A critical step in these strategies is the identification of unique conformers from the vast number of molecular configurations typically generated. This challenge can be effectively addressed using Graph Theory tools. Specifically, adjacency matrix analysis has been suc-cessfully applied to classify molecular configurations into different topological conformers in MD snapshots of individual solute molecules in solution or to distinguish topologically distinct, QM-optimized isomers . However, a comprehensive top-down approach that identifies individual aggregates coexisting in solution-potentially within the same snapshot-in terms of their isomorphic conformations, is still lacking. Such a framework is essential for accurately calculating populations in systems involving thousands of particles.