Metadata-Version: 2.1
Name: HTPolyNet
Version: 1.0.9
Summary: Automated MD System Builder for Amorphous Network Polymers
Project-URL: Source, https://github.com/AbramsGroup/HTPolyNet
Project-URL: Documentation, https://abramsgroup.github.io/HTPolyNet/
Project-URL: Bug Tracker, https://github.com/AbramsGroup/HTPolyNet/issues
Author-email: Cameron F Abrams <cfa22@drexel.edu>
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.9
Requires-Dist: gputil>=1.4
Requires-Dist: networkx>=3.2
Requires-Dist: numpy>=1.24
Requires-Dist: pandas>=2
Requires-Dist: parmed>=4
Requires-Dist: pyyaml>=6
Requires-Dist: requests>=2.28
Requires-Dist: scipy>=1.10
Description-Content-Type: text/markdown

# HTPolyNet
> High-Throughput Polymer Network Atomistic Simulations

HTPolyNet is a Python utility for generating atomistic models of cross-linked polymer networks together with appropriate topology and parameter files required for molecular dynamics simulations using Gromacs.  It is intended as a fully automated system builder requiring as inputs only the molecular structures of any monomer species, a description of the polymerization chemistry, and a handful of options describing desired system size and composition.  HTPolyNet uses the Generalized Amber Force Field for atom-typing and parameter generation.

## Installation

From PyPI:
```bash
pip install htpolynet
```

From source:
```bash
git clone git@github.com:AbramsGroup/HTPolyNet.git
cd HTPolyNet
pip install -e .
```

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

IMPORTANT NOTE: The programs ``antechamber``, ``parmchk2`` and ``tleap`` from AmberTools must be in your path.  These can be installed using the ``ambertools`` package from ``conda-forge`` or compiled from source.

## Documentation

Please consult documentation at [abramsgroup.github.io/HTPolyNet](https://abramsgroup.github.io/HTPolyNet/).

## Release History
* 1.0.9
   * ``minimum_bondcycle_length`` parameter added to allow for cyclic polymerization above a certain threshold length
   * bugfixes: 
     * rings not transferred from monomer templates if they are pre-parameterized
     * atom indexes in bondchain structure not remapped after atom deletion
* 1.0.8
    * uses ``chordless_cycles`` to find rings; ringidx no long unique atom attribute; improved ring-pierce detection
* 1.0.7.2
    * moved Library package to resources subpackage of HTPolyNet.HTPolyNet
* 1.0.6
    * gmx-style analyze subcommand added
* 1.0.5
    * Post-build MD simulations and plotting functionalities added
* 1.0.2
    * Enhanced molecule-network graph drawing in the plot subcommand
* 1.0.1
    * Fixed atom index assignment issue for systems with more than 100,000 atoms
* 1.0.0
    * First release
* 0.0.1
    * Initial beta version

## Meta

Cameron F. Abrams – cfa22@drexel.edu

Distributed under the MIT license. See ``LICENSE`` for more information.

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

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

## Contributing

1. Fork it (<https://github.com/AbramsGroup/HTPolyNet/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

