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chemconf-analysis

Combined Python/Linux scritp for conformational analysis of a xyz file containing multiple structures, based on RMSD and additional geometrical constrains

https://github.com/andresmacons/chemconf-analysis

Science Score: 67.0%

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    Found 11 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (11.8%) to scientific vocabulary

Keywords

chemistry conformational-analysis python
Last synced: 6 months ago · JSON representation ·

Repository

Combined Python/Linux scritp for conformational analysis of a xyz file containing multiple structures, based on RMSD and additional geometrical constrains

Basic Info
  • Host: GitHub
  • Owner: Andresmacons
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 374 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
chemistry conformational-analysis python
Created over 1 year ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

alt text

DOI

Combined Python/Linux scritp for conformational analysis of a xyz file containing multiple structures, based on RMSD and additional geometrical constrains.

Available for Jupyter Notebooks.

Instructions

  • Get your .xyz file with multiple structures. Make sure the .xyz file saved the geometries in the proper format, including atom number and energy. This is crucial for line counting and slicing the document.
  • Stablish the desired RMSD threshold (by default 1 Å is choosen) and the particular geometrical constrains
  • Run the script. It will create the required new folders (conformers and finalconformers_)
  • Once finishing, you will obtain the .xyz files for every "unique" conformer in the file.

Requirements

  • Python
  • Linux

License

ChemConf-Analysis is freely available under an MIT license

References

If you use ChemConf-Analysis, please include this citation: Álvarez-Constantino, A. M. (2024). ChemConf-Analysis (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.14266368

Additionally, please include the corresponding references for the following programs: - Chemcoord: paper and documentation - Pandas: documentation and Zenodo repository link - Numpy: paper and documentation

Related scientific works

References and examples will be added soon...

Owner

  • Name: Andres M. Álvarez-Constantino
  • Login: Andresmacons
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Álvarez-Constantino
    given-names: Andrés M.
    orcid: https://orcid.org/0000-0001-8948-1258
title: "ChemConf-Analysis"
version: 1.0.0
doi: 10.5281/zenodo.14266368
date-released: 2024-12-08
url: https://github.com/Andresmacons/ChemConf-Analysis

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