https://github.com/haschka/pdb2fasta

Extracts the fasta sequence from protein stored in a PDB file
https://github.com/haschka/pdb2fasta

Last synced: about 2 months ago
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Extracts the fasta sequence from protein stored in a PDB file

• Host: GitHub
• URL: https://github.com/haschka/pdb2fasta
• Owner: haschka
• License: gpl-3.0
• Created: 2022-07-22T15:32:11.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-01-31T22:56:30.000Z (almost 2 years ago)
• Last Synced: 2023-02-28T04:01:16.903Z (almost 2 years ago)
• Language: C
• Size: 26.4 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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/](https://cupnet.net/pdb2fasta/)

The tool outlined in this article however has several quriks and fails on 

PDB files such as [7VWC](https://www.rcsb.org/structure/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.