MDINSPECT(1)

📦 version 1.11.1.post1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 MDINSPECT(1) 💖

okay bestie, welcome to mdinspect, a User Command, and honestly? she's a whole vibe. this is the manual page for her, and yes i'm gonna walk you through every single crumb. no skipping. 🍓

✨ NAME ✨

mdinspect — sanity checking for molecular dynamics trajectories 🧚

like. she looks at your MD trajectories and goes "girl… are you okay?" and tells you the truth. it's giving quality control but make it cute.

🌸 DESCRIPTION 🌸

here's the literal usage, exactly as she wants it, no edits, periodt:

usage: mdinspect [-h] [-t TOPOLOGY] [--bond-low BOND_LOW]
       [--bond-high BOND_HIGH] [--rmsd-tolerance RMSD_TOLERANCE] files
       [files ...]

Sanity checking for molecular dynamics trajectories. This script is currently a work in progress — like, she's still growing, still evolving, main character development arc in progress 🦋. Contributions are encouraged!! so if you have ideas, bestie, bring them, she wants them. 🫶

🎀 positional arguments 🎀

  • files — Input trajectory file(s), in any supported format. yes, plural, you can hand her a whole little friend group of files and she'll deal with every single one. 💅

💜 optional arguments 💜

  • -h, --help — show this help message and exit. the classic "wait what do i do" button, no cap.
  • -t TOPOLOGY, --topology TOPOLOGY — Topology for the system (.prmtop/.pdb). this is the blueprint bestie, the map, the "who even are these atoms" document. 🗺️
  • --bond-low BOND_LOW — Minimum fraction of sum of covalent radii for bonded atoms. Default=0.4. she uses this to catch bonds that are suspiciously smol. 👀
  • --bond-high BOND_HIGH — Maximum fraction of sum of covalent radii for bonded atoms. Default=1.2. and this one catches bonds that have overextended themselves, honestly relatable. 😭
  • --rmsd-tolerance RMSD_TOLERANCE — Maximum tolerance for percent change in RMSD. Default=100.0. if your RMSD is out here changing more than this, that's not a vibe, that's a red flag. 🚩
⚠️ real talk, bestie: this tool is a work in progress, and the manpage says so directly. don't be weird about it. contributions welcome, always. 💖

and that's the whole page!! you ate that, honestly. 👑

MDTRAJ · October 2020 — that's the source, the version and the date, mwah, sign-off complete, go check those trajectories, ily, bye!! 💅✨🌈

📦 where this page comes from