PRODY(1)

🎀 NAME 🎀

ProDy — the Python Package for Protein Dynamics Analysis ✨ and yes bestie, this is the manual page for it, aka PRODY(1), section 1, the whole entire vibe 💖

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💅 DESCRIPTION 💅

okay so, when you run prody with no idea what to do next, this is the energy it gives:

usage: prody [-h] [-c] [-v]
              {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select,energy,clustenm}
              ...

and like, that's not just a wall of text, that's a menu 🫶:

ProDy: A Python Package for Protein Dynamics Analysis — say it with your chest 💜

✨ options: ✨

• -h, --help — the classic. shows you this help message and then dips, no cap 🙈
• -c, --cite — prints the citation info and exits, so you can credit people properly like the academic icon you are 👑
• -v, --version — prints the ProDy version and exits. one number, so much closure 💅

🦋 subcommands: 🦋

here's the whole roster, in a lil brace-y lineup bestie:

{anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select,energy,clustenm}

and one by one, because every single one of them deserves their moment:

• anm — perform anisotropic network model calculations 🌸
• gnm — perform Gaussian network model calculations ✨
• pca — perform principal component analysis calculations 💖
• eda — perform essential dynamics analysis calculations 🌈
• align — align models or structures 🧚
• blast — blast search Protein Data Bank 🔥
• biomol — build biomolecules 🍓
• catdcd — concatenate dcd files 🎀
• contacts — identify contacts between a target and ligand(s) 💜
• fetch — fetch a PDB file 🫶
• select — select atoms and write a PDB file ⭐
• energy — fix missing atoms, solvate, minimise and calculate energy 💀 (yes, all of that, in one command, main character energy fr fr)
• clustenm — run clustenm(d) simulations 👑

lowkey important, bestie: See 'prody <command> -h' for more information on a specific command. — like, each one has its own lore, go read it 📖

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and that's the whole page, we ate and left no crumbs 💅 This was ProDy 2.4.1, February 2024 — that version and that date, iconic, periodt. now go run something cute 🦋💖