Refactor molecule input handling to implement two-way synchronization and replace ReducedRouteCGR with SB-CGR, enhancing state management and visualization consistency.

Refactor route handling to replace ReducedRouteCGR with SB-CGR across multiple modules, enhancing clarity and consistency in clustering and visualization processes.

Prevent duplicate processing of atom pairs in lg_replacer function

Refactor code structure and remove redundant sections for improved readability and maintainability