lipid-plots 0.1.0

MD analysis tools for lipid membrane geometry: packing defects, depth-disorder, tilt-torsion.

lipid-plots

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

Three complementary analyses in one package:

Command	Analysis	X-axis	Y-axis
lipid-packing	Packing defects	Voronoi area per lipid (Ų)	Chain splay angle (°)
lipid-disorder	Depth–disorder	Z-depth relative to centre (Å)	Tail order parameter SCC
lipid-torsion	Tilt–torsion	Headgroup α-torsion (°)	P-N vector tilt (°)

---

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:

Type	Common formats
Topology	.tpr, .gro, .pdb, .psf, .mol2
Trajectory	.trr, .xtc, .dcd, .nc, .lammpstrj

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