| Name | fastpdb JSON |
| Version |
1.3.0
JSON |
| download |
| home_page | |
| Summary | A high performance drop-in replacement for Biotite's PDBFile. |
| upload_time | 2024-01-12 14:52:58 |
| maintainer | Patrick Kunzmann |
| docs_url | None |
| author | Patrick Kunzmann, Nick Coish |
| requires_python | >=3.7 |
| license | |
| keywords |
pdb-files
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
.. 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
Raw data
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