PDB_TOFASTA(1)

💖 PDB_TOFASTA 💖

okay bestie, so the manual name is pdb_tofasta and this is PDB_TOFASTA(1) — it's a User Commands situation, and we're on version 2.5.1. sit down, hydrate, let's get into it 🫶

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✨ NAME ✨

pdb_tofasta — the manual page for pdb_tofasta 2.5.1 💅

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🌸 DESCRIPTION 🌸

okay so first things first, if you mess up the invocation you get greeted with this, literally verbatim:

pdb_tofasta You provided an invalid option: '-help'

no cap, that's what it says. moving on 🦋

So what does it even do? It extracts the residue sequence in a PDB file to FASTA format. That's the whole vibe. ✨

The canonical amino acids and the nucleotides? They get represented by their one-letter code. Everything else — every single one of them — gets represented by 'X'. No exceptions, no notes. 💀

And then there's the -multi option, which is lowkey iconic: it splits the different chains into different records in the FASTA file. one chain, one record. separate. periodt. 👑

🎀 Usage:

python pdb_tofasta.py [-multi] <pdb file>

🍓 Example:

python pdb_tofasta.py 1CTF.pdb

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🌈 THE LORE 🌈

This program is part of the pdb-tools suite of utilities and should not be distributed isolatedly. fr fr, don't do that. 🙈

The pdb-tools were created to quickly manipulate PDB files using the terminal, and they can be used sequentially — one tool streaming data to another. it's giving pipeline main character energy. 🔥

They're based on old FORTRAN77 code that was taking too much effort to maintain and compile. RIP. 😭 we honor the fallen.

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sign-off time 🧚: this was pdb_tofasta 2.5.1, dated September 2024, and yeah — PDB_TOFASTA(1), that's us. mwah 💖✨