DeYonker lab scripts: new readme Sep 2025

Using scripts

1. Clone repo on bigblue
2. Add repo to your path by adding export PATH=$PATH:$HOME/git/DeYonker-lab-scripts into your ~/.bash_profile
3. Then scripts can be run as script.py [args] or script.sh [args] without needing to specify this dir's location

Please keep your useful scripts in here!

If you create scripts you use regularly or that might be useful for other people, please keep them in here.

• Create a directory for your own stuff
• Add your subdir to your path export PATH=$PATH:$HOME/git/DeYonker-lab-scripts/[name] into your ~/.bash_profile as well
• Keep a short readme file of what your scripts do/usage syntax (this should be in the scripts themselves too)

Contents of this directory:

DAW 09-25: I added this list of the directory contents and started sectioning it up/adding short descriptions of what the scripts do. Please contribute where you can too!

Setting up your hpc environment:

• alias_bash_profile.txt
  • this is a list of useful aliases for your bash_profile

Preparing jobs

• gen_irc.py

   usage: gen_irc.py
   prepares gaussian input files for irc1/irc2 from finished tsopt calc
  

• xtb_gen_irc.py

   usage: xtb_gen_irc.py
   same as gen_irc.py but for xtb calcs in gaussian
  

• xtb-g16-pdbfix.py

   usage: xtb-g16-pdbfix.py [pdb]
   creates 1.fix constraints file
  

• gen_jobscript_g16.sh

   usage: gen_jobscript_g16.sh
   creates 1 slurm submission script for gaussian input file with matching mem/cpu settings
  

• gen_jobscript_orca6.sh

   usage: gen_jobscript_orca6.sh [optional: orca inp file name]
   creates 1 slurm submission script for orca input file with matching mem/cpu settings
  

• gen_jobscript_psi4.sh

   usage: gen_jobscript_psi4.sh
   creates 1 slurm submission script for psi4 input file with matching cpu settings
  

• populate-submission-scripts.sh

   usage: populate-submission-scripts.sh
   adds 1 slurm submission script to any subdirs that don't have one using the gen_jobscript_[program] scripts
  

Managing jobs:

• test-completion.sh

   usage: test-completion.sh [dir(s) or "list" plus list file name]
   tests completion of gaussian 1.out files in current dir and its subdirs (or dirs specified in list file). files are labeled as complete/incomplete/failed
  

• check-opt.sh

   usage: check-opt.sh [file]
   extracts steps with smallest forces and lowest energy from gaussian output
   if no file specified, will extract from 1.out
  

• propagate_fails.sh

   usage: propagate_fails.sh [label]
   saves gaussian 1.inp, 1.out and 1.chk as [n]-[label]-inp, [n]-[label]-out and [n]-[label]-chk and so previous runs don't get overwritten
   increases count each time so files are kept in chronological order
  

• propagate_orca.sh

       usage: propagate_orca.sh [orca file name] [label]
       same as propagate_fails.sh but for orca jobs. saves the inp and out files and gbw/hess if present
  

Collecting outputs:

• extract.sh

   usage: extract.sh [warning/col/list] [list]
   extracts energies from 1.out files in dir and its subdirs
   arg "warning" - prints warnings
   arg "col" - prints in column format
   arg "list" - extracts from dirs specified in list txt file
  

MD stuff:

• add_chain.py

   usage: add_chain.py -list [file listing pdbs] -chain [startres/endres/chainletter ...]
   adds chain info to pdbs (for example ones created from MD runs with cpptraj)
  

Not yet sorted/described:

• avg_pdbs.py
• big-mol.sh
• car_to_pdb.py
• cerius_loader.py
• cerius-xyz-gen-from-moe.sh
• combifromcontacts.py
• CombiFromContacts.py
• convert-coords.sh
• create-simspec-ir.sh
• create-simspec-nmr.sh
• create-simspec-uv.sh
• cubegen.sh
• extract-geom-input.sh
• extract-geom-output.sh
• genmodelfiles.py
• GenResAtoms.py
• gopt_etrack.py
• gopt_pdb_transfer_mod.py
• gopt_pdb_transfer.py
• gout_extract.py
• identifiles.py
• interaction-info.py
• make-msi-series.sh
• make-msi.sh
• MDarpeggioFG.py
• MDarpeggioMaxModel.py
• MDarpeggioSIFT.py
• MDarpeggioWATNetwork.py
• MDprobeRIN.py
• measure.sh
• msi
• plot.sh
• prepare-list.py
• print-error-in-output.sh
• read_gout_xtb.py
• route-input.sh
• route.sh
• runcerius.sh
• simspec-ir
• simspec-nmr
• simspec-uv
• slurm-array-molpro.sh
• submit-all.sh
• submit-new.sh
• vec_calc.py
• write-matchmodel.sh
• write-openlog-pdb.sh
• write-openlog.sh

Use the newer RINRUS versions of these functions instead of these scripts

• distcalc.py (closest atom-atom distances done with RINRUS dist_rank.py)
• gopt_to_pdb.py