User Guide

Contents:

• Usage
  • Typical Usage
  • The htpolynet Directory Structure
  • htpolynet Subcommand Summaries
  • Parameterization caching
• Container Usage
  • Desktop Users (Docker)
  • HPC Users (Singularity/Apptainer)
• Molecular Structure Inputs
  • Before either path: valence conservation
  • In-config SMILES (recommended)
  • Supplying mol2 or pdb files directly
  • Atom-naming
• 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