# Chemprop
[](https://badge.fury.io/py/chemprop)
[](https://badge.fury.io/py/chemprop)
[](https://anaconda.org/conda-forge/chemprop)
[](https://github.com/chemprop/chemprop/actions/workflows/tests.yml)
[](https://chemprop.readthedocs.io/en/latest/?badge=latest)
[](https://opensource.org/licenses/MIT)
[](https://pepy.tech/project/chemprop)
[](https://pepy.tech/project/chemprop)
[](https://pepy.tech/project/chemprop)
Chemprop is a repository containing message passing neural networks for molecular property prediction.
Documentation can be found [here](https://chemprop.readthedocs.io/en/latest/).
There are tutorial notebooks in the [`examples/`](https://github.com/chemprop/chemprop/tree/main/examples) directory.
Chemprop recently underwent a ground-up rewrite and new major release (v2.0.0). A helpful transition guide from Chemprop v1 to v2 can be found [here](https://docs.google.com/spreadsheets/u/3/d/e/2PACX-1vRshySIknVBBsTs5P18jL4WeqisxDAnDE5VRnzxqYEhYrMe4GLS17w5KeKPw9sged6TmmPZ4eEZSTIy/pubhtml). This includes a side-by-side comparison of CLI argument options, a list of which arguments will be implemented in later versions of v2, and a list of changes to default hyperparameters.
**License:** Chemprop is free to use under the [MIT License](LICENSE.txt). The Chemprop logo is free to use under [CC0 1.0](docs/source/_static/images/logo/LICENSE.txt).
**References**: Please cite the appropriate papers if Chemprop is helpful to your research.
- Chemprop was initially described in the papers [Analyzing Learned Molecular Representations for Property Prediction](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00237) for molecules and [Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction](https://doi.org/10.1021/acs.jcim.1c00975) for reactions.
- The interpretation functionality (available in v1, but not yet implemented in v2) is based on the paper [Multi-Objective Molecule Generation using Interpretable Substructures](https://arxiv.org/abs/2002.03244).
- Chemprop now has its own dedicated manuscript that describes and benchmarks it in more detail: [Chemprop: A Machine Learning Package for Chemical Property Prediction](https://doi.org/10.1021/acs.jcim.3c01250).
- A paper describing and benchmarking the changes in v2.0.0 is forthcoming.
**Selected Applications**: Chemprop has been successfully used in the following works.
- [A Deep Learning Approach to Antibiotic Discovery](https://www.cell.com/cell/fulltext/S0092-8674(20)30102-1) - _Cell_ (2020): Chemprop was used to predict antibiotic activity against _E. coli_, leading to the discovery of [Halicin](https://en.wikipedia.org/wiki/Halicin), a novel antibiotic candidate. Model checkpoints are availabile on [Zenodo](https://doi.org/10.5281/zenodo.6527882).
- [Discovery of a structural class of antibiotics with explainable deep learning](https://www.nature.com/articles/s41586-023-06887-8) - _Nature_ (2023): Identified a structural class of antibiotics selective against methicillin-resistant _S. aureus_ (MRSA) and vancomycin-resistant enterococci using ensembles of Chemprop models, and explained results using Chemprop's interpret method.
- [ADMET-AI: A machine learning ADMET platform for evaluation of large-scale chemical libraries](https://www.biorxiv.org/content/10.1101/2023.12.28.573531v1): Chemprop was trained on 41 absorption, distribution, metabolism, excretion, and toxicity (ADMET) datasets from the [Therapeutics Data Commons](https://tdcommons.ai). The Chemprop models in ADMET-AI are available both as a web server at [admet.ai.greenstonebio.com](https://admet.ai.greenstonebio.com) and as a Python package at [github.com/swansonk14/admet_ai](https://github.com/swansonk14/admet_ai).
- A more extensive list of successful Chemprop applications is given in our [2023 paper](https://doi.org/10.1021/acs.jcim.3c01250)
## Version 1.x
For users who have not yet made the switch to Chemprop v2.0, please reference the following resources.
