lipid-plots

A Python package for analysing lipid membrane geometry from MD simulations using MDAnalysis.

Three complementary analyses in one package:

Install

pip install lipid-plots

Or from source:

git clone https://github.com/karagol-alper/lipid-plots
cd lipid-plots
pip install -e .

CLI — quick reference

Packing defects (Voronoi area vs. splay angle)

# Single structure file only (no trajectory):
lipid-packing -t system.gro

# With trajectory — default step=1 analyses every frame (recommended):
lipid-packing -t system.tpr -x traj.xtc

# --step N only for sub-sampling very long trajectories (trades accuracy for speed):
lipid-packing -t system.tpr -x traj.xtc --step 5   # every 5th frame only

# Custom lipid / chain atom names:
lipid-packing -t system.gro -x traj.xtc \
    --resname DPPC \
    --chain1-start C22 --chain1-end C29 \
    --chain2-start C32 --chain2-end C39 \
    --leaflet-z 0 \
    --output dppc_packing.png

Depth–disorder (Z-position vs. SCC)

lipid-disorder -t system.gro
lipid-disorder -t system.gro -x traj.xtc --resname POPC -o disorder.png

# Custom tail atom list:
lipid-disorder -t system.gro \
    --tail-atoms C22,C23,C24,C25,C26,C27,C28,C29,C210,C211,C212,C213,C214,C215,C216

Tilt–torsion map

lipid-torsion -t system.gro
lipid-torsion -t system.tpr -x fixed.trr -o tilt_torsion.png

# Custom dihedral atoms:
lipid-torsion -t system.gro --torsion-atoms O12,P,O13,C11

Umbrella command (all three via one entry point)

lipid-plots packing  -t system.gro -x traj.xtc --step 5
lipid-plots disorder -t system.gro
lipid-plots torsion  -t system.gro -x traj.xtc --step 5
lipid-plots --help

Python API

from lipid_plots.utils import load_universe
from lipid_plots import (
    analyze_packing_defects, plot_packing_defect,
    calculate_depth_disorder, plot_depth_disorder,
    get_torsion_and_tilt, plot_tilt_torsion,
)

# Trajectory is optional — omit for single-frame analysis
u = load_universe("system.gro")                  # single frame
u = load_universe("system.tpr", "traj.xtc")     # with trajectory

# --- Packing defects ---
areas, splays = analyze_packing_defects(u, step=5)
plot_packing_defect(areas, splays, output="packing.png")

# --- Depth–disorder ---
depths, orders = calculate_depth_disorder(u)
plot_depth_disorder(depths, orders, output="disorder.png")

# --- Tilt–torsion ---
torsions, tilts = get_torsion_and_tilt(u)
plot_tilt_torsion(torsions, tilts, output="tilt_torsion.png")

Supported input formats

The --topology and --trajectory arguments accept any format supported by MDAnalysis:

The trajectory (-x) is always optional. If omitted, only the single frame in the topology is analysed.

Configuration

All atom names, residue names, and chain definitions can be overridden via CLI flags or keyword arguments in the Python API. The defaults follow CHARMM36 / GROMACS POPC nomenclature.

License

MIT