gmxtopology 0.1.0

A Python library for parsing and editing GROMACS topology files.

gmxtopology

Description

gmxtopology is a Python package for parsing and editing GROMACS topology files.

Package layout

The main flow is organized around a few top-level modules:

• gmxtopology.topology: topology data models
• gmxtopology.io: topology file reading and writing
• gmxtopology.parser: section parsing and dispatch
• gmxtopology.lookup: parameter lookup and virtual-site reduction helpers
• gmxtopology.schema: schema objects used by the parser
• gmxtopology.interaction_specs: GROMACS interaction tables

Installation

pip install gmxtopology

This installs ipykernel as well, so the environment is ready for Jupyter and IPython kernel use.

From source:

pip install git+https://github.com/vojtechkostal/gmxtopology.git

Usage

See examples/example.ipynb for a fuller walkthrough.

from gmxtopology import Topology

# load topology from file
fn_top = "./examples/topol.top"
top = Topology(fn_top)

# modifying topology parameters
for atom in top.molecules['POPC'][0].atoms:
    atom.update(charge=0.0)

for atomtype in top.atomtypes:
    atomtype.update(sigma=0.31)

# remove virtual sites from a molecule
top.molecules['SOL'][0].remove_vsites()

# write topology into a file
top.write("./examples/topol-processed.top", overwrite=True)

Publishing

GitHub Trusted Publishing is set up via publish.yml. The one-time PyPI and TestPyPI configuration steps are documented in docs/publishing.md.