CIF_COD_NUMBERS(1)

🦋 CIF_COD_NUMBERS — bestie's guide to finding COD numbers 💖

okay so first things first: this is the General Commands Manual page for the command cif_cod_numbers, section 1. It's a lil' tool that goes and hunts down COD numbers for the CIF files chilling in whatever directories or file lists you hand it. No cap, that's the whole job. 🌸

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✨ NAME ✨

cif_cod_numbers — find COD numbers for the CIF files in given directories of file lists.

it's giving "matchmaker but for crystallography files" fr fr 💅

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🌈 SYNOPSIS 🌈

so you pass it your options and then a bunch of CIF files (globs are very much invited to the party) 🎀

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💜 DESCRIPTION 💜

Find COD numbers for the CIF files in given directories of file lists. That's it, that's the vibe. You feed it files, it goes and asks the COD database who these structures actually are. 👑

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🎀 OPTIONS 🎀

• --platform 'SQLite' — use the SQL database platform 'SQLite' to query structures (default: 'mysql'). pick your fighter ✨
• -d, --database — use database "cod" to query for structures.
• -h, --host — the host value is www.crystallography.net 💖
• -s, --server — query the COD database on the host 'www.crystallography.net'. yes bestie, that's the default host, iconic behavior 🫶
• -l, --localhost — use the database server on the localhost to query the COD database. stay home, query local 🏠
• -p, --port — use the specified port to query structures (default: 3306). the value shown is 3306, so that's the port you're knocking on 🔥
• -t, --table — use SQL table "data" to query for structures.
• -u, --user — use user name "cod_reader" to access the COD database. This user should have at least the SELECT privilege, i.e. should be able to read the COD database without supplying a password. lowkey the chillest login ever 🧚
• --password — use the specified password to connect (default: ''). empty string, mind you — that's the default, not a secret 💀
• -P, --print-datablock-name — print the data block name as the fifth column. extra column, extra drama 📊
• -P-, --no-print-datablock-name, --dont-print-datablock-name — do not print data block names (this is the default). no datablock names, we're being mysterious 🙈
• -S, --series — check only COD entries starting with 9 (the so called 9* series). Default: check the whole COD database. Set series to "" (empty string) to restore the default behaviour. so if you set it to 9, you're only looking at the 9* girlies ⭐
• --max-cell-length-difference — maximum difference of unit cell lengths allowed for entries regarded as the same, in angstroms (default: 0.5). the value shown is 0.5 📏
• --max-cell-angle-difference — maximum difference of unit cell angles allowed for entries regarded as the same, in angstroms (default: 1.2). yep, it says angstroms, we're just reporting what the page says 💅 the value shown is 1.2 📐
• --check-bibliography — only CIFs that have different bibliography data are declared different if all other parameters match. CIFs with missing bibliographies are assumed to have matching bibliographies (this is the default). citations matter, bestie 📚
• --no-check-bibliography, --dont-check-bibliography — ignore bibliographic data of all CIFs; thus even files with different bibliographies will be regarded the same if their cells, chemical formulae and measurement conditions match. bibliography? never heard of her 🙈
• --use-sigma, --no-ignore-sigma, --dont-ignore-sigma — use standard deviations (sigmas) when comparing unit cell constants (this is the default). respect the sigma ✨
• --no-use-sigma, --dont-use-sigma, --ignore-sigma — ignore standard deviations (sigmas) when comparing unit cell constants. sigma? blocked 🚫
• --check-sample-history — only CIFs that have different sample history data (as recorded in the _exptl_crystal_thermal_history and _exptl_crystal_pressure_history tags) are declared different if all other parameters match. the lore is in the tags, iykyk 🧚
• --no-check-sample-history, --dont-check-sample-history, --disregard-sample-history — ignore sample history of all CIFs; thus even files with different sample histories will be regarded the same if their cells, chemical formulae and measurement conditions match (this is the default). sample history? we don't know her 💀
• --check-compound-source — only CIFs that have different compound source (as recorded in the _chemical_compound_source) are declared different if all other parameters match. where did this compound come from? we're asking 🍓
• --no-check-compound-source, --dont-check-compound-source, --disregard-compound-source — ignore compound source of all CIFs; thus even files with different compound sources will be regarded the same if other conditions match (this is the default). origin story: deleted 🫶
• --use-attached-hydrogens — include the number of implicit hydrogens, specified using the _atom_site_attached_hydrogens tag, into the formula sum (this is the default). hydrogens are literally invited to the function 🔥
• --no-use-attached-hydrogens, --dont-use-attached-hydrogens, --ignore-attached-hydrogens — ignore the number of implicit hydrogens, specified using the _atom_site_attached_hydrogens tag, in calculation of the formula sum. hydrogens? not counted, not today 😭
• --use-perl-parser — use the Perl-only CIF parser. old reliable, in Perl 🐪
• --use-c-parser — use the speed-optimised C/Perl parser (this is the default). fast mode, main character energy ⚡
• --cif-input — use CIF format for input (this is the default). 📄
• --json-input — use JSON format for input. 🧾
• --help, --usage — output a short usage message (this message) and exit. your lil' cheat sheet 💖
• --version — output version information and exit. 👑

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🫶 REPORTING BUGS 🫶

found a bug? not the vibe. report cif_cod_numbers bugs using e-mail: cod-bugs@ibt.lt 📧

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and that's the whole page, bestie!! we made it through every single option, no skips, no cap 💖 this was the cif_cod_numbers manual page, from the General Commands Manual (section 1), footer signed CIF_COD_NUMBERS(1) — so if you ever see that name floatin' around, it's us. slay, go match some structures ✨👑🌸