ngpb4py 0.5.4

Thin Python wrapper for NextGenPB

ngpb4py

ngpb4py is a Python wrapper for running NextGenPB through a containerized workflow.

It provides:

• a typed configuration object for .prm files
• a high-level runner that stages inputs and executes NextGenPB
• structured parsing of key log sections and supported output files

Installation

If Apptainer is already installed on your system, install the package normally:

pip install ngpb4py

If Apptainer is not installed, prefer the Conda-based setup provided by this repository so both ngpb4py and apptainer are installed together:

wget https://raw.githubusercontent.com/pedrishi/ngpb4py/refs/heads/main/environment.yml
conda env create -f environment.yml
conda activate ngpb4py

For development or local docs/testing, install the project with its development dependencies:

uv sync --group dev

ngpb4py expects an Apptainer runtime to be available locally.

Quick Start

Using an existing .prm file:

from ngpb4py import NgpbConfig, NgpbRunner

config = NgpbConfig.from_prm("examples/exercise1/options.prm")
result = NgpbRunner(nproc=4).run(config=config, verbose=1)

print(result.log.energies.total_electrostatic_energy_kt)

Or running with defaults directly on a new .pdb file:

from ngpb4py import NgpbRunner

result = NgpbRunner(nproc=4).run(config={"filetype": "pdb", "filename": "examples/simple_4LZT/4LZT.pdb"})

print(result.log.energies.total_electrostatic_energy_kt)

Documentation

Documentation can be found here

License

This project is licensed under the GNU GPL v3.0.

ngpb4py is a separate Python wrapper project. It is not the NextGenPB solver itself, and its license statement applies to the wrapper code in this repository.

NextGenPB is the upstream solver project. That project is distributed separately, includes its own copyright notices, and is also marked there as GPL-3.0 licensed.