Menger_Curvature Documentation

Menger_Curvature is a Python package that calculates the Menger curvature of polymeric backbones along molecular trajectories, particularly useful for analyzing protein backbone conformations.

Scientific Background

The Menger curvature is a geometric measure that characterizes how much a curve passing through 3 points deviates from being straight. For a triplet of points, it is calculated as the reciprocal of the radius of the circumscribed circle passing through these points.

In protein analysis, this metric provides: Local geometric information about backbone conformation Insights into structural flexibility when analyzed across trajectories Quantitative measures for comparing different protein regions of the backbone

Computational Approach

The package implements: JIT-accelerated calculations using Numba for performance Parallel computation support for large trajectories Integration with MDAnalysis for efficient trajectory handling Memory-efficient array operations with NumPy

Installation

Quick installation using pip:

pip install menger-curvature

For development installation:

git clone https://github.com/EtienneReboul/menger_curvature.git
cd menger_curvature
pip install -e .

Basic Usage

Calculate Menger curvature for a protein trajectory:

import MDAnalysis as mda
from menger.analysis.mengercurvature import MengerCurvature
from menger.data import files

# replace by your own filepaths
topology = files.TUBULIN_CHAIN_A_PDB
trajectory = files.TUBULIN_CHAIN_A_DCD
u = mda.Universe(topology, trajectory)

# run analysis in serial mode
menger_analyser = MengerCurvature(
   u,
   select="name CA and chainID A",
   spacing=2
   )
menger_analyser.run()

# retrieve results data
average_curvature = menger_analyser.results.local_curvatures
flexibility = menger_analyser.results.local_flexibilities
menger_curvature = menger_analyser.results.curvature_array

Contents

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