CIF_FIX_VALUES(1)

💖 CIF_FIX_VALUES 💖

okay bestie, welcome to cif_fix_values from the General Commands Manual — she's a whole glow-up artist for your CIF files and she's about to fix EVERYTHING 🔥

✨ NAME ✨

cif_fix_values — corrects various CIF file values and outputs the changes she made straight into the standard I/O streams. She's lowkey a full makeover montage, and here's her roster of corrections:

• Converting temperature from degrees Celsius to kelvins, removing temperature units of measurement, and processing other undefined temperature values 🥵➡️🥶
• Fixing misspelled values by using the provided replacement value file 📝
• Fixing enumeration values in the CIF file against CIF dictionaries 📚
• Correcting values of '_exptl_crystal_density_meas' data item ⚖️

And the tea: all of these corrections are enabled by default, but you can turn any of them off by prefixing the corresponding option with '--do-not', '--dont' or '--no' — for example, '--no-fix-temperature'. Not her being customizable AND gorgeous 💅

🌈 SYNOPSIS 🌈

cif_fix_values --options input1.cif input*.cif

🦋 DESCRIPTION 🦋

Correct various CIF file values and output the made changes into the standard I/O streams. (Yes she's repeating herself, she's thorough, she contains multitudes ✨)

The script is capable of making these corrections:

• Converting temperature from degrees Celsius to kelvins, removing temperature units of measurement, processing other undefined temperature values
• Fixing misspelled values by using the provided replacement value file
• Fixing enumeration values in CIF file against CIF dictionaries
• Correcting values of '_exptl_crystal_density_meas' data item

All described corrections are enabled by default, but can be disabled by prefixing the corresponding options by '--do-not', '--dont' or '--no' (for example, '--no-fix-temperature').

bestie she is doing the MOST by default. if you wanted a chill, do-nothing script, wrong number 💀

👑 OPTIONS 👑

• --fix-temperature — Corrects temperature values which have units specified, or converts between degrees Celsius and kelvins. Changes 'room/ambiante temperature' to the appropriate numeric value. Changes other undefined values ('none', 'not given') to the '?' symbol. No more vibes-based temperatures, we're doing numbers now 🔢
• --fix-misspelled replacement_value.lst file — Corrects misspelled values in the CIF file. Provide a file for the check.
• --fix-dois — Removes URL or DOI: prefixes from values of DOI data items. bye bye prefix, you're not invited 🫶
• --fix-enums — Corrects enumeration values in the CIF against CIF dictionaries. Provide dictionaries using option --dictionaries (or -d), otherwise the script uses a built-in table derived from the CIF Core dictionary.
• --treat-as-set — Treats certain enumeration values as set data type in the CIF against CIF dictionaries (default). Provide dictionaries using --dictionaries (or -d) option, otherwise the script uses a built-in table derived from the CIF Core dictionary.
• --fix-density-meas — Corrects the value of data item '_exptl_crystal_density_meas'. Values which are perceived as 'not measured' are changed to '?'. The correct units are deleted. The new data item is created if there are information about temperature.
• --fix-weighting-scheme — Changes the value of the data item '_refine_ls_weighting_scheme' to the value 'calc' if it contains details which seems to have a formula, and creates new data item '_refine_ls_weighting_details' to store that information. If value is equal to number one, then it is changed to the enumeration value 'unit'. the way she catches that formula hiding in plain sight… iconic 🕵️‍♀️
• --fix-atom-sites-solution — Corrects the most frequent mistakes in the values of data items '_atom_sites_solution_primary', '_atom_sites_solution_secondary' and '_atom_sites_solution_hydrogens'.
• -d, --dictionaries 'cif_core.dic,cif_cod.dic' — A list of CIF dictionary files (according to DDL1) to be used in CIF file validation. List elements are separated either by ',' or by ' '. To include dictionaries with filenames containing these symbols, the --add-dictionary option is used.
• -D, --add-dictionary 'cif new dictionary.dic' — Add additional CIF dictionary to the list.
• --clear-dictionaries — Remove all CIF dictionaries from the list. poof, gone, no notes 💨
• --use-perl-parser
• --use-c-parser — Specify parser to parse CIF files (default: C parser). (both of these bad boys share that one job, pick your fighter ⚔️)
• --help, --usage — Output a short usage message (this message) and exit.
• --version — Output version information and exit.

😭 REPORTING BUGS 😭

Report cif_fix_values bugs using e-mail: cod-bugs@ibt.lt

not her asking you to email her about bugs, she wants the feedback fr fr 📬

and that's the whole page bestie!! she's cif_fix_values(1), she lives in the General Commands Manual section 1, and she came from the CIF_FIX_VALUES(1) era — go fix those values, you absolute main character 🎀✨💜