PEPNET(1e)

📦 version 6.6.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 PEPNET(1e) — the EMBOSS Manual for Debian, but make it a group chat 💖

okay bestie, sit down, hydrate, because we're about to talk about pepnet, a lil command line program living in the EMBOSS family — that's "the European Molecular Biology Open Software Suite", yes the whole name, yes it's a mouthful, drink some water. 🫶

It hangs out in the "Display,Protein:2D Structure" command group(s), which is exactly the kind of niche that makes it iconic. This page is PEPNET(1e), and she's serving Debian, EMBOSS 6.4.0, dated 05/11/2012. Periodt.

✨ NAME ✨

pepnet — draw a helical net for a protein sequence. that's it. that's the whole job. she draws nets. 🕸️

🌸 SYNOPSIS 🌸

the way you summon her:

pepnet -sequence sequence -amphipathic toggle -squares string
       -diamonds string -octags string -graph graph

and if you just need a lil help moment:

pepnet -help

🦋 DESCRIPTION 🦋

pepnet is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). lowkey a legend, highkey a workhorse. 💅

She's part of the "Display,Protein:2D Structure" command group(s). so if you're out here trying to see your protein's structure instead of just squinting at letters, she's your girl. no cap.

🎀 OPTIONS 🎀

💜 Input section 💜

  • -sequence sequence — this is your input sequence, bestie. the raw material. the main character. feed her the protein and she'll do the rest. 🌈

🍓 Output section 🍓

  • -amphipathic toggle — if this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. 👑 heads up though: this overrides any other markup that you may have specified using the qualifiers -squares, -diamonds and -octags. so like, pick a lane, she can't do both.
  • -squares string — by default the aliphatic residues ILVM are marked with squares. ⬜ Default value: ILVM
  • -diamonds string — by default the residues DENQST are marked with diamonds. 🔷 Default value: DENQST
  • -octags string — by default the positively charged residues HKR are marked with octagons. 🛑 (octagons, not octagons-of-doom, we're being scientific) Default value: HKR
  • -graph graph — the graph output. that's the whole vibe. ✨

💀 BUGS 💀

found a bug? not me being shook but okay, here's where you report it:

please be nice to them, they're doing their best. 🙈

🧚 SEE ALSO 🧚

pepnet is fully documented via the tfm(1) system. iykyk. 📖

👑 AUTHOR 👑

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

  • Wrote the script used to autogenerate this manual page. honestly? slay. 🤖💖

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. so like, share responsibly, bestie. 🫶

and that's the whole page!! every flag, every default, every residue string, all of it, nothing dropped. ate and left no crumbs. 💅✨

okay so this was PEPNET(1e), from the EMBOSS 6.4.0 era, dated 05/11/2012, shipped for Debian by the Debian Med Packaging Team. go draw a helical net, you absolute icon. 🎀🦋💖

📦 where this page comes from