Shape Descriptor Toolkit

This toolkit provides Python scripts for analyzing peptide self-assembly simulations.

Scripts

adi_analysis.py: Aggregate Dynamics Index (ADI)
sfi_analysis.py: Sheet Formation Index (SFI)
vfi_analysis.py: Vesicle Formation Index (VFI)
tfi_analysis.py: Tube Formation Index (TFI)
ffi_analysis.py: Fiber Formation Index (FFI)
shape_tracker.py: Tracks structural changes over time

Installation

Using Conda

conda env create -f environment.yml
conda activate descriptors

Using pip

pip install -r requirements.txt

Usage

Place your topology and trajectory files in the data/ directory.

Run Analysis Scripts

python adi_analysis.py -t data/your_topology.gro -x data/your_trajectory.xtc -s 'resname PEP' -o results/adi_results
python sfi_analysis.py -t data/your_topology.gro -x data/your_trajectory.xtc -s 'resname PEP' -o results/sfi_results
python vfi_analysis.py -t data/your_topology.gro -x data/your_trajectory.xtc -s 'resname PEP' -o results/vfi_results
python tfi_analysis.py -t data/your_topology.gro -x data/your_trajectory.xtc -s 'resname PEP' -o results/tfi_results
python ffi_analysis.py -t data/your_topology.gro -x data/your_trajectory.xtc -s 'resname PEP' -o results/ffi_results

Run Tracking Script

python shape_tracker.py \
-adi results/adi_results \
-sfi results/sfi_results \
-vfi results/vfi_results \
-tfi results/tfi_results \
-ffi results/ffi_results \
-o results/tracking_results

Requirements

Install the required Python packages:

numpy
scipy
pandas
matplotlib
MDAnalysis
scikit-image

These are listed in requirements.txt and environment.yml.