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biotite-dev / fastpdb

A high performance drop-in replacement for Biotite's PDBFile.
BSD 3-Clause "New" or "Revised" License
32 stars 2 forks source link

readme

.. image:: https://raw.githubusercontent.com/biotite-dev/fastpdb/main/logo.svg :width: 300 :align: center :alt: fastpdb

A high performance drop-in replacement for Biotite's PDBFile written in Rust.

Installation

fastpdb can be installed via

.. code-block:: console

$ pip install fastpdb

Usage

You can simply replace biotite.structure.io.pdb.PDBFile by fastpdb.PDBFile. The methods and their parameters are the same.

.. code-block:: python

import fastpdb

in_file = fastpdb.PDBFile.read("path/to/file.pdb")
atom_array = in_file.get_structure(model=1)

out_file = fastpdb.PDBFile()
out_file.set_structure(atom_array)
out_file.write("path/to/another_file.pdb")

Note that fastpdb does not yet support the hybrid-36 PDB format.

Performance

fastpdb is multiple times faster than biotite.

.. image:: https://raw.githubusercontent.com/biotite-dev/fastpdb/main/benchmark.svg :width: 800 :align: center