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README.md

protein-science - Scripts and Tools

PDB to FASTA

Sebastian Raschka, 09/01/2014
Version 1.0



I would be happy to hear your comments and suggestions. Please feel free to drop me a note via [twitter](https://twitter.com/rasbt), [email](mailto:[email protected]), or [google+](https://plus.google.com/+SebastianRaschka).


A script that converts amino acid residues from PDB files into a FASTA string



Requirements:

  • Python 2.7.x or Python 3.x


Usage:

run python pdb_to_fasta.py --help for the usage information:

usage: pdb_to_fasta.py [-h] [-l] [-o out.fasta] PDBfile

Converts amino acid residues from PDB file into a FASTA string

positional arguments:
  PDBfile

optional arguments:
  -h, --help            show this help message and exit
  -l, --ligand          includes HETATM residues.
  -o out.fasta, --out out.fasta
                        writes FASTA strings to an output file instead of printing it to the screen


Example

command:

python pdb_to_fasta.py 3B7V.pdb -o 3B7V.fasta