CIF_GUESS_...ATOM_TYPES(1)

📦 version 3.12.0, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 CIF_GUESS_...ATOM_TYPES 💖

okay so bestie, welcome to the CIF_GUESS_...ATOM_TYPES(1) page — yeah that's the whole title, the ellipsis is doing a lot of heavy lifting and honestly? iconic. this is a page from the General Commands Manual, section 1, and it's all about one little program that reads your CIF and guesses what your atoms are. let's get into it 🧚

✨ NAME ✨

cif_guess_AMCSD_atom_types — read the CIF file, assuming that it follows AMCSD atom naming conventions, and assign atom types and attached hydrogen counts as follows:

  • for 'Wat' atoms (with or without a number) assign atom type 'O' and hydrogen count 2.
  • for 'O-H' atoms assign atom type 'O' and hydrogen count 1.
  • for 'OH' atoms assign atom type 'O' and hydrogen count 0 (hydrogen atoms are usually given explicitly in such cases).
  • For other 'O[a-rt-z]' matching atoms, assign type 'O' and no attached hydrogens.

🌸 SYNOPSIS 🌸


yes she takes options AND as many CIF files as you wanna throw at her. glob queen. 💅

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# 🦋 DESCRIPTION 🦋

Read the CIF file, assuming that it follows AMCSD atom naming conventions, and assign atom types and attached hydrogen counts as follows:

- for <yellow>`'Wat'`</yellow> atoms (with or without a number) assign atom type <mint>`'O'`</mint> and hydrogen count <mint>`2`</mint>.

- for <yellow>`'O-H'`</yellow> atoms assign atom type <mint>`'O'`</mint> and hydrogen count <mint>`1`</mint>.

- for <yellow>`'OH'`</yellow> atoms assign atom type <mint>`'O'`</mint> and hydrogen count <mint>`0`</mint> (hydrogen atoms are usually given explicitly in such cases).

- For other <yellow>`'O[a-rt-z]'`</yellow> matching atoms, assign type <mint>`'O'`</mint> and no attached hydrogens.

so basically: water gets two hydrogens, `O-H` gets one, bare `OH` gets zero because the H is already out there living its truth in the file, and everything else that matches `O[a-rt-z]` gets typed as `O` with nothing attached. no cap. ✨

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# 🎀 OPTIONS 🎀

- **`--keep-tag-order`** — Keep the original tag order in CIF file (default).
- **`--sort-tags`** — Reorder tags in CIF file according to COD.
- **`--use-perl-parser`** — Use Perl parser to parse CIF files.
- **`--use-c-parser`** — Use C parser to parse CIF files (default).
- **`--help`, `--usage`** — Output a short usage message (this message) and exit.
- **`--version`** — Output version information and exit.

lowkey the defaults are `--keep-tag-order` and `--use-c-parser`, so if you just run it with no vibes specified, that's what you get. 🫶

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# 😭 REPORTING BUGS 😭

Report <pink>`cif_guess_AMCSD_atom_types`</pink> bugs using e-mail: <cyan>`cod-bugs@ibt.lt`</cyan>

> fr fr, if something's broken, tell the cod people. they wanna know. do not suffer in silence bestie 💀

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and that's the whole page!! <rainbow>slay</rainbow> 🌈 this was `CIF_GUESS_...ATOM_TYPES(1)`, straight out of the <purple>General Commands Manual</purple>, and it's giving very much section-1 energy. go type your atoms, you got this 👑💖
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