PSIZE(1)

📦 version 2.1.1, in ubuntu jammy

💖 PSIZE(1) — the pqrfile dimension tea 💖

okay bestie, welcome to psize, a lil tool from the PDB2PQR Manual that's here to spill all the deets about your PQR files. it's giving main character energy for electrostatics setup, fr fr. 🦋

✨ NAME ✨

psize — get dimensions and other information from PQR files 👑

🌸 SYNOPSIS 🌸

psize [--cfact=value] [--fadd=value] [--space=value] [--gememfac=value]
      [--gememceil=value] [--ofrac=value] [--redfac=value] {pqrfile}

psize {--help | -h}

💅 DESCRIPTION 💅

so basically psize pulls info out of PQR files so you can prep models of proteins and chemicals for electrostatics calculations. she's the get-ready-with-me of grid math, no cap. 🎀

here's what she figures out for you:

  • dimensions for coarse and fine grids
  • grid spacings
  • box size
  • an estimate of the memory you're gonna need to run an electrostatics calculation

and the way that you can influence all of that? you just hand her constraints as parameters. iconic. ✨

🔥 OPTIONS 🔥

psize accepts the following options, bestie, and yes you're gonna want to know every single one:

  • --help, -h — prints a help message and dips. that's it, that's the whole job. 🙈
  • --cfact=value — the factor you multiply the molecule dimensions by to get the coarse grid dimensions. expand her. 💜
  • --fadd=value — how much you add to the molecule dimensions to get the fine grid dimensions. just a lil top-up. 🍓
  • --space=value — the fine mesh resolution you want. your vibe, your call. 🌈
  • --gememfac=value — number of bytes per grid point needed for a sequential MG calculation. yes, bytes. she counts them. 🧚
  • --gememceil=value — the maximum MB allowed for a sequential MG calculation. crank this to force the script into faster calculations, which — heads up — require more parallelism. faster but thirstier, iykyk. 🔥
  • --ofrac=value — the overlap factor between mesh partitions. she likes her space, but not that much space. 🫶
  • --redfac=value — the maximum factor by which a domain dimension can be reduced during focusing. the limit, the ceiling, the "girl know your bounds". 💅

👑 SEE ALSO 👑

go read those next, they're the supporting cast and they ate. ⭐

🌟 AUTHOR 🌟

Manuel Prinz <debian@pinguinkiste.de> wrote this manpage for the Debian System. thank you for your service, king. 🫡

Copyright © 2008 Manuel Prinz

and that's the whole page, bestie!! this one shipped as part of the PDB2PQR manual, version vibes from 2008-06-04 — literally a classic, a vintage, an heirloom. go calculate those grids, you got this. 💖✨🎀🦋🌸

📦 where this page comes from