Metadata-Version: 2.4
Name: mdna
Version: 0.0.1
Summary: Software module for DNA structure analysis and generation
Project-URL: Homepage, https://github.com/heezch/mdna
Author-email: Thor van Heesch <t.vanheesch@uva.nl>
License: MIT License
        
        Copyright (c) [2024] [Thor van Heesch]
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Keywords: Molecular Dynamics,Molecular Toolkit,Structuer Generation Tool,Structure Analysis
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.10
Requires-Dist: biopython
Requires-Dist: matplotlib
Requires-Dist: mdtraj
Requires-Dist: numba
Requires-Dist: numpy
Requires-Dist: scipy
Description-Content-Type: text/markdown

# MDNA: Molecular DNA Structure Generation and Analysis Toolkit

## Description
MDNA is a powerful molecular modeling tool designed to bridge the gap in generating starting structures for DNA and DNA-protein complexes for molecular dynamics (MD) simulations. By leveraging rigid body models, this tool enhances the precision in representing DNA structures, allowing for the inclusion of non-canonical bases, the adjustment of Watson-Crick to Hoogsteen configurations, methylation patterns, and structural extensions. It also provides robust analytical capabilities for MD simulations, calculating geometric properties, curvature, and protein-DNA interaction profiles.

## Installation
To install MDNA, follow these steps:
```bash
git clone --recurse-submodules https://github.com/heezch/mdna.git
```
After that go to the 'mdna' project folder and do:
```bash
pip install .
```

## Usage

See our [documentation page](https://heezch.github.io/mdna/)

## Contributing

We welcome contributions from the community! To contribute:

- Fork the repository.
- Create a new branch (`git checkout -b feature-branch`).
- Make your changes and commit them (`git commit -am 'Add new feature'`).
- Push to the branch (`git push origin feature-branch`).
- Create a new Pull Request.

Please ensure your code adheres to our coding standards and includes relevant tests.


## License

This project is licensed under the MIT License. See the LICENSE file for details.
