CIF2COD(1)

💖 CIF2COD(1) 💖

okay bestie, welcome to cif2cod from the General Commands Manual — yeah that's the manual name, it's giving classic Unix royalty 👑

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✨ NAME ✨

cif2cod — parse a CIF file and prep a COD database table entry out of it. that's it, that's the whole job 🫶

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🌸 SYNOPSIS 🌸

cif2cod --options input.cif inputs*.cif

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🦋 DESCRIPTION 🦋

Parse a CIF file, prepare a COD database table entry from it. literally what it says on the tin, no plot twist ✨

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💅 OPTIONS 💅

• -C, --cod-number 1000000 — use the number you give it (like 1000000 in this example, bestie) as the COD number for this structure. do not take the number from the data block name. main character energy: you decide the number 👑
• -c, --always-continue — keep going and return a successful return status even if errors get diagnosed. she's resilient 💪
• -c-, --always-die — stop and return error status if errors get diagnosed. dramatic exit, no cap 💀
• -h, --print-header — print a header with the data column names on the first line for CSV output format. Default.
• -h-, --no-print-header, --dont-print-header — do not print the column names on that first (header) line for CSV output format. shy mode 🙈
• -k, --keywords — print values on separate lines, each one prefixed with keywords.
• --include-keywords-with-undefined-values — print the keyword line with an empty value even if the value is undefined. showing up empty-handed but still showing up 🫶
• --exclude-keywords-with-undefined-values — do not print the keyword line at all if the value is undefined. Default.
• --use-attached-hydrogens — include the number of implicit hydrogen atoms, specified using the _atom_site_attached_hydrogens data item, into the formula sum. Default.
• --no-use-attached-hydrogens, --dont-use-attached-hydrogens, --ignore-attached-hydrogens — ignore the number of implicit hydrogen atoms, specified using the _atom_site_attached_hydrogens data item, in calculation of the formula sum.
• --reformat-space-group — correct the formatting of the Hermann-Mauguin 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 space group symbol. Default.
• --use-datablocks-without-coordinates, --use-all-datablocks — do not filter out data blocks without coordinates. everyone's invited to the party 🎀
• --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. Default.
• --require-only-doi — do not require all the bibliographic details (authors, journal name, title, year, volume and first page of the publication) to be present if the publication DOI is specified. DOI girlies get a pass 💅
• --require-full-bibliography — require author names, journal name, volume, publication title, year and first page to be present. Default.
• --columns file,flags,Robs
• --columns "file flags Robs" — print only the columns specified in this option. choose your faves 💖
• --validate-by-schema doc/CODDictionary.xml — validate the output by the supplied XML schema, where the SQL data types are given in the following manner:

<CODDictionary>
  <CODParameter name="file">
    <SQLDataType>mediumint(7) unsigned</SQLDataType>
    ...
  </CODParameter>
</CODDictionary>

• --continue-on-errors — do not 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. Default.
• --continue-on-warnings — do not terminate the script if warnings are raised. Default.
• --die-on-warnings — terminate the script immediately if warnings are raised.
• --continue-on-notes — do not terminate the script if notes are raised. 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. Default. fast AND iconic 🔥
• --cif-input — use CIF format for input. Default.
• --json-input — use JSON format for input.
• --help, --usage — output a short usage message (this message) and exit.
• --version — output version information and exit.

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😭 REPORTING BUGS 😭

Found a bug? report cif2cod bugs using e-mail: cod-bugs@ibt.lt — go tell them, bestie, they wanna know 🫶

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and that's the whole page, fr fr. CIF2COD(1), General Commands Manual, from the COD crew — ily, go parse something pretty 💜🌈