Metadata-Version: 2.4
Name: molnetpack
Version: 1.2.0
Summary: 3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
Author: Yuhui Hong, Sujun Li, Christopher J Welch, Shane Tichy, Yuzhen Ye, Haixu Tang
Maintainer-email: Yuhui Hong <yuhhong@iu.edu>
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
License-File: LICENSE
Requires-Dist: absl-py
Requires-Dist: beautifulsoup4
Requires-Dist: filelock
Requires-Dist: gdown
Requires-Dist: grpcio
Requires-Dist: importlib-metadata
Requires-Dist: lxml
Requires-Dist: markdown
Requires-Dist: markupsafe
Requires-Dist: molmass
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: protobuf
Requires-Dist: pysocks
Requires-Dist: pyteomics
Requires-Dist: soupsieve
Requires-Dist: tensorboard
Requires-Dist: PyYAML
Requires-Dist: rdkit
Requires-Dist: matplotlib
Requires-Dist: pillow
Project-URL: Changelog, https://github.com/JosieHong/3DMolMS/blob/main/CHANGE_LOG.md
Project-URL: Homepage, https://github.com/JosieHong/3DMolMS/
Project-URL: Issues, https://github.com/JosieHong/3DMolMS/issues

# 3DMolMS

[![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa] (free for academic use) 

**3D** **Mol**ecular Network for **M**ass **S**pectra Prediction (3DMolMS) is a deep neural network model to predict the MS/MS spectra of compounds from their 3D conformations. This model's molecular representation, learned through MS/MS prediction tasks, can be further applied to enhance performance in other molecular-related tasks, such as predicting retention times (RT) and collision cross sections (CCS). 

[Paper](https://academic.oup.com/bioinformatics/article/39/6/btad354/7186501) | [Document](https://3dmolms.readthedocs.io/en/latest/) | [Workflow on Konia](https://koina.wilhelmlab.org/docs#post-/3dmolms_qtof/infer) | [PyPI package](https://pypi.org/project/molnetpack/)

🆕 3DMolMS v1.2.0 is now available for inference on **Konia**, and **PyPI**! 

The changes log can be found at [./CHANGE_LOG.md](./CHANGE_LOG.md). 

## Citation

```
@article{hong20233dmolms,
  title={3DMolMS: prediction of tandem mass spectra from 3D molecular conformations},
  author={Hong, Yuhui and Li, Sujun and Welch, Christopher J and Tichy, Shane and Ye, Yuzhen and Tang, Haixu},
  journal={Bioinformatics},
  volume={39},
  number={6},
  pages={btad354},
  year={2023},
  publisher={Oxford University Press}
}
@article{hong2024enhanced,
  title={Enhanced structure-based prediction of chiral stationary phases for chromatographic enantioseparation from 3D molecular conformations},
  author={Hong, Yuhui and Welch, Christopher J and Piras, Patrick and Tang, Haixu},
  journal={Analytical Chemistry},
  volume={96},
  number={6},
  pages={2351--2359},
  year={2024},
  publisher={ACS Publications}
}
```

## License

This work is licensed under a
[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa].

[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa]

[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0/
[cc-by-nc-sa-image]: https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png
[cc-by-nc-sa-shield]: https://img.shields.io/badge/License-CC%20BY--NC--SA%204.0-lightgrey.svg
