Metadata-Version: 2.4
Name: chromdyn
Version: 0.2.0
Summary: Tools for chromosome dynamics modeling and analysis
Author-email: Sumitabha Brahmachari <b.sumitabha@gmail.com>
License-Expression: MIT
Project-URL: Homepage, https://github.com/s-brahmachari/chromdyn
Project-URL: Source, https://github.com/s-brahmachari/chromdyn
Project-URL: Issues, https://github.com/s-brahmachari/chromdyn/issues
Keywords: chromosome,dynamics,biophysics,polymer
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy==1.26
Requires-Dist: scipy>=1.11
Requires-Dist: pandas>=2.0
Requires-Dist: openmm>=8.0
Requires-Dist: h5py>=3.15
Dynamic: license-file

# chromdyn
*A Python library for chromosome dynamics simulation and analysis with options to integrate Hi-C data.*

## Overview

`chromdyn` provides tools for building, simulating, and analyzing 3D chromosome structures.  
It uses **OpenMM** for fast CPU/GPU simulations and includes:

- Polymer topology generation  
- Customizable force fields  
- Hi-C-based restraints  
- Simulation utilities  
- Analysis tools

## Installation

### From PyPI

```
pip install chromdyn
```

### From source (development)

```
git clone https://github.com/s-brahmachari/chromdyn
cd chromdyn
pip install -e .
```

## Verify Installation

Run the built-in test script:

```
python -m chromdyn.check_install
```

## Quick Example

```python
from chromdyn import ChromatinDynamics, TopologyGenerator

gen = TopologyGenerator()
gen.gen_top([100])

sim = ChromatinDynamics(
    gen.topology,
    name="demo",
    platform_name="CPU",
)

sim.force_field_manager.add_harmonic_bonds()
sim.simulation_setup(
    init_struct="randomwalk",
    integrator="langevin",
    temperature=300.0,
    timestep=0.01,
)

sim.run(1000)
```

## Tutorials

See the `notebooks/` directory for examples on:

- Building polymer models  
- Running simulations  
- Using Hi-C restraints  
- Analyzing trajectories  


## License

MIT License.
