MBN-tools 1.0.0

Useful tools for use with MBN Explorer simulations, files, and their analysis

MBN Tools

MBN Tools provides a set of utilities for running, processing, and analysing simulations with MBN Explorer.

Features

• Run MBN Explorer simulations
  Run MBN Explorer simulation tasks directly from Python.

• File handling utilities
  Create, read, modify, and convert simulation input/output files including .task, .xyz, .dcd, and.pdb.

• Trajectory analysis
  Analyze simulation outputs, including radial distribution functions (RDF), mean squared displacement (MSD), RMSD, and more.

• Crystallography utilities
  Group atoms by crystallographic planes, translate coordinates to planes, and remove atoms near simulation boundaries.

• 3D visualisation
  Render atoms, planes, and simulation boxes in 3D using VisPy with customisable colours, sizes, and markers.

Installation

pip install MBN-tools

Usage

import MBN_tools as MBN
from MBN_tools import analysis, crystallography, visualise

# Run an MBN Explorer simulation
stdout, stderr = MBN.run_task("example.task", "/path/to/MBN_Explorer")

# Read an XYZ file
xyz_data = MBN.read_xyz("simulation.xyz")

# Compute RMSD
rmsd_values = analysis.calculate_rmsd(xyz_data, box_size=[50, 50, 100])

# Group atoms by a crystalline plane
planes = crystallography.group_atoms_by_plane(xyz_data, hkl=(1,1,0), tolerance=0.5)

# Visualize atoms in 3D
canvas = visualise.create_canvas()
visualise.draw_atoms(xyz_data['coordinates'], parent=canvas.central_widget.add_view())

Dependencies

• numpy >= 1.26
• scipy >= 1.12
• mdtraj
• vispy