FishMol Documentation

FishMol is a pure-Python package for analysing molecular dynamics (MD) trajectories. It is designed for researchers working with periodic systems and aims to make common post-processing tasks — radial distribution functions, diffusion coefficients, hydrogen-bond lifetimes, vector reorientation dynamics — accessible with a clean, composable API.

Key Features

Feature	Module
Fast trajectory I/O (XYZ format, memory-mapped)	fishmol.trj
Atom/molecule selection and PBC-aware geometry	fishmol.atoms
Automatic molecule recognition by bond topology	fishmol.sel_tools
RDF, ADF, DDF, CDF distribution functions	fishmol.funcs
Vector Reorientation Dynamics (Legendre l = 1, 2, 3) with KWW fitting	fishmol.funcs
MSD and diffusion coefficient (FFT algorithm)	fishmol.msd
Diffusion anisotropy via spherical MSD projection	fishmol.msd
Hydrogen-bond recognition and lifetime autocorrelation	fishmol.dimer
Dimer lifetime–displacement distribution function	fishmol.dimer
Voronoi-based diffusion channel assignment	fishmol.utils
Interactive 3-D visualisation (ASE backend)	fishmol.vis

Tutorial Notebooks

The following notebooks walk through complete analysis workflows using a model cage-compound system with water molecules, trifluoroacetate anions, phenols, and amines.

• I/O of Molecular Dynamics Trajectories
• Mean Square Displacement and Diffusion Coefficient
• Diffusion Anisotropy
• Hydrogen Bond Recognition and Lifetime Analysis
• Vector Reorientation Dynamics (VRD)

Quick Install

git clone https://github.com/Lei-Lei-alpha/fishmol.git
cd fishmol
pip install -e ./

Then verify:

fishmol

Contact

Lei Lei — Lei.Lei@durham.ac.uk