#### NOTE [Go to the end](#sphx-glr-download-auto-examples-structure-analysis-plot-loop-analysis-py) to download the full example code. # Loop Finding and Analysis This example demonstrates how to find and analyze loops in polymer networks using pylimer-tools. ```none Number of loops found (max length 2*(46+1)): 2 Loop length counts: {322: 1, 92: 1, 46: 2, 138: 1} Shortest loop involving atom 1: [] ```
```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 'network.gml' with your file) 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) # 1. Find loops in the network loops = universe.find_loops( crosslinker_type, skip_self_loops=True, max_length=2 * (46 + 1) ) # restrict for large networks print(f"Number of loops found (max length 2*(46+1)): {len(loops)}") # 2. Count loop lengths loop_length_counts = universe.count_loop_lengths(max_length=7 * (46 + 1)) print(f"Loop length counts: {loop_length_counts}") # plot the loop length counts plt.bar(list(loop_length_counts.keys()), list(loop_length_counts.values())) plt.xlabel("Loop Length") plt.ylabel("Count") plt.show() # 3. Find shortest loop for a specific atom (e.g., atom 0) shortest_loop = universe.find_minimal_order_loop_from( loop_start=1, loop_step1=1) print(f"Shortest loop involving atom 1: {shortest_loop}") ``` **Total running time of the script:** (0 minutes 0.071 seconds) [`Download Jupyter notebook: plot_loop_analysis.ipynb`](_downloads/2597fa1b568165054f9ecb58cad97e96/plot_loop_analysis.ipynb) [`Download Python source code: plot_loop_analysis.py`](_downloads/517fdf36ddecba1a12587474d4a82381/plot_loop_analysis.py) [`Download zipped: plot_loop_analysis.zip`](_downloads/6199f131c5a0e9e3f49d9c04d17856b4/plot_loop_analysis.zip) [Gallery generated by Sphinx-Gallery](https://sphinx-gallery.github.io)