CIF_SORT_ATOMS(1)

✨ CIF_SORT_ATOMS ✨

okay bestie, welcome to cif_sort_atoms from section 1 of the General Commands Manual — she's a little command-line icon who reorganises the atoms in a CIF file into whatever order you want, and she does not make you pick just one sorting criterion. more than one? sure babe, stack 'em. 💅

🌸 NAME 🌸

cif_sort_atoms — sort atoms in a CIF file in given order. accepts more than one sorting criterion. periodt.

🎀 SYNOPSIS 🎀

cif_sort_atoms --options input1.cif input*.cif

🦋 DESCRIPTION 🦋

So like. You hand her a CIF file, you tell her how you want the atoms arranged, and she arranges them. That's the whole vibe. And the slay part? She accepts more than one sorting criterion — you're not limited to a single sort, you can stack your criteria and let her cook. 👑

💖 OPTIONS 💖

• -l, --lexicographic — sort by lexicographic order. this is the default, so if you say nothing she just does this. lowkey her comfort zone. ✨
• -Z, --atomic-number — sort by atomic number. chemistry girlies rise. 🧪
• --ascending-numerical _atom_site_occupancy — sort by the values of the CIF data item you name, in ascending numerical order. the example data item is _atom_site_occupancy, but it's a placeholder, iykyk. 🔢
• --descending-numerical _atom_site_occupancy — same deal but going down: sort by the values of the CIF data item in descending numerical order. 💫
• --ascending-lexical _atom_site_label — sort by the values of the CIF data item in ascending lexical order. example data item here is _atom_site_label. 🔤
• --descending-lexical _atom_site_label — sort by the values of the CIF data item in descending lexical order. Z to A energy. 🌀
• -r, --reverse — reverse the ordering. just flip the whole thing, no cap. 🔄
• --order-child-loops — also order loops with data items referencing _atom_site_label. matching the vibes of the parent, as she should. 🫶
• --no-order-child-loops — preserve the original order of loops with data items referencing _atom_site_label. this is the default, so loops stay exactly where they were unless you say otherwise. 🙈
• --record-original-order — record the original atom order. so you can remember where everyone started. 📝
• --no-record-original-order — do not record the original atom order. this is the default. ⭐
• --use-perl-parser — use the Perl parser for CIF parsing. 🐪
• --use-c-parser — use the Perl & C parser for CIF parsing. this one is the default, so it's what you get if you don't specify. 🔥
• --help, --usage — output a short usage message (this message) and exit. she tells you how she works, then she dips. 💜
• --version — output version information and exit. 👑

😭 REPORTING BUGS 😭

Found a bug? don't suffer in silence bestie — report cif_sort_atoms bugs using e-mail: cod-bugs@ibt.lt 📧

ngl the wrap on --descending-numerical in the original is giving "descending numerical order", so that's exactly what she does. no details lost, no details invented. 🎀

and that's the whole page, bestie — cif_sort_atoms(1), straight out of the General Commands Manual, section 1. go forth and sort ur atoms. slay. 💅✨🦋🌸