CIF_FIND_DUPLICATES(1)

💖 CIF_FIND_DUPLICATES(1) 💖

okay bestie, welcome to the General Commands Manual page for cif_find_duplicates — she's a little script with big main character energy and she's about to find your duplicates for you ✨

🌸 NAME 🌸

cif_find_duplicates — finds COD numbers for the .cif files sitting in the directories (or file lists) you hand her 🫶

🎀 SYNOPSIS 🎀

cif_find_duplicates --options my-cif-dir1/ my-cif-dir2/files*.cif COD-cif-dir/

like. that's it. that's the whole summoning ritual 💅

🦋 DESCRIPTION 🦋

Find COD numbers for the .cif files in given directories of file lists. literally her entire job. she's booked and busy and she's doing exactly one thing 👑

✨ OPTIONS ✨

• -c, --always-continue — keep on processing and hand back a successful return status even if errors got diagnosed. she's forgiving like that 🥺
• -c-, --always-die — the moment errors get diagnosed she stops and returns an error status. dramatic? yes. correct? also yes 💀
• --max-cell-length-difference 0.5 — the biggest difference in unit cell lengths that still counts as "same entry", measured in angstroms. default is 0.5 ⭐
• --max-cell-angle-difference 1.2 — the biggest difference in unit cell angles that still counts as "same entry", in angstroms. default is 1.2 ⭐
• --check-bibliography — CIFs only get declared different if their bibliography data differs, when everything else matches. and ngl, CIFs with missing bibliographies get assumed to have matching ones — this is the default 🎀
• --no-check-bibliography, --dont-check-bibliography — straight up ignore everyone's bibliographic data, so even files with different bibliographies count as the same as long as their cells, chemical formulae and measurement conditions line up 🙈
• --use-sigma, --dont-ignore-sigma, --no-ignore-sigma — actually use the standard deviations (sigmas) when comparing unit cell constants. default behavior, bestie ✨
• --no-use-sigma, --dont-use-sigma, --ignore-sigma — ignore the standard uncertainties (sigmas) when comparing unit cell constants. not today, sigma 💅
• --check-sample-history — CIFs only get declared different if their sample history data differs, where that data lives in the _exptl_crystal_thermal_history and _exptl_crystal_pressure_history tags, assuming all other parameters match 🌡️
• --no-check-sample-history, --dont-check-sample-history, --disregard-sample-history — ignore sample history for everyone, so files with different sample histories still count as the same when their cells, chemical formulae and measurement conditions match. this one's the default 🍓
• --use-attached-hydrogens — count the implicit hydrogen atoms when working out the summary chemical formula. those implicit H's are specified with the _atom_site_attached_hydrogens data item 🧪
• --no-use-attached-hydrogens, --ignore-attached-hydrogens — skip the implicit hydrogen atoms when calculating the summary chemical formula. again, implicit H's come from the _atom_site_attached_hydrogens data item. default, babes 🧚
• --continue-on-errors — don't terminate the script when errors get raised 🙏
• --die-on-errors, --dont-continue-on-errors, --do-not-continue-on-errors, --no-continue-on-errors — terminate the script immediately when errors get raised. default 🚨
• --continue-on-warnings — don't terminate the script when warnings get raised. default 😌
• --die-on-warnings — terminate the script immediately when warnings get raised ⚠️
• --continue-on-notes — don't terminate the script when notes get raised. default 📝
• --die-on-notes — terminate the script immediately when notes get raised 📌
• --use-perl-parser — parse CIF files with the Perl parser 🐪
• --use-c-parser — parse CIF files with the C parser. default 💪
• --help, --usage — print a short usage message (this exact message, yes) and exit 👋
• --version — print version info and exit 🏷️

🐛 REPORTING BUGS 🐛

Found a bug in cif_find_duplicates? spill it to the group chat, aka send e-mail to: cod-bugs@ibt.lt 📧 she wants to know fr fr

and that's the whole page, bestie!! this was CIF_FIND_DUPLICATES(1) from the General Commands Manual, and the footer said CIF_FIND_DUPLICATES(1) right back at us — so yeah, she signs off as herself, iconic behavior honestly. no cap, go find those duplicates 💖✨🎀🦋