gmxtopology 0.2.0

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

For Jupyter/IPython kernel support, install the optional notebook extra:

pip install "gmxtopology[notebook]"

From source:

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

Usage

See examples/example.ipynb for a fuller walkthrough. The packaged walkthrough uses the single self-contained examples/example.top file.

from gmxtopology import Topology

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

# modifying topology parameters
for atom in top.molecules['MOL'][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)

Topology preprocessing

The reader follows local #include directives relative to the including file and preserves conditional topology sections when writing a modified topology. Supported directives include:

• #define NAME and #define NAME replacement text
• #ifdef NAME and #ifndef NAME
• #else and #endif, including nested blocks
• #include "relative/path.itp"

Missing includes remain errors unless they occur inside a conditional block. This allows topologies with absent optional restraint files to load when those files are referenced only behind flags such as #ifdef REST_ON.

For free-energy topologies, [ atoms ] records and supported bonded interactions may also include the optional topology-B parameters documented by GROMACS. They are exposed with _b suffixes, such as charge_b, b0_b, and kb_b.

Sections that gmxtopology does not edit are carried through as opaque records when writing a flattened topology. This preserves force-field-specific data such as CHARMM [ cmaptypes ], [ implicit_genborn_params ], and molecular [ cmap ] sections.

Written topologies contain only the [ atomtypes ] used by molecules in the [ molecules ] section or referenced by preserved opaque global sections. Bonded parameter tables such as [ bondtypes ], [ angletypes ], and [ dihedraltypes ] are resolved onto molecular interactions and omitted from the output. Relevant [ nonbond_params ] entries remain global because they cannot be expanded onto bonded records.

Testing

Run the parser regression suite with:

python -m pytest

The repository test suite includes pinned official GROMACS fixtures covering SPC/E, TIP3P, TIP4P, and urea topologies, plus prosECCo75 CHARMM36-derived fixtures covering POPC and CMAP tables. A curated ParmEd GmxTests snapshot adds real-world water, peptide, solvated protein, mixed-solvent, and DPPC cases.

PyPI distributions intentionally contain only the package code, documentation, the example notebook, and its small self-contained topology. Clone the repository explicitly when you need the larger examples and regression fixtures:

git clone --depth 1 https://github.com/vojtechkostal/gmxtopology.git

Changelog

See CHANGELOG.md for release highlights.

Publishing

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