# Structure Analysis pylimer-tools offers various tools to manipulate and analyze the topology of polymer networks. Here you can find examples of some of the functionality provided by the package. ## Decomposing Crosslinked Networks to Chains There are a number of ways how a given [`Universe`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe) can be decomposed. The most common use case is to decompose a crosslinked network into its constituent chains, which can then be used for further analysis or processing. To find the chains, there are two main approaches: - Removing the crosslinkers and analysing the remaining polymer strands using [`get_molecules()`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_molecules) - Decomposing the network to chains, but keeping the crosslinkers in place, possibly being repeated in all the chains it is associated with. This decomposition can be done using the [`get_chains_with_crosslinker()`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_chains_with_crosslinker) method. pylimer-tools provides two more advanced methods for decomposing networks: - If you removed the junctions yourself, you can use [`get_clusters()`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_clusters) If you want even more control, you could assemble your own decomposition algorithm using the [`Universe`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe) class and its methods, such as [`get_atoms_connected_to()`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.get_atoms_connected_to). ## Finding Loops You can also find loops in the network using the [`find_loops()`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.find_loops) method. If you want to count the number of loops present in the network, as a function of their length, you can use the [`count_loop_lengths()`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.count_loop_lengths) method. Finally, to find the shortest loop a specific atom is involved in, you can use the [`find_minimal_order_loop_from()`](../../api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe.find_minimal_order_loop_from) method. #### CAUTION There are exponentially many paths between two crosslinkers of a network, and you may run out of memory when using these functions, if your network is lattice-like.
![](auto_examples/structure_analysis/images/thumb/sphx_glr_plot_decompose_structure_thumb.png) [Decompose/Split Structure](plot_decompose_structure.html.md)
Decompose/Split Structure
![](auto_examples/structure_analysis/images/thumb/sphx_glr_plot_loop_analysis_thumb.png) [Loop Finding and Analysis](plot_loop_analysis.html.md)
Loop Finding and Analysis
![](auto_examples/structure_analysis/images/thumb/sphx_glr_plot_end_to_end_distribution_thumb.png) [End-to-End Distribution](plot_end_to_end_distribution.html.md)
End-to-End Distribution
![](auto_examples/structure_analysis/images/thumb/sphx_glr_plot_structure_analysis_thumb.png) [Extract Synthesis Parameters](plot_structure_analysis.html.md)
Extract Synthesis Parameters