Metadata-Version: 2.4
Name: hashrope-bio
Version: 0.1.0
Summary: Computational biology applications of hash rope data structures
Author-email: Muntaser Syed <muntaser@ieee.org>
License-Expression: MIT
License-File: LICENSE
Keywords: bioinformatics,drug-discovery,genomics,hash-rope,sequence-comparison
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: hashrope>=0.1.0
Provides-Extra: bench
Requires-Dist: biopython>=1.83; extra == 'bench'
Requires-Dist: matplotlib>=3.8; extra == 'bench'
Requires-Dist: mdanalysis>=2.7; extra == 'bench'
Requires-Dist: numpy>=1.26; extra == 'bench'
Requires-Dist: pandas>=2.0; extra == 'bench'
Requires-Dist: pysam>=0.22; extra == 'bench'
Requires-Dist: rdkit; extra == 'bench'
Provides-Extra: cheminformatics
Requires-Dist: rdkit; extra == 'cheminformatics'
Provides-Extra: dev
Requires-Dist: pytest-benchmark>=4.0; extra == 'dev'
Requires-Dist: pytest>=8.0; extra == 'dev'
Provides-Extra: genomics
Requires-Dist: biopython>=1.83; extra == 'genomics'
Requires-Dist: pysam>=0.22; extra == 'genomics'
Provides-Extra: proteomics
Requires-Dist: mdanalysis>=2.7; extra == 'proteomics'
Requires-Dist: numpy>=1.26; extra == 'proteomics'
Description-Content-Type: text/markdown

# hashrope-bio

Computational biology applications of [hashrope](https://github.com/jemsbhai/hashrope) —
O(log w) substring hashing for genomic region comparison, mutation localization,
tandem repeat compression, MD trajectory indexing, and drug resistance screening.

## Install

```bash
pip install -e ".[genomics,bench,dev]"
```

## Project structure

```
src/hashrope_bio/
├── genomics/          # FASTA loading, region queries, mutation search, tandem repeats
├── proteomics/        # MD trajectory frame comparison, periodic detection
└── cheminformatics/   # SMILES/InChI compound lookup, resistance panels
benchmarks/            # Experiment scripts (E-G1 through E-CG1)
scripts/               # Dataset download helpers
data/                  # Downloaded datasets (gitignored)
tests/                 # Unit tests
```

## Experiments

See `../../experiments/EXPERIMENTS.md` for the full protocol.

Run a benchmark:
```bash
python benchmarks/bench_region_query.py
```

## Depends on

- [hashrope](https://pypi.org/project/hashrope/) (PyPI) — core data structure
- pysam / biopython — FASTA I/O
- MDAnalysis — trajectory I/O
- RDKit — cheminformatics

## License

MIT
