Metadata-Version: 2.4
Name: pestifer
Version: 2.1.4
Summary: A NAMD topology/coordinate system preparation tool
Project-URL: Source, https://github.com/cameronabrams/pestifer
Project-URL: Documentation, https://pestifer.readthedocs.io/en/latest/
Project-URL: Bug Tracker, https://github.com/cameronabrams/pestifer/issues
Author-email: Cameron F Abrams <cfa22@drexel.edu>
License-File: LICENSE
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.12
Requires-Dist: colorist
Requires-Dist: docutils<0.22,>=0.20
Requires-Dist: filelock
Requires-Dist: fsspec
Requires-Dist: gputil
Requires-Dist: joblib
Requires-Dist: matplotlib
Requires-Dist: mmcif
Requires-Dist: networkx
Requires-Dist: numpy>=1.24
Requires-Dist: pandas
Requires-Dist: pidibble>=1.5.2
Requires-Dist: platformdirs
Requires-Dist: progressbar2
Requires-Dist: pydantic
Requires-Dist: pyyaml>=6
Requires-Dist: scipy
Requires-Dist: sphinx>=8.2.3
Requires-Dist: unidiff
Requires-Dist: ycleptic>=2.0.1
Description-Content-Type: text/markdown

# Pestifer
> NAMD System Preparation Tool

[![PyPI](https://img.shields.io/pypi/v/pestifer.svg)](https://pypi.org/project/pestifer/)
[![PyPI Downloads](https://static.pepy.tech/badge/pestifer)](https://pepy.tech/projects/pestifer)
[![Docs](https://readthedocs.org/projects/pestifer/badge/?version=latest)](https://pestifer.readthedocs.io/en/latest/)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16051498.svg)](https://doi.org/10.5281/zenodo.16051498)

Pestifer is a fully automated simulation-ready MD system preparation tool, requiring as inputs only biomolecular structures (e.g., PDB IDs, PDB files, mmCIF files, alphafold IDs) and a handful of customization parameters, to generate NAMD-compatible input files (PSF, PDB, and xsc).  It is basically a highly functionalized front end for VMD's `psfgen` utility.  It also has a few handy subcommands for working with NAMD output.

## Installation

```bash
pip install pestifer
```

Once installed, the user has access to the main `pestifer` command. 

Pestifer also requires access to the following executables:

1. `namd3` and `charmrun`
2. `vmd` and `catdcd`
3. `packmol`

Pestifer **includes a copy of** the [July 2024 Charmm36 force field](https://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul24.tgz).

## Documentation

Please visit [readthedocs](https://pestifer.readthedocs.io/en/latest) for full documentation.

## Version History

See the [CHANGELOG](./CHANGELOG.md) for full details.

## Meta

[https://github.com/cameronabrams](https://github.com/cameronabrams/)

Pestifer is maintained by Cameron F. Abrams.

Pestifer is distributed under the MIT license. See ``LICENSE`` for more information.

Pestifer was developed with support from the National Institutes of Health via grants GM100472, AI154071, and AI178833.

## Contributing

1. Fork it (<https://github.com/cameronabrams/pestifer/fork>)
2. Create your feature branch (`git checkout -b feature/fooBar`)
3. Commit your changes (`git commit -am 'Add some fooBar'`)
4. Push to the branch (`git push origin feature/fooBar`)
5. Create a new Pull Request

