CIF_COD_CHECK(1)

💖 CIF_COD_CHECK — the manual page, but make it make sense 💖

okay bestie, gather round, because this is cif_cod_check from section 1 of the General Commands Manual, and she is that girl. she parses your CIF files and checks whether your data values are actually serving COD requirements and IUCr data validation criteria. no cap.

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✨ NAME ✨

cif_cod_check — parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09, https://www.iucr.org/__data/iucr/ftp/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests)

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🦋 SYNOPSIS 🦋

cif_cod_check --options input1.cif input*.cif

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🌸 DESCRIPTION 🌸

so basically: she parses a CIF file and checks if certain data values match COD requirements and IUCr data validation criteria. that's the whole vibe. Version: 2000.06.09, and the validation criteria live at https://www.iucr.org/__data/iucr/ftp/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests. 💅

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👑 OPTIONS 👑

💀 the "do we keep going or do we perish" options

• -c, --always-continue — keep processing and return a successful return status, even if errors are diagnosed. she's unbothered, moisturized, in her lane.
• -c-, --always-die — stop and return error status if errors are diagnosed. dramatic exit, iconic.
• --continue-on-errors — do not terminate the script if errors are raised.
• --die-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.

🧚 parser + input vibes

• --use-perl-parser — use the Perl parser for CIF parsing.
• --use-c-parser — use the Perl & C parser for CIF parsing (default).
• --cif-input — use CIF format for input (default).
• --json-input — use JSON format for input.

🌈 the meta-options for every check

fr fr, for every --check-xyz option there are these corresponding related options:

• --check-only-xyz — switch off any other checks and check ONLY xyz (the last option on the command line wins, so don't be messy about it).
• --no-check-xyz, --do-not-check-xyz, --dont-check-xyz — switch off checks of the xyz condition. three names, one energy.

🔥 the check options themselves

• --check-authors — check if the author names comply with the COD name syntax requirements. Default.
• --check-bibliography — check if the bibliographical information referring to the original source is present in the file. Default.
• --require-only-doi — treat the presence of the DOI as sufficient bibliographic information.
• --require-full-bibliography — require a more detailed set of bibliographic information containing items such as publication journal, year, volume, page numbers, etc. Default.
• --check-chemical-formula-sum — check if the summary chemical formula complies with the chemical formula syntax requirements. this check uses a simple syntax that does not take into account things such as chemical element types, chemical element order, etc. Default.
• --check-pd-block-relations — check if the relations between powder diffractogram and phase data blocks are properly described. Default.
• --check-spacegroup-info
• --check-operators, --check-symmetry-operators
• --check-unit-cell
• --check-symmetry
• --check-simultaneous-presence — check if data items from a certain data item grouping (e.g. atomic coordinates, anisotropic displacement parameters, etc.) are all simultaneously present in a data block. missing data items are reported only if at least one data item from the grouping is already present in the data block. Default.
• --check-limits
• --print-limits
• --add-limits limits.lst
• --limits-file limits.lst
• --reset-limits
• --check-adp-presence — check if each data block contains the atomic displacement parameters. the check may optionally be applied only to data files that were published after a certain year (see --max-year-adp-presence-is-optional). Default.
• --max-year-adp-presence-is-optional 1969 — check the presence of atomic displacement parameters only in data files published after the specified year. modifies the behaviour of --check-adp-presence. use --no-max-year-adp-presence-is-optional to override this option. Default: 1969.
• --no-max-year-adp-presence-is-optional — check the presence of atomic displacement parameters in all data files regardless of the publication year. modifies the behaviour of --check-adp-presence.
• --check-temperature-factors — alias of the --check-adp-presence option. Deprecated.
• --max-year-temperature-factors-optional 1969 — alias of the --max-year-adp-presence-is-optional option. Deprecated.
• --no-max-year-temperature-factors-optional — alias of the --no-max-year-adp-presence-is-optional option. Deprecated.
• --check-shelx-checksums — validate the checksums of embedded SHELX files. Default.
• --check-embedded-file-integrity
• --check-z
• --check-disorder
• --check-unquoted-strings — check if unquoted strings start or end with unusual characters such as ";" or "'". the presence of such features is a likely indication of an incorrectly formatted multi-line text field or a quoted string. Disabled by default.
• --check-all — enable all available checks. she's doing everything, all at once, and she's slaying.
• --check-none, --dont-check-any, --do-not-check-any, --no-check-any — disable all available checks.
• --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? don't be shy, report cif_cod_check bugs using e-mail: cod-bugs@ibt.lt 📧

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ok that's the whole page bestie, you ate that. now go validate some CIFs 💖

this was CIF_COD_CHECK(1) from the General Commands Manual, Version 2000.06.09 — that's the source/version energy, periodt. 🫶🌸✨