cif-validate(1)

📦
version 2.0.0 · 5 versions
, in ubuntu stonking

💖 cif-validate — validate the content of a mmCIF file, bestie 💖

okay so this is a User Commands situation, and it's literally called cif-validate, and it's about to be your new best friend if you ever touch mmCIF files. buckle up 🎀

✨ NAME ✨

cif-validate — validate the content of a mmCIF file. yes that's the whole job. she validates. she's the vibe check for your mmCIF, no cap. 💅

🌸 SYNOPSIS 🌸

cif-validate [OPTION] file [output-file]

like, you give her a file, you may also give her an output-file, and you sprinkle in whatever [OPTION]s your heart desires. that's the whole ritual 🦋

🫶 DESCRIPTION 🫶

okay so story time: the mmCIF format is not really new, but the way it's been implemented has been taken up slowly. 😭 and unfortunately — and we're saying this with love — the knowledge of the ins and outs of the format is still poorly understood, and so many files written contain errors. it's giving chaos, honestly.

that's where our girl comes in. cif-validate can be used to help debug the creation of mmCIF files. 🛠️

by default she uses the dictionary provided by libcifpp — which may be updated automatically, depending on your installation, so keep that in mind, bestie. but you can also specify your own dictionary file using the --dict option. main character energy honestly, letting you bring your own dictionary to the function. 👑

✨ OPTIONS ✨

  • --dict=<file> — the mmCIF dictionary file to use. the default is mmcif_pdbx.dic. 📖

and here's a lil trick, okay: you can specify multiple dictionaries by concatenating their names separated by a semicolon, like this:

--dict='mmcif_pdbx.dic;dssp-extension.dic'

iconic. obsessed. semicolons as separators, slay. 💅

  • --validate-links — validate all links. she'll output information about missing parent category items. 🔗
  • --strip — strip all categories and/or items that are not valid according to the specified dictionary. 🧹 and heads up: this implies the --print option. she's not asking, she's telling.
  • --verbose,-v — be more verbose, which is useful to diagnose validation errors. 💬 you can specify it multiple times to increase the verbosity level. stack 'em, bestie, go feral with the -vs.
  • --print — print a formatted version of the input file to stdout, or to output-file if you specified one. 🖨️✨

🎀 AUTHOR 🎀

written by Maarten L. Hekkelman <maarten@hekkelman.com> — ty for your service 🫡💖

🙈 REPORTING BUGS 🙈

report bugs at https://github.com/PDB-REDO/cif-tools/issues — the devs do want to hear about it, fr fr. not me gatekeeping your bug reports, go tell them 🐛💌

🌈 SEE ALSO 🌈

cif-diff, cif-grep, cif-merge, cif2pdb, mmcql, pdb2cif. the whole friend group fr — go say hi to the rest of the squad 👯‍♀️

💀 real talk for a sec: this is version 1.0.8, dated 2023-01-06, and it's the cif-validate(1) page, so like — that's the era we're in, yk? if your install pulls a newer libcifpp dictionary automatically, that's just the universe updating itself, no drama. 💜

later bestie, go validate something iconic ✨🦋🌸

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