xyz_to_pdb.py

Usage and arguments 

usage: xyz_to_pdb.py [-h] [-xyz XYZ] [-pdb PDBF] [-frame FRAME] [-name NAME]

generate pdbfiles from orca xyz file

options:
  -h, --help    show this help message and exit
  -xyz XYZ      xyz structure file
  -pdb PDBF     template pdb file
  -frame FRAME  select frame: -1 (final=default) or integer (count starts at 0) or "all"
  -name NAME    filename for output pdb

Inputs

  • -xyz: xyz file to extract geometry from (required)
    • Given as filename, default is orca.xyz
    • Example: -xyz orca.xyz
  • -pdb: Template pdb to put optimised geometry into (required)
    • Given as filename
    • Example: -pdb model_N_template.pdb
  • -frame: Which structure from the output to convert
    • Given as integer or ‘all’ or -1 for just the final structure (default)
    • Examples: -frame all or -frame 10
  • -name: base name to use for converted structure

    • Given as string (with or without “.pdb” ending), default is basename of given xyz file (or ‘orca’ if xyz argument also left unspecified)

    • Examples: -name model_13_ts_opt or -name model_13_reactant_opt.pdb

Outputs

  • [name].pdb if making only final frame, [name].f[num].pdb if using -frame all or -frame [num]