CIF_DISTANCES(1)

💫 CIF_DISTANCES — ok bestie, let's talk atom distance math 💫

This is the manual page for cif_distances, a little icon from the General Commands Manual collection. Pull up a chair, grab a boba, we're measuring atoms. 🧚

✨ NAME ✨

cif_distances — calculate minimal distance between atoms read from a CIF file.

No cap, that's literally the whole job. 🫶

🌸 SYNOPSIS 🌸

cif_distances --options input1.cif input*.cif

🦋 DESCRIPTION 🦋

Calculate minimal distance between atoms read from a CIF file.

That's it. That's the vibe. Give it CIF files, it gives you distances. 💅

👑 OPTIONS 👑

Bestie, this is the part where you take notes. Every single one of these matters. ✨

• -P, --pairwise-distance — sets the pairwise distance output format. This is the default, so if you just run it and say nothing, this is what you get. Main character energy, honestly.
• -M, --distance-matrix — sets the distance matrix output format. A whole grid of distances. It's giving spreadsheet but make it slay.
• --format "%8.6f" — use the specified format for the distance matrix and the pairwise printout format. Defaults? "%-11.3f" for the matrix and "%-6.3f" for pairwise. Yes, they're different. Yes, that's on purpose. 🙈
• -l, --matrix-line-length "80" — maximum length of an output line in distance matrix format. Default is 80, because some things are sacred.
• -F, --add-filename — adds a filename field at the end of pairwise distance format lines. Now you know which file each line came from. Iconic.
• --no-add-filename, --do-not-add-filename — does not add a filename field at the end of pairwise distance format lines. This one's the default, so it's already the chill option.
• --process-disordered-structures, --include-disordered-structures — forces processing of disordered structures. Default behaviour, so it's already on. 🎀
• --no-process-disordered-structures, --exclude-disordered-structures, --skip-disordered-structures — skips disordered structures entirely. Bye. 👋
• --process-duplicate-structures, --include-duplicate-structures — forces processing of structures that are flagged as duplicates with the '_cod_duplicate_entry' or '_[local]_cod_duplicate_entry' tags.
• --no-process-duplicate-structures, --exclude-duplicate-structures, --skip-duplicate-structures — skips duplicate structures. This is the default, so dupes get filtered out unless you say otherwise.
• --include-null-distances — includes entries of the null distance relationship between atoms from different disorder groups of the same disorder assembly, in the pairwise distances output format. Whew, that was a mouthful. 🍓
• --no-null-distances, --exclude-null-distances — excludes those null distance entries between atoms from different disorder groups of the same disorder assembly in the pairwise distances output format. Default behaviour, bestie.
• --include-self-distances — includes entries of distances between symmetry-related instances of the same atom. Yes, an atom vs. its own symmetry twin. Default. 🌈
• --no-self-distances, --exclude-self-distances — excludes entries of distances between symmetry-related instances of the same atom. No selfies allowed. 📵
• -U, --include-unknown-types — includes entries containing atoms of undetermined chemical type. Those atom types get marked as 'UN'. Mysterious. Love that for them. 💀
• --no-unknown-types, --exclude-unknown-types — excludes entries containing atoms of undetermined chemical type. Default, so the mystery atoms stay home. 🏠
• --uniquify-atoms — makes atom labels unique. This is the default. 💖
• --no-uniquify-atoms — does not make atom labels unique. Chaos mode, respect.
• --use-perl-parser — use the Perl parser to parse CIF files. 🐪
• --use-c-parser — use the C parser to parse CIF files. This is the default one. 🅒
• --help, --usage — outputs a short usage message (this message, basically) and exits. Your "hey what was that flag again" button. ✨
• --version — outputs version information and exits. For when you need receipts.

🔥 REPORTING BUGS 🔥

Found a bug? First of all, I'm so sorry. Second of all, report cif_distances bugs using e-mail: cod-bugs@ibt.lt 💌

Okay bestie, that's the whole page. This one's from the General Commands Manual family, the page was dated 2024-01-01... just kidding, the footer just says CIF_DISTANCES(1) — but you know the drill, the source, version and date live down there at the bottom of the original. Go measure some atoms. Slay. 💅👑🦋