Connected Substructures [1]
This analyzer counts the number of connected subgraphs (molecules) and classifies each as a chain or ring. A subgraph is considered a chain if its backbone has free ends after removing 1-order nodes, otherwise it is classified as a ring.
Command line
-NoSub--NoSubgraphsCalculate molecule, chain, and ring counts. Optionally provide an output filename.
Default: noSubGraphs.csv
Example
MakroLyzer -xyz polymer.xyz -NoSub myNoSubOutput.csv
Output
The output file contains one row per frame:
Column |
Description |
|---|---|
Frame |
Frame index in the trajectory |
Molecule count |
Number of connected subgraphs |
Chain count |
Number of chain subgraphs |
Ring count |
Number of ring subgraphs |