User GuideΒΆ Contents: Usage Typical Usage The htpolynet Directory Structure htpolynet Subcommand Summaries Container Usage Desktop Users (Docker) HPC Users (Singularity/Apptainer) Molecular Structure Inputs Configuration Files Configuration Files for htpolynet run Configuration Files for htpolynet postsim Configuration Files for htpolynet analyze Program Flow The Connect-Update-Relax-Equilibrate (CURE) algorithm Identifying allowable bonds: Bondsearch filters