cheminformatics-microservice

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

https://github.com/steinbeck-lab/cheminformatics-microservice

Science Score: 85.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 7 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
1 of 7 committers (14.3%) from academic institutions
✓
Institutional organization owner
Organization steinbeck-lab has institutional domain (cheminf.uni-jena.de)
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (7.5%) to scientific vocabulary

Keywords

cheminformatics chemistry chemistry-development-kit docker microservices-architecture openbabel rdkit reactjs

Keywords from Contributors

standardization meshing pde pinn interpretability projections polygons sequences parallel simulations

Scientific Fields

Artificial Intelligence and Machine Learning Computer Science - 83% confidence

Last synced: 6 months ago · JSON representation ·

Repository

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

Basic Info

Host: GitHub
Owner: Steinbeck-Lab
License: mit
Language: JavaScript
Default Branch: main
Homepage: https://app.naturalproducts.net
Size: 21.3 MB

Statistics

Stars: 48
Watchers: 2
Forks: 7
Open Issues: 5
Releases: 48

Topics

cheminformatics chemistry chemistry-development-kit docker microservices-architecture openbabel rdkit reactjs

Created almost 3 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

README.md

Cheminformatics Microservice & UI

🌐 Overview

A comprehensive cheminformatics solution consisting of:

Backend Microservices API that provides cheminformatics functionality through API calls:
- Translating between different machine-readable representations
- Calculating Natural Product (NP) likeliness scores
- Visualizing chemical structures
- Generating descriptors
- Hosting instances of DECIMER for optical chemical structure recognition
Modern React Frontend that provides an intuitive user interface for:
- Chemical structure analysis and validation
- Format conversion (SMILES, InChI, IUPAC, etc.)
- 2D and 3D molecular visualization
- Optical Chemical Structure Recognition (OCSR)
- Molecular property calculation

Important Note: STOUT (Smiles-TO-iUpac-Translator) is currently unavailable due to legal issues.

📚 Documentation

Backend API

Comprehensive documentation is available at: https://docs.api.naturalproducts.net/

API Swagger Docs

Production: https://api.naturalproducts.net/latest/docs
Development: https://dev.api.naturalproducts.net/latest/docs

⚛️ Frontend Application

The frontend application provides a modern, user-friendly interface to the cheminformatics microservices.

Key Features

Chemical Analysis Tools:
- Structure validation and standardization
- Molecular descriptor calculation
- Stereoisomer generation
- Natural product likeness scoring
- Functional group detection (Ertl)
- Tautomer standardization
- HOSE code generation
- Tanimoto similarity calculation
Format Conversion:
- SMILES to various chemical formats (InChI, InChIKey, SELFIES, etc.)
- IUPAC name to SMILES conversion
- 2D/3D coordinate generation (Molblock)
Molecule Depiction:
- 2D molecule visualization with customizable settings
- Interactive 3D molecule visualization
- Batch depiction for multiple molecules
OCSR (Optical Chemical Structure Recognition):
- Convert chemical structure images to SMILES notation

Technical Stack

React 18: Core UI library
React Router 6: Client-side routing
Tailwind CSS: Utility-first styling
Framer Motion: Enhanced UI animations
Axios: API communication
React Dropzone: File upload handling

Frontend Architecture

Component-Based Design: Modular components for reusability and maintainability
Service Layer: Specialized services for API interaction
Context API: Global state management for theme, recent molecules, etc.
Responsive Design: Mobile-first approach with responsive layouts
Dark/Light Theme: Full theme support with Tailwind dark mode

