#### NOTE [Go to the end](#sphx-glr-download-auto-examples-structure-analysis-plot-end-to-end-distribution-py) to download the full example code. # End-to-End Distribution This example demonstrates how to analyze the end-to-end distribution of polymer chains using pylimer-tools. It reads a structure file, computes the end-to-end distances, and plots the distribution of these distances. ```Python import os from pathlib import Path import matplotlib.pyplot as plt from pylimer_tools.io.read_lammps_output_file import read_data_file from pylimer_tools_cpp import Universe # Replace with your crosslinker type crosslinker_type = 2 # Load your network (replace path accordingly) def _find_fixtures_dir() -> Path: for cur in ( [Path(__file__).resolve().parent] if "__file__" in globals() else [] ) + [Path.cwd()]: for p in [cur] + list(cur.parents): candidate = p / "tests" / "pylimer_tools" / "fixtures" if candidate.is_dir(): return candidate return Path("tests/pylimer_tools/fixtures").resolve() _fixtures_dir = _find_fixtures_dir() universe = read_data_file( str(_fixtures_dir / "structure/network_100_a_46.structure.out") ) assert isinstance(universe, Universe) # Compute end-to-end distances for all chains, # including crosslinkers. # Two options are available: end_to_end_distances_derived = [ m.compute_end_to_end_distance_with_derived_image_flags() for m in universe.get_chains_with_crosslinker(crosslinker_type) ] end_to_end_distances = [ m.compute_end_to_end_distance() for m in universe.get_chains_with_crosslinker(crosslinker_type) ] # Plot the end-to-end distance distribution plt.figure() plt.hist( end_to_end_distances_derived, bins=50, alpha=0.5, label="End-to-End Distances (Derived Image Flags)", ) plt.hist( end_to_end_distances, bins=50, alpha=0.5, label="End-to-End Distances (Original Image Flags)", ) plt.xlabel("End-to-End Distance") plt.ylabel("Frequency") plt.show() ``` **Total running time of the script:** (0 minutes 0.071 seconds) [`Download Jupyter notebook: plot_end_to_end_distribution.ipynb`](_downloads/b16387431e9b9e37a924b860f0c52f55/plot_end_to_end_distribution.ipynb) [`Download Python source code: plot_end_to_end_distribution.py`](_downloads/5d785a30c2c538854433711b98b5cacb/plot_end_to_end_distribution.py) [`Download zipped: plot_end_to_end_distribution.zip`](_downloads/40c40441682b4b36d3efb2e6b64ed7a4/plot_end_to_end_distribution.zip) [Gallery generated by Sphinx-Gallery](https://sphinx-gallery.github.io)