pdb2fasta

Convert PDB and mmCIF structure files to FASTA format.

Features

• Parse PDB format files
• Parse mmCIF format files
• Auto-detect file format
• Configurable output options
• C++ library with Python bindings
• Command-line interface

Installation

Python Package

pip install pdb2fasta

From Source

Requirements:

• CMake >= 3.15
• C++17 compiler
• Python >= 3.10
• pybind11

Build and install:

# Install in development mode (recommended for testing)
pip install -e .

# Or install normally
pip install .

# With test dependencies
pip install -e ".[test]"

Build the C++ extension:

The Python package uses scikit-build-core to automatically build the C++ extension during installation. However, if you need to rebuild:

# Clean and rebuild
pip install --no-build-isolation --force-reinstall -e .

C++ Library Only

mkdir build && cd build
cmake .. -DBUILD_CLI=ON -DBUILD_PYTHON=OFF
make
make install

Usage

Python

import pdb2fasta

# Convert a file
fasta = pdb2fasta.convert("structure.pdb")
print(fasta)

# Convert from string
pdb_content = open("structure.pdb").read()
fasta = pdb2fasta.pdb_to_fasta(pdb_content)

# Convert mmCIF
cif_content = open("structure.cif").read()
fasta = pdb2fasta.mmcif_to_fasta(cif_content)

# With options
fasta = pdb2fasta.pdb_to_fasta(
    pdb_content,
    line_width=60,
    include_chain_id=True
)

# Using the Converter class
options = pdb2fasta.ConversionOptions()
options.line_width = 80
converter = pdb2fasta.Converter(options)
fasta = converter.convert_file("structure.pdb")

# Parse and inspect structure
parser = pdb2fasta.PDBParser()
structure = parser.parse(pdb_content)
for chain in structure.chains:
    print(f"Chain {chain.id}: {len(chain.residues)} residues")

Command Line

# Basic usage
pdb2fasta-cli structure.pdb

# Multiple files
pdb2fasta-cli *.pdb *.cif

# With options
pdb2fasta-cli -w 60 -f mmcif structure.cif

# Options:
#   -h, --help          Show help message
#   -f, --format <fmt>  Force input format (pdb, mmcif, auto)
#   -w, --width <n>     Line width for FASTA output (default: 80)
#   -n, --no-chain      Don't include chain ID in header

C++

#include <pdb2fasta/pdb2fasta.hpp>
#include <iostream>

int main() {
    // Simple conversion
    std::string fasta = pdb2fasta::convert("structure.pdb");
    std::cout << fasta;
    
    // With options
    pdb2fasta::ConversionOptions options;
    options.line_width = 60;
    
    pdb2fasta::Converter converter(options);
    fasta = converter.convert_file("structure.cif");
    
    return 0;
}

Development

Running Tests

First, build and install the package:

pip install -e ".[test]"

Then run tests:

pytest
# or
uv run pytest

Troubleshooting

If you get ModuleNotFoundError: No module named '_pdb2fasta':

1. Make sure you've installed the package: pip install -e .
2. Check that the build completed successfully
3. Verify CMake and a C++ compiler are available
4. Try a clean rebuild: pip install --no-build-isolation --force-reinstall -e .

Supported Formats

Input

• PDB (.pdb, .ent)
• mmCIF (.cif, .mmcif)

Output

• FASTA format

License

MIT License