Installation & Setup (Frontend)

```bash

Clone the repository

git clone https://github.com/Steinbeck-Lab/cheminformatics-microservice.git cd cheminformatics-microservice/frontend

Install dependencies

npm install

Start development server

npm start

Build for production

npm run build ```

For detailed frontend configuration options, see the Frontend Documentation.

💻 Backend Installation

You can run Cheminformatics Microservice in multiple ways:

As a standalone application using a Python virtual environment
Via Docker
Deploy to a Kubernetes cluster using Helm charts

For detailed instructions, please refer to:

📈 Load Ramping Test Results

View the latest load ramping test results from September 29, 2023: Test Results Discussion

📜 License

This project is licensed under the MIT License. See the LICENSE file for details.

📰 Citation

Paper

Chandrasekhar, V., Sharma, N., Schaub, J. et al. Cheminformatics Microservice: unifying access to open cheminformatics toolkits. J Cheminform 15, 98 (2023). https://doi.org/10.1186/s13321-023-00762-4

Software

Venkata, C., Sharma, N., & Rajan, K. (2023). Cheminformatics Microservice (Version v2.6.0) [Computer software]. https://zenodo.org/records/13867839

🔧 Maintenance

Cheminformatics Microservice and Natural Products Online are developed and maintained by the Steinbeck group at the Friedrich Schiller University Jena, Germany.

💡 Acknowledgments

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI4Chem – Project number: 441958208 and ChemBioSys (Project INF) - Project number: 239748522 - SFB 1127.

Owner

Name: Steinbeck-Lab
Login: Steinbeck-Lab
Kind: organization

Website: https://cheminf.uni-jena.de
Repositories: 28
Profile: https://github.com/Steinbeck-Lab

Official GitHub organization for the Steinbeck group Jena, Germany

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Venkata"
  given-names: "Chandrasekhar"
  orcid: "https://orcid.org/0000-0002-2564-3243"
- family-names: "Sharma"
  given-names: "Nisha"
  orcid: "https://orcid.org/0009-0006-4755-1039"
- family-names: "Schaub"
  given-names: "Jonas"
  orcid: "https://orcid.org/0000-0003-1554-6666"
- family-names: "Steinbeck"
  given-names: "Christoph"
  orcid: "https://orcid.org/0000-0001-6966-0814"
- family-names: "Rajan"
  given-names: "Kohulan"
  orcid: "https://orcid.org/0000-0003-1066-7792"
title: "cheminformatics-microservice"
version: v3.3.0
doi: 10.5281/zenodo.15575699
date-released: 2025-06-02
url: "https://github.com/Steinbeck-Lab/cheminformatics-microservice"

GitHub Events

Total

Create event: 22
Release event: 9
Issues event: 25
Watch event: 19
Delete event: 11
Issue comment event: 65
Member event: 1
Push event: 193
Pull request review comment event: 9
Pull request review event: 48
Pull request event: 124
Fork event: 3

Last Year

Create event: 22
Release event: 9
Issues event: 25
Watch event: 19
Delete event: 11
Issue comment event: 65
Member event: 1
Push event: 193
Pull request review comment event: 9
Pull request review event: 48
Pull request event: 124
Fork event: 3

Committers

Last synced: about 2 years ago

All Time

Total Commits: 548
Total Committers: 7
Avg Commits per committer: 78.286
Development Distribution Score (DDS): 0.571

Past Year

Commits: 532
Committers: 6
Avg Commits per committer: 88.667
Development Distribution Score (DDS): 0.558

Top Committers

Name	Email	Commits
Kohulan	k**n@u**e	235
NishaSharma14	s**4@g**m	168
Venkata Chandra Sekhar Nainala	m**6@g**m	97
Nisha Sharma	5****4	29
github-actions[bot]	4****]	8
NRayya	8****a	7
dependabot[bot]	4****]	4

Committer Domains (Top 20 + Academic)

uni-jena.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 72
Total pull requests: 154
Average time to close issues: 3 months
Average time to close pull requests: 3 days
Total issue authors: 8
Total pull request authors: 9
Average comments per issue: 0.51
Average comments per pull request: 0.47
Merged pull requests: 128
Bot issues: 0
Bot pull requests: 10

Past Year

Issues: 13
Pull requests: 69
Average time to close issues: 7 days
Average time to close pull requests: 2 days
Issue authors: 6
Pull request authors: 8
Average comments per issue: 0.31
Average comments per pull request: 0.35
Merged pull requests: 52
Bot issues: 0
Bot pull requests: 4

View more stats

Top Authors

Issue Authors

CS76 (35)
vcnainala (12)
Kohulan (11)
NishaSharma14 (11)
sriramkanakam87 (3)
cthoyt (2)
alexey-krasnov (1)
fbaensch-beilstein (1)

Pull Request Authors

Kohulan (132)
NishaSharma14 (42)
dependabot[bot] (20)
CS76 (16)
sriramkanakam87 (2)
fbaensch-beilstein (2)
vcnainala (1)
egonw (1)
steinbeck (1)

Top Labels

Issue Labels

enhancement (17) bug (12) wip (11) wontfix (5) documentation (5) needs further discussion (3)

Pull Request Labels

dependencies (20) autorelease: pending (20) javascript (10) python (9) autorelease: tagged (7) wip (2) testing (1)

Dependencies

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google-github-actions/release-please-action v3 composite

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Dockerfile docker

continuumio/miniconda3 latest build

docker-compose.yml docker

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prom/prometheus latest

ops/docker-compose-dev.yml docker

caffeinejena/cheminformatics-python-microservice dev-latest
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traefik v2.10

ops/docker-compose-prod.yml docker

caffeinejena/cheminformatics-python-microservice v1.0.0
grafana/grafana latest
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traefik v2.10

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package.json npm

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