CODCIF2SDF(1)

📦 version 3.12.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 CODCIF2SDF(1) 💖

okay bestie, so this is codcif2sdf, and it lives in the General Commands Manual (section 1, as the (1) is giving ✨manual page✨). she's a little command-line girlie whose whole job is turning crystal-structure CIFs into molecule SDFs. sit down, hydrate, let's go 🫶

🌸 NAME 🌸

codcif2sdf — convert CIFs with crystal description (similar to those obtained from the COD) to an SDF file with a molecule description. Intended to be suitable for upload to PubChem.

like literally, that's the whole personality. CIF in, SDF out, PubChem-ready. no cap 💅

✨ SYNOPSIS ✨

three ways to run her, pick your fighter:

codcif2sdf --options < file1.cif
codcif2sdf --options file1.cif
codcif2sdf --options file1.cif file2*.cif

so you can pipe it in with <, hand it one file, or just throw a whole glob at it and let her cook 🔥

🦋 DESCRIPTION 🦋

Convert CIFs with crystal description (similar to those obtained from the COD) to an SDF file with a molecule description. Intended to be suitable for upload to PubChem.

fr fr that's it. crystal description → molecule description, and the output is meant to be suitable for upload to PubChem. main character energy, honestly 👑

🎀 OPTIONS 🎀

  • -i, --ignore-bumps — Ignore atomic bumps while running cif_molecule. yes bestie, let her ignore the bumps, she's unbothered 💅
  • --tmp-dir /tmp — Use the specified temporary directory (default: '/tmp'). the default is literally '/tmp', so if you don't say anything she just chills there 🍓
  • --help, --usage — Output a short help message (this message) and exit. she tells you what's up and then dips 🙈
  • --version — Output version information and exit. just the version, then she's gone ✨

💀 REPORTING BUGS 💀

Report codcif2sdf bugs using e-mail: cod-bugs@ibt.lt

like pls tell her, she wants to be better 😭

and that's the whole page, bestie 🧚 the header said CODCIF2SDF(1) and the footer said CODCIF2SDF(1) too (General Commands Manual, section 1 — no version or date on this one, she's keeping it mysterious), so consider this your cute lil sign-off. go convert some crystals 💜

📦 where this page comes from