cif-grep(1)

💖 cif-grep(1) — the manual page, but make it cute 💖

okay bestie, welcome to cif-grep, a User Command and honestly a whole vibe. she's a tool kinda like grep, except she's out here printing fields in mmCIF files that match your patterns. let's get into it 🦋

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✨ NAME ✨

cif-grep — a tool like grep to print fields in mmCIF files that match patterns

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🌸 SYNOPSIS 🌸

cif-grep [OPTION] pattern file1 [file2..]

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💅 DESCRIPTION 💅

so basically, this tool tries to work in a similar way as grep — but instead of scanning lines, she's searching mmCIF files and comparing the content of fields to your patterns. same energy, different target. iconic, honestly. 🎀

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🔥 OPTIONS 🔥

first up, some ground rules before we get to the flags, bestie:

• You can specify multiple files to search. more files, more fun. 🫶
• If you specify a directory name, then <em>all files in that directory</em> will be searched. slay.
• Want to go deeper? Use the --recursive flag to do a recursive search. she'll go all the way down the tree, no cap. 🌈

now the actual options, one by one, no skips:

• --item=<item>, -i <item> — limits the search to only the item you named in <item>. Default is to search all items. and listen, the item should be of the form _category.item, with the leading underscore. do not forget the underscore, I am begging 🙈
• --quiet, -q — prints only the file names that match the pattern. minimal. clean. main character energy. 👑
• --count, -c — only shows the number of hits. just the digits, bestie, nothing else. 🔢
• --invert-match, -v — only selects the fields that do not match the pattern. flips the whole thing, very contrarian of her, we love that. 💀
• --line-number, -n — prints the line numbers. so you know exactly where the tea is. 🍓
• --no-filename, -h — do not print the filename. anonymous era. 🧚
• --with-filename, -H — do print the filename. okay so she's back to being known. 💜
• --files-with-matches, -l — prints only the names of the files containing matches. not the matches themselves, just the receipts. ✨
• --recursive, -r — search recursively. down the directory tree we go, bestie. 🌸
• --verbose,-V — be more verbose, useful to diagnose validation errors. she'll tell you everything, and honestly? sometimes you need that. 😭

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👑 AUTHOR 👑

Written by Maarten L. Hekkelman <maarten@hekkelman.com> 💖

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😭 REPORTING BUGS 😭

Report bugs at https://github.com/PDB-REDO/cif-tools/issues

(if something's broken, tell the devs, not me — I'm just the messenger, fr fr)

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🌈 SEE ALSO 🌈

cif-diff, cif-merge, cif-validate, cif2pdb, mmCQL, pdb2cif.

go read those too, they're all part of the friend group. 🫶

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and that's the whole page, bestie!! this was version 1.0.5, dated 2022-11-20, and it's the cif-grep(1) manual — mwah, periodt. 💅✨