PARMED:(1)

✨ PARMED:(1) ✨

okay bestie, welcome to the PARMED:(1) manual page, the one and only. pull up a chair, grab a strawberry 🍓, and let's get into it.

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🌸 NAME 🌸

parmed — parameter file editor. that's it, that's the whole vibe. it edits your parameter files. iconic behavior tbh. 💅

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🦋 DESCRIPTION 🦋

here's how you summon it, exactly as written:

usage: parmed [-h] [-v] [-i FILE] [-p <prmtop>] [-c <inpcrd>] [-O] [-l
FILE]

       [--prompt PROMPT] [-n] [-e] [-s] [-r] [<prmtop>] [<script>]

she's long, she's detailed, she ate. let's break down every single piece because we do NOT skip details in this house. no cap. 🫶

🎀 positional arguments

• <prmtop> — the topology file you want to analyze. the main character, lowkey.
• <script> — a file stuffed with a whole series of ParmEd commands to execute. like a to-do list but for your molecules.

💅 options

• -h, --help — shows this help message and dips. the classic "wait what does this do" move.
• -v, --version — shows the program's version number and exits. quick lil flex.

🌈 Input Files

• -i FILE, --input FILE — a script full of ParmEd commands to execute. by default it reads from stdin. you can drop this flag multiple times to process multiple input files. stacking? we love to see it.
• -p <prmtop>, --parm <prmtop> — the list of topology files to load into ParmEd. yes you can specify it multiple times to process multiple topologies. go off.
• -c <inpcrd>, --inpcrd <inpcrd> — the list of inpcrd files to load into ParmEd. these get paired up with the topology files in the exact same order that each set of files is specified on the command-line. so order matters bestie, keep them lined up like a choreo. 👑

🧚 Output Files

• -O, --overwrite — lets ParmEd overwrite files that already exist. permission granted, use responsibly.
• -l FILE, --logfile FILE — a log file containing every single command executed during an interactive ParmEd session. the default is parmed.log. receipts for everything, we keep them.

🔥 Interpreter Options

these options affect how the ParmEd interpreter behaves in certain cases. (so: vibes control. 🎛️)

• --prompt PROMPT — the string to use as a command prompt. customize it, make it cute.
• -n, --no-splash — prevents printing the greeting logo. skipping the intro, straight to business.
• -e, --enable-interpreter — allows arbitrary single Python commands, or whole blocks of Python code, to be run. by default Python commands will not be run, and that's a safeguard for your system. so fr fr, make sure you trust the source of the ParmEd command before you turn this option on. 🚨

seriously bestie, -e is the "let a stranger drive my car" flag. trust the source first. 😭

💜 Error Handling

these options control how ParmEd handles the various errors and warnings that show up during the course of Action execution. pick your coping mechanism:

• -s, --strict — prevents scripts from running past unrecognized input and actions that end with an error. in interactive mode, actions with unrecognized inputs and failed actions prevent any changes from being made to the topology, but it does not quit the interpreter. this is the default behavior. she's cautious, she's protected, she's the responsible friend. 🎀
• -r, --relaxed — scripts ignore unrecognized input and simply skip over failed actions, executing the rest of the script. unrecognized input in the interactive interpreter emits a non-fatal warning. she's chill like that. 🌈

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and that's the whole page, bestie. every flag, every default, every caveat, all of it. 💖

signing off with the receipts: this was parmed: Version 4.1.0, dated September 2023, filed under PARMED:(1). periodt. 👑✨