CIF2RDF(1)

💖 CIF2RDF(1) 💖

okay bestie, welcome to cif2rdf — it lives in the General Commands Manual (that's section 1, the one for commands, iykyk). pull up a chair, grab a boba, and let's get into it 🧋✨

🌸 NAME 🌸

cif2rdf — parse a CIF file and describe its properties in RDF format. that's the whole gig. no cap.

✨ SYNOPSIS ✨

ugh the formatting, let me just show you:

so like. options first, then a CIF file, then as many more CIF files as your little heart desires 🦋

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# 🎀 DESCRIPTION 🎀

Parse a CIF file and describe its properties in RDF format. it takes your crystallography data and spins it into RDF, which is honestly giving main character energy 🔥

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# 💅 OPTIONS 💅

so many flags. all of them valid. let's go one by one, no skipping, I promise 🫶

- **`-C`, `--cod-number` *1000000*** — use the number you give here (the example uses `1000000`) as the COD number for this structure. like, do **not** take the number from the data block name. you're overriding it, periodt.

- **`-c`, `--always-continue`** — keep on processing and still return a *successful* return status even if errors get diagnosed. yes, even then. she's unbothered 💅

- **`-c-`, `--always-die`** — stop and return an *error* status if errors are diagnosed. the dramatic one of the pair 💀

- **`--use-attached-hydrogens`** — include the number of implicit hydrogens (the ones specified with the `_atom_site_attached_hydrogens` tag) into the formula sum. this is the **default**, bestie ✨

- **`--no-use-attached-hydrogens`**, **`--dont-use-attached-hydrogens`**, **`--ignore-attached-hydrogens`** — ignore that number of implicit hydrogens from the `_atom_site_attached_hydrogens` tag when calculating the formula sum. not today 🚫

- **`--reformat-space-group`** — correct the formatting of the Hermann-Mauguin symmetry space group symbol. glow-up for your space group ✨

- **`--no-reformat-space-group`**, **`--dont-reformat-space-group`**, **`--leave-space-group`** — do **not** correct the formatting of the Hermann-Mauguin symmetry space group symbol. this one is the **default** 🙈

- **`--use-datablocks-without-coordinates`**, **`--use-all-datablocks`** — don't filter out data blocks that have no coordinates. all datablocks welcome 🌈

- **`--no-use-datablocks-without-coordinates`**, **`--do-not-use-datablocks-without-coordinates`**, **`--dont-use-datablocks-without-coordinates`**, **`--skip-datablocks-without-coordinates`** — filter out data blocks without coordinates. this is the **default**, so yes, they get skipped by default 👑

- **`--require-only-doi`** — don't require all the bibliographic details (that's authors, journal name, title, year, volume and first page of the publication) to be present, as long as the publication DOI is specified. DOI girlies, this one's for you 💜

- **`--require-full-bibliography`** — require author names, journal name, volume, publication title, year and first page to all be present. this is the **default**, and she's thorough 📚

- **`--columns` *file,flags,Robs*** and **`--columns "file flags Robs"`** — print only the columns you list in this option. two ways to write it, same vibe 🎀

- **`--vocabulary-namespace` *cod*** — use vocabulary namespace `"cod"` to prefix properties that are native to the queried database.

- **`--vocabulary-url-prefix` *http://www.crystallography.net/cod/doc/rdf/*** — specify the URL prefix for the database's native namespace.

- **`--prefix`**, **`--db-url-prefix`** *http://www.crystallography.net/cod/* — specify the URL prefix for all objects in the queried database.

- **`--postfix`**, **`--db-url-postfix`** *.html* — specify the URL postfix for all objects in the queried database.

- **`--split-author-names`** — split author names in the internal database representation at semicolons (`';'`) so you get an RDF-parsable list of author names. each author in that list gets marked with the `"author"` property instead of `"authors"` (which is what gets used for the non-split value). this one is the **default** ✂️✨

- **`--no-split-author-names`**, **`--dont-split-author-names`** — make **no** assumptions about the internal database representation of the author list. she's neutral, she's chill 😌

- **`--xml-output`** — output RDF in XML carrier format. this is the **default** 💖

- **`--n3-output`** — output RDF in N3 (Notation3) carrier format.

- **`--turtle-output`** — output RDF in Turtle carrier format. 🐢

- **`--ntriples-output`**, **`--n-triples-output`** — output RDF in N-Triples carrier format.

- **`--replace-utf-codepoints-from`** — replace Unicode code points starting at the specified point with carrier format-specific entities.

- **`--no-replace-utf-codepoints`**, **`--dont-replace-utf-code-points`** — leave Unicode code points unescaped. this is the **default** 🌸

- **`--html-utf-escapes`** — escape Unicode code points using HTML hexadecimal format, corresponding to the `'&#x%04X;'` formatted string. this is the **default** 🔥

- **`--internal-utf-escapes`** — escape Unicode code points using internal format, corresponding to the `'\u%04X'` formatted string.

- **`--utf-escape-format`** — escape Unicode code points using a format corresponding to the formatted string you provide.

- **`--no-header`** — skip the header of the corresponding format. lowkey useful for generating catenable output 👀

- **`--no-footer`** — skip the footer of the corresponding format. also useful for generating catenable output 👀

- **`--only-header`** — print the header of the corresponding format and exit. that's it, that's the whole job ✨

- **`--only-footer`** — print the footer of the corresponding format and exit.

- **`--continue-on-errors`** — don't terminate the script if errors are raised.

- **`--die-on-errors`**, **`--no-continue-on-errors`**, **`--do-not-continue-on-errors`**, **`--dont-continue-on-errors`**, **`--exit-on-errors`** — terminate the script immediately if errors are raised. this is the **default** 💀

- **`--continue-on-warnings`** — don't terminate the script if warnings are raised. this is the **default** 🫶

- **`--die-on-warnings`** — terminate the script immediately if warnings are raised.

- **`--continue-on-notes`** — don't terminate the script if notes are raised. this is the **default** 📝

- **`--die-on-notes`** — terminate the script immediately if notes are raised.

- **`--use-perl-parser`** — use the Perl parser for parsing CIFs.

- **`--use-c-parser`** — use the faster C parser for parsing CIFs. this is the **default** ⚡

- **`--help`**, **`--usage`** — output a short usage message (this message, the one you're reading the vibes of) and exit.

- **`--version`** — output version information and exit. slay 💅

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# 🦋 REPORTING BUGS 🦋

found a bug? don't suffer in silence, bestie. report `cif2rdf` bugs using e-mail: `cod-bugs@ibt.lt` 📧

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okay that's the whole page!! <rainbow>cif2rdf</rainbow>, from the **General Commands Manual** (section 1, iconic behavior), brought to you by the version-and-date energy of this here footer. go parse something and be great 👑💖✨