorithm in Java.

  Java

  •

  MIT License

  •2•0•0•0•Updated Jul 3, 2024Jul 3, 2024

• DECIMER-Image-Segmentation

  Public
  https://decimer.ai

  Jupyter Notebook

  •

  MIT License

  •36•0•0•0•Updated Mar 4, 2024Mar 4, 2024

• classify_homologues

  Public
  A cheminformatics algorithm to classify homologous chemical series

  Python

  •

  Apache License 2.0

  •5•0•0•0•Updated Jan 30, 2024Jan 30, 2024

• GlycosylationStatistics

  Public
  Systematic detection of sugar moieties in COCONUT using the Sugar Removal Utility

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Jan 24, 2024Jan 24, 2024

• scaffold-graph-vis

  Public
  Basic utilities for visualising cdk-scaffold graphs using GraphStream

  Java

  •

  GNU Lesser General Public License v2.1

  •1•0•0•0•Updated Dec 19, 2023Dec 19, 2023

• FragmentFingerprints

  Public
  A library to generate fingerprints for molecular structures based on a set of fragments

  Java

  •

  MIT License

  •1•0•0•0•Updated Dec 19, 2023Dec 19, 2023

• ScaffoldGenerator

  Public
  A CDK-based library for generating Scaffold Trees and Scaffold Networks

  Java

  •

  GNU Lesser General Public License v2.1

  •6•0•0•0•Updated Nov 3, 2023Nov 3, 2023

• cloud-surge

  Public
  Massively parallel computation of chemical spaces in cloud environments with surge

  cheminformaticsdrug-discoverykubernetes-jobs+ 3chemical-spaceschemical-structure-generatornew-drug-research

  Jupyter Notebook

  •

  MIT License

  •0•1•1•1•Updated Oct 13, 2023Oct 13, 2023

• NaturalProductsOnline

  Public
  Website code for COCONUT

  JavaScript

  •11•0•0•0•Updated Oct 4, 2023Oct 4, 2023

• cheminformatics-be

  Public
  Cheminformatics browser extension brings a suite of powerful tools and features directly to your web pages.

  Vue

  •

  MIT License

  •1•0•0•0•Updated Sep 14, 2023Sep 14, 2023

• lightweight-registration

  Public
  Python

  •

  MIT License

  •17•1•0•0•Updated Aug 29, 2023Aug 29, 2023

• chemical_page_segmentation_dataset

  Public
  Artificial data generation for DECIMER-Segmentation

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Aug 22, 2023Aug 22, 2023

• MAW

  Public
  Metabolome Annotation Workflow

  Jupyter Notebook

  •8•0•0•0•Updated Aug 3, 2023Aug 3, 2023

• NMR_Chemical_Shift-Automation

  Public
  Automated NMR Chemical Shift Calculation

  Python

  •

  MIT License

  •2•0•0•0•Updated Jul 24, 2023Jul 24, 2023