hfold 0.0.2

HFold: Python bindings for the HFold C++ library

How to test the hfold python package

1. Make sure you have ViennaRNA installed on your system

ViennaRNA package installation

The hfold package requires ViennaRNA to be installed before compilation.

1. Download the ViennaRNA package: ViennaRNA-2.7.0.tar.gz

2. Install the Package:

tar -zxvf ViennaRNA-2.7.0.tar.gz
cd ViennaRNA-2.7.0
./configure --without-perl
sudo make -j$(nproc)              # Linux
sudo make -j$(sysctl -n hw.ncpu)  # macOS
sudo make install

More info: ViennaRNA GitHub

2. Setup a Virtual Environment

Make sure you're in a virtual environment

python3 -m venv venv
source venv/bin/activate

3. Install Python Dependencies

Make sure you have pybind11 and setuptools installed

sudo apt install pybind11-dev # linux
brew install pybind11 # MacOS
python3 -m pip install pybind11 setuptools scikit-build

4. Build the Python Extension

From the project root:

cd ./pylib
python3 setup.py build_ext --inplace

5. Start Python (From the pylib Directory)

python3

6. Run Test Commands

Once in the Python shell, you can test hfold:

import hfold

# Basic sequence folding
hfold.hfold("AGGGCUAUCCUU", param_file="../params/rna_DirksPierce09.par")[0][0]

# Folding with suboptimal structures
hfold.hfold("AGGGCUAUCCUU", subopt=5, param_file="../params/rna_DirksPierce09.par")[0]

# Folding sequences from file
hfold.hfold(subopt=2, fileI="./sample_inputs/sample.txt", param_file="../params/rna_DirksPierce09.par")

Full List of Parameters

Parameter	Type	Description
sequence	str	RNA sequence
restriction	str	Folding constraint
pk_free	bool	Exclude pseudoknots
pk_only	bool	Only allow pseudoknots
dangles	int	Dangle configuration
subopt	int	Number of suboptimal structures
fileI	str	Input file path
fileO	str	Output file path
param_file	str	Thermodynamic parameters file
noConv_given	bool	Do not convert DNA into RNA
suppress_output	bool	Suppress console output

Build wheels

python -m pip install --upgrade cibuildwheel scikit-build-core twine pybind11 setuptools # install pre-req
cibuildwheel pylib --output-dir dist # build
python -m twine upload dist/* # upload