applyhtreat Command Help

Command: $SCHRODINGER/utilities/applyhtreat

Usage: applyhtreat applyhtreat.py input_file output_file [options]
  Supported input formats: Maestro, SD, Mol2, or PDB.
  Supported output formats: Maestro, SD, Mol2, PDB or SMILES.

  Allowed treatment names for -treatment(-t) option are:
    "All-atom with Osp3/Nsp3-Lp"
    "All-atom with No-Lp"
    "Csp3 United-atom with S-Lp"
    "Csp3 United-atom with No-Lp"
    "All-atom with S-Lp"
    "C sp2/sp3 United-atom with No-Lp"
    "C sp2/sp3, N,O,S United-atom with No-Lp" 

Options:
  -v, -version          Show the program's version and exit.
  -h, -help             Show this help message and exit.
  -t TREATMENT, -treatment TREATMENT
                        Name of the treatment to use (Default is "All-atom
                        with No-Lp").
  -a ASL, -asl ASL      Restrict htreatment to atoms matching the ASL
                        expression (default all atoms).
  -s, -use_stereo       Adjust atom numbers in chirality strings (default
                        off).