pdb2fasta in C

Extracts the fasta sequence from protein stored in a PDB file.

This is a tool inspired by Pierre Poulain's pdb2fasta in bash article c.f.: https://cupnet.net/pdb2fasta/ The tool outlined in this article however has several quriks and fails on PDB files such as 7VWC . Actually it is also pdb2fasta in bash,awk,sed,etc. than pdb2fasta simply in bash.

I thought it is time to join the pdb2fasta game and write my own.

As such, here, a hopefully better, more standard conformant tool in C. ( and nothing but C )

Compilation:

compile with the c compilier of your choice, here gcc

gcc pdb2fasta.c -o pdb2fasta

you may add compilier flags, for a ultra high performant converter tool.

Usage:

./pdb2fasta yourpdbfile.pdb

should print a fasta formatted file to stdout with one sequence specification per chain.

Special Features:

The tool omits strcmp() or other string comparisons functions by usage of 4 bytes integers that can store just enough data to hold a 3 character long C-string.