https://github.com/deepmodeling/reacnetgenerator

an automatic reaction network generator for reactive molecular dynamics simulation
https://github.com/deepmodeling/reacnetgenerator

hmm md network python reaction reactive

Last synced: about 2 months ago
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an automatic reaction network generator for reactive molecular dynamics simulation

• Host: GitHub
• URL: https://github.com/deepmodeling/reacnetgenerator
• Owner: deepmodeling
• License: lgpl-3.0
• Created: 2018-04-06T15:07:56.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2025-03-17T19:52:40.000Z (about 2 months ago)
• Last Synced: 2025-03-17T20:39:30.708Z (about 2 months ago)
• Topics: hmm, md, network, python, reaction, reactive
• Language: Python
• Homepage: https://docs.deepmodeling.com/projects/reacnetgenerator/
• Size: 32.1 MB
• Stars: 83
• Watchers: 7
• Forks: 41
• Open Issues: 18
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

        
#  ReacNetGenerator

[![DOI:10.1039/C9CP05091D](https://img.shields.io/badge/DOI-10.1039%2FC9CP05091D-blue)](https://doi.org/10.1039/C9CP05091D)

[![Citations](https://citations.njzjz.win/10.1039/C9CP05091D)](https://doi.org/10.1039/C9CP05091D)

[![Research Group](https://img.shields.io/website-up-down-green-red/https/computchem.cn.svg?label=Research%20Group)](https://computchem.cn)

An automatic reaction network generator for reactive molecular dynamics simulation.

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamic simulations, Phys. Chem. Chem. Phys., 2020, 22 (2): 683–691, doi: [10.1039/C9CP05091D](https://dx.doi.org/10.1039/C9CP05091D)

[email protected] (Jinzhe Zeng), [email protected] (Tong Zhu)

## Features

- Processing of MD trajectory containing atomic coordinates or bond orders

- Hidden Markov Model (HMM) based noise filtering

- Isomers identifying accoarding to SMILES

- Generation of reaction network for visualization using force-directed algorithm

- Parallel computing

## Guide and Tutorial

The latest version requires Python 3.7 or later.

You can install ReacNetGenerator with `conda`:

```sh

conda install reacnetgenerator -c conda-forge

reacnetgenerator -h

```

See [the guide](https://docs.deepmodeling.com/projects/reacnetgenerator/en/latest/guide/) to learn how to install and use ReacNetGenerattor. We also provide [a series of tutorials](https://docs.deepmodeling.com/projects/reacnetgenerator/en/latest/tutorial/) to help you learn ReacNetGenerator.

## Awards

- The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students

- The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students

## Acknowledge

- National Natural Science Foundation of China (Grants No. 91641116)

- National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)

- ECNU Multifunctional Platform for Innovation (No. 001)