MOLCIF2SDF(1)

💖 MOLCIF2SDF 💖

okay bestie, welcome to molcif2sdf — it's a General Commands Manual page, section 1, and it's lowkey one of the most useful little glow-ups you can do to a CIF file. sit down, grab a strawberry 🍓, let's go.

✨ NAME ✨

molcif2sdf — convert CIFs with multiple molecules (similar to those obtained from the 'cif_molecule' script) to an SDF file with a molecule description. Intended to be suitable for upload to PubChem. 🧪✨

🌸 SYNOPSIS 🌸

molcif2sdf --options < file1.cif

molcif2sdf --options file1.cif

molcif2sdf --options file1.cif file2*.cif

like. three whole ways to feed it. stdin, one file, or a whole lil glob squad. pick your fighter 💅

🦋 DESCRIPTION 🦋

okay so here's the whole vibe: you take CIFs with multiple molecules — the kind that look similar to those obtained from the 'cif_molecule' script — and you convert them into an SDF file with a molecule description. 🎀

and why do we care?? because it's intended to be suitable for upload to PubChem. that's the whole point, bestie. that's the assignment and it ate. 👑

🌈 OPTIONS 🌈

• -C, --cod-cif 1000000.cif — hand over the original COD CIF so it can extract structure metadata. yes, you literally pass it the file, like 1000000.cif. it's giving receipts 📎
• --tmp-dir /tmp — use the temporary directory you specify. the default is '/tmp', so if you say nothing it's just chillin' in /tmp like always 💀
• --help, --usage — outputs a short help message (this message!! the one you're reading, iconic) and then exits. 🫶
• --version — outputs version information and then exits. simple. clean. slay. ⭐

😭 REPORTING BUGS 😭

found a bug?? don't suffer in silence bestie, report molcif2sdf bugs using e-mail:

cod-bugs@ibt.lt

they wanna hear it, fr fr 📧

and that's the page!! it's MOLCIF2SDF(1) from the General Commands Manual, and that's the whole thing — no cap, every last option accounted for. now go convert something and make PubChem proud 💜🦋🌸