Welcome to drugforge's documentation!
=========================================
<img src="_static/drugforge_logo.png" width="200">

All pandemics are global health threats. Our best defense is a healthy global antiviral discovery community with a robust pipeline of open discovery tools.

The toolkit in this repo is a batteries-included drug discovery pipeline being actively developed in a transparent open-source way, with a focus on computational chemistry and informatics support for medicinal chemistry.

This project is a fork of  [ASAPDiscovery](https://github.com/asapdiscovery/asapdiscovery) by the ASAP Discovery Consortium. We thank the original authors for their work and for making it available under MIT license.

This fork is now developed and maintained independently by the [Chodera Lab](https://www.choderalab.org/).

```{note}
drugforge is not designed as a one size fits all solution for drug discovery, rather it is our opinionated tooling designed with our targets in mind. Your mileage will vary if not using an ASAP target. We will be working towards more general solutions in future releases.
```

```{warning}
The implementation of drugforge-ML is still in the works and will be available in the next release. If you want to use ML scoring please refer to the original version of this code under [asapdiscovery](https://github.com/asapdiscovery/asapdiscovery).
```

The `drugforge` toolkit is focused around the following core competencies, organised into submodules:

 - `drugforge-alchemy`: Free energy calculations using [OpenFE](https://openfree.energy/) and [Alchemiscale](https://github.com/openforcefield/alchemiscale)

 - `drugforge-cli`: Command line tools uniting the whole repo.

 - `drugforge-data`: Core data models and integrations with services such as [postera.ai](https://postera.ai/) , [Collaborative Drug Discovery Vault](https://www.collaborativedrug.com/)`, and Diamond Light Source's [Fragalysis](https://fragalysis.diamond.ac.uk/viewer/react/landing) database

 - `drugforge-dataviz`: Data and structure visualization using [3DMol](https://3dmol.csb.pitt.edu) and [PyMOL](https://pymol.org/)

 - `drugforge-docking`: Docking and compound screening with the [OpenEye toolkit](https://docs.eyesopen.com/toolkits/python/index.html)

 - `drugforge-spectrum`: Working with sequence and fitness information and conducting protein structure inference

 - `drugforge-ml`: Structure and graph based ML models for predicting compound activity and other endpoints

 - `drugforge-modelling`: Structure prep and standardisation

 - `drugforge-simulation`: MD simulations and analysis using [OpenMM](https://openmm.org/)

 - `drugforge-workflows`: Workflows that combine components to enable end to end project support


The `drugforge` toolkit is currently focused on [ASAP's targets](https://asapdiscovery.org/pipeline/), which are enumerated on the ASAP website.

See `future` for more information on our roadmap and future plans for the toolkit.


Disclaimer
----------
drugforge is pre-alpha and is under very active development, we make no guarantees around correctness and the API is liable to change rapidly at any time.


```{toctree}
:maxdepth: 5
:hidden:
installation
tutorials/index
guides/index
ecosystem/index
future/index
API/index
```