semvec/pypi-packages huggingface dataset:
aleph 1.6.0
ALEPH is a bioinformatics tool for structure interpretation and generation of fragment-based library for Molecular Replacement.
Keywords: crystallography macromolecular bioinformatics networks

# ALEPH
ALEPH is a bioinformatics tool to generate fragment-based libraries for molecular replacement

ALEPH is a bioinformatics tool to generate customised fold libraries for fragment-based molecular replacement.
It provides several algorithms to interpret and analyse protein structures.

References:

ALEPH: a network-oriented approach for the generation of fragment-based
libraries and for structure interpretation
Medina A, Trivino J, Borges R, Millan C , Uson I and Sammito MD
(2019) Acta Cryst. D Study Weekend
                        
Exploiting tertiary structure through local folds for ab initio phasing
Sammito M, Millan C, Rodriguez DD, M. de Ilarduya I, Meindl K, De Marino I,
Petrillo G, Buey RM, de Pereda JM, Zeth K, Sheldrick GM and Uson I
(2013) Nat Methods. 10, 1099-1101.
                        
Email support: alephbugs@gmail.com
Bug tracking: https://gitlab.com/arcimboldo-team/ALEPH/-/issues
chromdyn 0.2.0
Tools for chromosome dynamics modeling and analysis
Requires Python: >=3.9
Keywords: chromosome, dynamics, biophysics, polymer

# 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.