DDLM_VALIDATE(1)

📦
version 3.12.0 · 3 versions
, in ubuntu stonking

💖 DDLM_VALIDATE 💖

okay bestie, so this is ddlm_validate — it lives in the General Commands Manual (section 1, the classics ✨), and it's the little tool that checks your CIF files against DDLm-compliant CIF dictionaries. think of it as a vibe check for your crystal data 💅

✨ NAME ✨

ddlm_validate — validate CIF files against DDLm-compliant CIF dictionaries.

like, it takes your CIF files and goes "hmm, does this match the dictionary rules tho?" 👑

🌸 SYNOPSIS 🌸

ddlm_validate --dictionaries 'cif_core.dic,cif_cod.dic' --options
input1.cif input*.cif

yes, that's the whole glow-up. dictionaries first, then your files, no cap 🫶

🦋 DESCRIPTION 🦋

Validate CIF files against DDLm-compliant CIF dictionaries.

that's literally it, that's the job. she validates. she slays. periodt ✨

💅 OPTIONS 💅

  • -d, --dictionaries 'cif_core.dic,cif_cod.dic' — bestie this is THE list of DDLm-compliant CIF dictionary files that your CIF files should be validated against. list elements get separated either by , or by . hmm and if you have dictionary filenames that literally contain those symbols? 💀 then you gotta use the --add-dictionary option instead, sorry.
  • -D, --add-dictionary 'cif new dictionary.dic' — adds one more CIF dictionary to the list. one at a time, queen, stack 'em up 🎀
  • --clear-dictionaries — yeets every single CIF dictionary off the list. clean slate energy.
  • -I, --add-ddlm-import-path './ddlm/cod/' — prepends an additional directory to the dictionary import path. and what even is the dictionary import path, you ask? it's the list of directories where we go looking for files that get imported by DDLm-compliant CIF dictionaries. directories you give with this option get the highest priority — they're searched before the directories listed in the COD_TOOLS_DDLM_IMPORT_PATH environment variable, or the default import path (which is the directory of the importing dictionary). main character priority fr fr 👑
  • --clear-ddlm-import-path — removes all the directories from the dictionary import path that were added using the --add-ddlm-import-path option. important: neither the COD_TOOLS_DDLM_IMPORT_PATH environment variable nor the default import path is affected by this option. she's surgical with it 💅
  • --max-message-count 5 — the maximum number of validation messages that get reported for each unique combination of validation criteria and validated data items. wanna see EVERYTHING? provide a negative value (e.g. -1) and she'll output all of the generated validation messages. Default: -1.
  • --range-su-multiplier 3.5 — the multiplier applied to the standard uncertainty (s.u.) when we're deciding if a numeric value actually resides in the specified range. for example: a multiplier of 3.5 means the value is treated as valid if it falls inside the interval of [lower bound - 3.5 * s.u.; upper bound + 3.5 * s.u.]. math girlies rise 🧚 Default: 3.
  • --treat-as-set _atom_site_refinement_flags — treats values of given data items as a set. okay so due to historical reasons 🙈 data values of some data items are sometimes formed by concatenating several of the available enumeration values. any number of data items can be specified, like this:
ddlm_validate --treat-as-set _tag_1 --treat-as-set _tag_2

Default: '_atom_site_refinement_flags' and '_atom_site.refinement_flags'.

  • --no-treat-as-set — do not treat values of any data items as sets (see --treat-as-set). so... the opposite, obviously 💜
  • --report-deprecated — reports the presence of data items that are marked as deprecated in the dictionaries. and what does deprecation mean? usually that the data item has been replaced with another data item. she's giving you the heads up, not just gossip 💅
  • --no-report-deprecated, --ignore-deprecated — do not report the presence of data items marked as deprecated in the dictionaries. this is the Default. shhh, we don't talk about those 🤫
  • --report-local-tags — reports the presence of local data items. spill the tea ☕
  • --no-report-local-tags, --ignore-local-tags — do not report the presence of local data items. Default. quiet luxury energy.
  • --report-missing-su — reports measurand data items that aren't accompanied by standard uncertainty values. this behaviour follows the requirements imposed by the DDLm reference dictionary prior to version 4.0.1. vintage rules, retro vibes 🌈
  • --no-report-missing-su, --ignore-missing-su — do not report measurand data items that aren't accompanied by standard uncertainty values. this behaviour follows the requirements imposed by the DDLm reference dictionary since version 4.0.1. Default. glow-up complete ✨
  • --follow-iucr-style-guide — do not report missing recommended attributes if they fit the criteria defined in the IUCr DDLm dictionary style guide version 1.4.0, rule 3.1.6. very specific, very cunty, very correct 🎀
  • --no-follow-iucr-style-guide — do not make any validation exceptions based on the IUCr DDLm dictionary style guide. Default. no special treatment here 💅
  • --continue-on-errors — do not terminate the script if errors are raised. she's resilient, she's bouncing back 🦋
  • --die-on-errors — terminate the script immediately if errors are raised. Default. dramatic exit, honestly iconic 💀
  • --continue-on-warnings — do not terminate the script if warnings are raised. Default. we move on 🫶
  • --die-on-warnings — terminate the script immediately if warnings are raised. lights out, bestie 😭
  • --continue-on-notes — do not terminate the script if notes are raised. Default. notes? little notes? she can handle it 🌸
  • --die-on-notes — terminate the script immediately if notes are raised. even the lil notes can end it all 💀
  • --help, --usage — output a short usage message (this message) and exit. your girl loves a lil help 🥰
  • --version — output version information and exit. numbers! dates! slay! ⭐

🌈 ENVIRONMENT 🌈

  • COD_TOOLS_DDLM_IMPORT_PATH — a list of directories in which to look for the DDLm-compliant CIF dictionaries that are imported by other DDLm-compliant CIF dictionaries. list elements are separated by the colon symbol (':'). directories listed in COD_TOOLS_DDLM_IMPORT_PATH have a lower priority than those provided using the command line option (--add-dictionary-import-path), but higher than the default import path directory (directory of the importing dictionary). hierarchy, but make it cute 🧚

💀 REPORTING BUGS 💀

found a bug? bestie, report ddlm_validate bugs using e-mail: cod-bugs@ibt.lt 📧 she wants to know, fr fr 🫶

and that's the whole page 💖 this was the DDLM_VALIDATE(1) command from the General Commands Manual, and the footer down there is just the title all over again — DDLM_VALIDATE(1) on its own, no version, no date, just her name in lights ✨ obsessed. go validate something, bestie 🎀

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