COOT(1)

💖 COOT(1) — pyrogen 💖

okay bestie, welcome to the General Commands Manual page that ships as COOT(1) but is actually all about pyrogen. yes the name is a whole little plot twist, we love that for it. 🌸

✨ NAME ✨

pyrogen — a crystallographic dictionary restraints generating tool 🧚

like, that's the whole job description. it makes restraints. for crystals. for dictionaries. iconic behaviour, no notes. 💅

🎀 SYNOPSIS 🎀

pyrogen [OPTIONS] file-or-SMILES

so you hand it OPTIONS plus either a file or a SMILES string, and it does its little magic. periodt. ✨

💅 OPTIONS 💅

• -h, --help — show this help message and exit. the "hello, what is this" button. 🫶
• -c FILE, --mmcif=FILE — make restraints from an input mmcif FILE. feed it the mmcif, get restraints back. 💖
• -m FILE, --mol=FILE — make restraints from an input sdf/mol FILE. same energy, different file type. 🍓
• -r COMP_ID, --residue-type=COMP_ID — create restraints for this type. the default is LIG. so if you don't say anything, it assumes LIG, iykyk. 👑
• -4, --quartet-planes — use 4-atom plane restraints. heads up bestie, this forces --quartet-hydrogens on. they're a package deal. 😭
• -H, --quartet-hydrogens — use 4-atom hydrogen plane restraints. hydrogens getting their own plane era. ✨
• -b, --no-shift-hydrogen-atoms — stop the addition or deletion of hydrogen atoms for formally-charged atoms. leaving those hydrogens exactly where they are. 🛑
• -n, --no-mogul — don't run CSD Mogul to update bond and angle restraints. skipping the glow-up pass entirely. 🙈
• -N COMPOUND_NAME, --name=COMPOUND_NAME — compound name. give your baby a name. 🎀
• -S, --smiles — write the SMILES for the input molecule. just the SMILES, thank you. 💜
• -t, --tautomers — show SMILES for tautomers, and don't generate restraints. it's a look-only situation, no restraint generation. 👀
• -T MOGUL_DIR, --tmp-directory=MOGUL_DIR — the directory where the tmp files (e.g. for mogul) get written. 🗂️
• -d OUTPUT_DIR, --directory=OUTPUT_DIR — the directory where the output files (e.g. mmCIF and PDB) get written. this is where the good stuff lands. 🌈
• -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX — a string to add to output file names. the default is "pyrogen". ⭐
• -p, --picture — additionally output a chemical diagram PNG. yes, a picture. we're doing visuals now. 🖼️
• -P, --preserve-input-coordinates — preserve the input coordinates (if possible). only if possible, so don't come for it. 💀
• -v, --version — print version information. the "who even are you" flag. 🦋
• -a, --no-match-vs-reference-dictionaries — don't match atom names vs. dictionary molecules. the default is False. 🚫
• -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH — try to match the atom names of the output molecule to this dictionary in these files (a comma-separated list). 🌸
• -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH — try to match the atom names of the output molecule to these comp-ids (a comma-separated list). 🧚
• -w, --wwPDB — fetch the wwPDB ligand definition and use that. just grab the official one, easy. 💖
• -f FETCH — (just) fetch from the PDBe the CCD entry for the given compound-id. fetch mode only, nothing else. 🐕
• -q, --quiet — print less messages. for when the chatter is simply too much. 🤫

🌟 DESCRIPTION 🌟

Pyrogen is a command-line tool for the generation of crystallographic dictionary restraints. that's the whole vibe: you run it, it generates restraints. 💅

Pyrogen is based on the RDKit. 👑

👑 AUTHOR 👑

Paul Emsley

and that's a wrap, bestie ✨ this page came to you as COOT(1) from the General Commands Manual — go generate some restraints, you absolute main character 🫶💖🎀