DOMAINREP(1e)

📦 version 0.1.660, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 DOMAINREP(1e) — the EMBOSS Manual for Debian, bestie edition 💖

okay so. picture this: it's DOMAINREP(1e), it's a page from the EMBOSS Manual for Debian, and it's here to serve. let's get into it 🫶

✨ NAME ✨

domainrep — reorder a DCF file so you can clock which structures are the representative ones. that's the whole vibe. 👑

🌸 SYNOPSIS 🌸

domainrep -dcfinfile infile -node list -dcfoutfile outfile

domainrep -help

like, two moods. one does the thing, one asks for help. both iconic. 💅

🦋 DESCRIPTION 🦋

domainrep is a command line program from EMBOSS (which stands for "the European Molecular Biology Open Software Suite", no cap, that's the actual name).

it lives in the "Protein:3D Structure" command group(s). that's its little friend group. it belongs there. 🎀

🌈 OPTIONS 🌈

🍓 Input section

  • -dcfinfile infile — this one names the DCF file (that's your domain classification file) coming in as input. so what even is a 'domain classification file', you ask? it's a file holding classification and other data for domains from SCOP or CATH, all in DCF format (which is EMBL-like, iykyk). you generate these files using SCOPPARSE and CATHPARSE, and if you want domain sequence info in there too, you add it with DOMAINSEQS. periodt. 💖

💜 Required section

  • -node list — this specifies the node for reordering the file (the original says "fore" but we all know what she meant, bestie 😭). you can reorder for any specified node in the SCOP or CATH hierarchies. for example, by selecting 'Class', entries belonging to the same Class get reordered in turn. Default value: 1 ✨

🧚 Output section

  • -dcfoutfile outfile — this names the DCF file (domain classification file again, same lore) coming out as output. and yes, same deal: a 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). generated with SCOPPARSE and CATHPARSE, and domain sequence information can be added by using DOMAINSEQS. Default value: test.scop 🌸

💀 BUGS 💀

found a bug? not the vibe, but okay, tell someone:

they want to know. genuinely. 🫶

👑 SEE ALSO 👑

domainrep is fully documented via the tfm(1) system. so if you need more, that's where the full lore lives. go read it, it ate. 🔥

🎀 AUTHOR 🎀

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

  • Wrote the script used to autogenerate this manual page. slay, honestly. 💅

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. respect the terms, bestie. 🌈

so yeah, that's domainrep. reorder your DCF, find your representative structures, live your truth. no notes. 💖

and that's a wrap, my love 🫶 this lil page is signed off from DOMALIGN 0.1.0+20100721, dated 08/11/2010, and yes the footer really does say DOMALIGN even though we've been talking about DOMAINREP the whole time — not me pointing that out, but also, iconic of the manpage to keep us on our toes. 💀✨ bye bestie!

📦 where this page comes from