CSB-HHFRAG(1)

📦 version 1.2.5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ CSB-HHFRAG ✨

okay bestie, gather round, because this is the csb-hhfrag manual page (that's manual section 1, for the record 💅) and it is genuinely iconic.

💖 NAME 💖

csb-hhfrag — build a dynamic variable-length fragment library for protein structure

🌸 DESCRIPTION 🌸

here's the vibe, fr fr:

usage: csb-hhfrag [-h] [-H HHSEARCH] -d DATABASE [-m MIN] [-M MAX] [-s STEP]
                  [-c CPU] [-g GAP_FILLING] [-F FILTERED_FILLING] [-f] [--c-alpha]
                  [-t CONFIDENCE_THRESHOLD] [-v VERBOSITY] [-o OUTPUT] QUERY

HHfrag: build a dynamic variable-length fragment library for protein structure prediction with Rosetta AbInitio. that's the whole main character job, no cap 🫶

🎀 positional arguments 🎀

  • QUERY — the query profile HMM (like, e.g. one you made with csb.apps.buildhmm). this is your moment, bestie ✨

🦋 optional arguments 🦋

  • -h, --help — show this help message and exit. the classic. the icon. the "help me help you" 💖
  • -H HHSEARCH, --hhsearch HHSEARCH — path to the HHsearch executable (default=hhsearch)
  • -d DATABASE, --database DATABASE — database directory (containing PDBS25.hhm). lowkey essential, it's required, so don't skip it 🙈
  • -m MIN, --min MIN — minimum query segment length (default=6)
  • -M MAX, --max MAX — maximum query segment length (default=21)
  • -s STEP, --step STEP — query segmentation step (default=3)
  • -c CPU, --cpu CPU — maximum degree of parallelism (default=4). multitasking queen behavior 👑
  • -g GAP_FILLING, --gap-filling GAP_FILLING — path to a fragment file (e.g. CSfrag or Rosetta NNmake), which will be used to complement lowconfidence regions (when specified, a hybrid fragment library be produced) 🧚
  • -F FILTERED_FILLING, --filtered-filling FILTERED_FILLING — path to a filtered fragment file (e.g. filtered CSfrag-ments), which will be mixed with the HHfrag-set and then filtered, resulting in a double-filtered library. double-filtered?? she's doing the most and we love her for it 💅
  • -f, --filtered-map — make an additional filtered fragment map of centroids and predict torsion angles (default=False)
  • --c-alpha — include also C-alpha vectors in the output (default=False)
  • -t CONFIDENCE_THRESHOLD, --confidence-threshold CONFIDENCE_THRESHOLD — confidence threshold for gap filling (default=0.7)
  • -v VERBOSITY, --verbosity VERBOSITY — verbosity level (default=2)
  • -o OUTPUT, --output OUTPUT — output directory (default=.)

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. shoutout to the author, absolute legend for real 🫶

and that's the whole page, bestie!! this was csb-hhfrag version 1.2.5, from November 2017 — yeah, a vintage queen, and she still ate 💅✨🌸

📦 where this page comes from