### v1 Documentation
- Documentation of Chemprop v1 is available [here](https://chemprop.readthedocs.io/en/v1.7.1/). Note that the content of this site is several versions behind the final v1 release (v1.7.1) and does not cover the full scope of features available in chemprop v1.
- The v1 [README](https://github.com/chemprop/chemprop/blob/v1.7.1/README.md) is the best source for documentation on more recently-added features.
- Please also see descriptions of all the possible command line arguments in the v1 [`args.py`](https://github.com/chemprop/chemprop/blob/v1.7.1/chemprop/args.py) file.
### v1 Tutorials and Examples
- [Benchmark scripts](https://github.com/chemprop/chemprop_benchmark) - scripts from our 2023 paper, providing examples of many features using Chemprop v1.6.1
- [ACS Fall 2023 Workshop](https://github.com/chemprop/chemprop-workshop-acs-fall2023) - presentation, interactive demo, exercises on Google Colab with solution key
- [Google Colab notebook](https://colab.research.google.com/github/chemprop/chemprop/blob/v1.7.1/colab_demo.ipynb) - several examples, intended to be run in Google Colab rather than as a Jupyter notebook on your local machine
- [nanoHUB tool](https://nanohub.org/resources/chempropdemo/) - a notebook of examples similar to the Colab notebook above, doesn't require any installation
- [YouTube video](https://www.youtube.com/watch?v=TeOl5E8Wo2M) - lecture accompanying nanoHUB tool
- These [slides](https://docs.google.com/presentation/d/14pbd9LTXzfPSJHyXYkfLxnK8Q80LhVnjImg8a3WqCRM/edit?usp=sharing) provide a Chemprop tutorial and highlight additions as of April 28th, 2020
### v1 Known Issues
We have discontinued support for v1 since v2 has been released, but we still appreciate v1 bug reports and will tag them as [`v1-wontfix`](https://github.com/chemprop/chemprop/issues?q=label%3Av1-wontfix+) so the community can find them easily.
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"description": "\n# Chemprop\n\n[](https://badge.fury.io/py/chemprop)\n[](https://badge.fury.io/py/chemprop)\n[](https://anaconda.org/conda-forge/chemprop)\n[](https://github.com/chemprop/chemprop/actions/workflows/tests.yml)\n[](https://chemprop.readthedocs.io/en/latest/?badge=latest)\n[](https://opensource.org/licenses/MIT)\n[](https://pepy.tech/project/chemprop)\n[](https://pepy.tech/project/chemprop)\n[](https://pepy.tech/project/chemprop)\n\nChemprop is a repository containing message passing neural networks for molecular property prediction.\n\nDocumentation can be found [here](https://chemprop.readthedocs.io/en/latest/).\n\nThere are tutorial notebooks in the [`examples/`](https://github.com/chemprop/chemprop/tree/main/examples) directory.\n\nChemprop recently underwent a ground-up rewrite and new major release (v2.0.0). A helpful transition guide from Chemprop v1 to v2 can be found [here](https://docs.google.com/spreadsheets/u/3/d/e/2PACX-1vRshySIknVBBsTs5P18jL4WeqisxDAnDE5VRnzxqYEhYrMe4GLS17w5KeKPw9sged6TmmPZ4eEZSTIy/pubhtml). This includes a side-by-side comparison of CLI argument options, a list of which arguments will be implemented in later versions of v2, and a list of changes to default hyperparameters.\n\n**License:** Chemprop is free to use under the [MIT License](LICENSE.txt). The Chemprop logo is free to use under [CC0 1.0](docs/source/_static/images/logo/LICENSE.txt).\n\n**References**: Please cite the appropriate papers if Chemprop is helpful to your research.\n\n- Chemprop was initially described in the papers [Analyzing Learned Molecular Representations for Property Prediction](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00237) for molecules and [Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction](https://doi.org/10.1021/acs.jcim.1c00975) for reactions.\n- The interpretation functionality (available in v1, but not yet implemented in v2) is based on the paper [Multi-Objective Molecule Generation using Interpretable Substructures](https://arxiv.org/abs/2002.03244).\n- Chemprop now has its own dedicated manuscript that describes and benchmarks it in more detail: [Chemprop: A Machine Learning Package for Chemical Property Prediction](https://doi.org/10.1021/acs.jcim.3c01250).\n- A paper describing and benchmarking the changes in v2.0.0 is forthcoming.\n\n**Selected Applications**: Chemprop has been successfully used in the following works.\n\n- [A Deep Learning Approach to Antibiotic Discovery](https://www.cell.com/cell/fulltext/S0092-8674(20)30102-1) - _Cell_ (2020): Chemprop was used to predict antibiotic activity against _E. coli_, leading to the discovery of [Halicin](https://en.wikipedia.org/wiki/Halicin), a novel antibiotic candidate. Model checkpoints are availabile on [Zenodo](https://doi.org/10.5281/zenodo.6527882).\n- [Discovery of a structural class of antibiotics with explainable deep learning](https://www.nature.com/articles/s41586-023-06887-8) - _Nature_ (2023): Identified a structural class of antibiotics selective against methicillin-resistant _S. aureus_ (MRSA) and vancomycin-resistant enterococci using ensembles of Chemprop models, and explained results using Chemprop's interpret method.\n- [ADMET-AI: A machine learning ADMET platform for evaluation of large-scale chemical libraries](https://www.biorxiv.org/content/10.1101/2023.12.28.573531v1): Chemprop was trained on 41 absorption, distribution, metabolism, excretion, and toxicity (ADMET) datasets from the [Therapeutics Data Commons](https://tdcommons.ai). The Chemprop models in ADMET-AI are available both as a web server at [admet.ai.greenstonebio.com](https://admet.ai.greenstonebio.com) and as a Python package at [github.com/swansonk14/admet_ai](https://github.com/swansonk14/admet_ai).\n- A more extensive list of successful Chemprop applications is given in our [2023 paper](https://doi.org/10.1021/acs.jcim.3c01250)\n\n## Version 1.x\n\nFor users who have not yet made the switch to Chemprop v2.0, please reference the following resources.\n\n### v1 Documentation\n\n- Documentation of Chemprop v1 is available [here](https://chemprop.readthedocs.io/en/v1.7.1/). Note that the content of this site is several versions behind the final v1 release (v1.7.1) and does not cover the full scope of features available in chemprop v1.\n- The v1 [README](https://github.com/chemprop/chemprop/blob/v1.7.1/README.md) is the best source for documentation on more recently-added features.\n- Please also see descriptions of all the possible command line arguments in the v1 [`args.py`](https://github.com/chemprop/chemprop/blob/v1.7.1/chemprop/args.py) file.\n\n### v1 Tutorials and Examples\n\n- [Benchmark scripts](https://github.com/chemprop/chemprop_benchmark) - scripts from our 2023 paper, providing examples of many features using Chemprop v1.6.1\n- [ACS Fall 2023 Workshop](https://github.com/chemprop/chemprop-workshop-acs-fall2023) - presentation, interactive demo, exercises on Google Colab with solution key\n- [Google Colab notebook](https://colab.research.google.com/github/chemprop/chemprop/blob/v1.7.1/colab_demo.ipynb) - several examples, intended to be run in Google Colab rather than as a Jupyter notebook on your local machine\n- [nanoHUB tool](https://nanohub.org/resources/chempropdemo/) - a notebook of examples similar to the Colab notebook above, doesn't require any installation\n - [YouTube video](https://www.youtube.com/watch?v=TeOl5E8Wo2M) - lecture accompanying nanoHUB tool\n- These [slides](https://docs.google.com/presentation/d/14pbd9LTXzfPSJHyXYkfLxnK8Q80LhVnjImg8a3WqCRM/edit?usp=sharing) provide a Chemprop tutorial and highlight additions as of April 28th, 2020\n\n### v1 Known Issues\n\nWe have discontinued support for v1 since v2 has been released, but we still appreciate v1 bug reports and will tag them as [`v1-wontfix`](https://github.com/chemprop/chemprop/issues?q=label%3Av1-wontfix+) so the community can find them easily.\n",
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