Installation

Requirements

Biotite requires a modern Python installation (at least the last two years are supported) and the following packages:

• numpy

• requests

• msgpack

• networkx

Installation of the biotite package will also automatically install these dependencies if not already present.

Some functionalities require extra packages:

• matplotlib - Required for plotting purposes.

Installation from PyPI

Biotite is available as wheels for a variety of platforms (Windows, Linux, OS X). Simply type

$ pip install biotite

If pip finds an appropriate wheel for your system configuration on PyPI, it will download and install it. If no fitting wheel is found, pip will fall back to the source distribution. In this case, installation will take longer, because extension modules need to be compiled first. Note that this requires a C-compiler (typically GCC) installed on your system.

Installation via Conda

Biotite is also available via Conda.

$ conda install -c conda-forge biotite

Installation from source

You can also install Biotite from the project repository. After cloning the repository, navigate to its top-level directory (the one setup.py is in) and type the following:

$ pip install .

Having the Biotite installation always pointing to your repository clone is also possible. Type the following in the top-level directory:

$ pip install -e .

Updating the Chemical Component Dictionary

The biotite.structure.info subpackage contains a subset from the PDB Chemical Component Dictionary (CCD). The repository ships a potentially outdated version of this subset. To update this subset to the current upstream CCD version, run

$ python setup_ccd.py

Afterwards, install Biotite again.

Common issues and solutions

Compiler error when building Biotite

There is a known problem with GCC compiler errors in some Linux distributions (e.g. Arch Linux) when building Biotite from source. Among other error lines the central error is the following:

unable to initialize decompress status for section .debug_info

While the exact reason for this error is still unknown, this can be fixed by using a GCC installed via Conda:

$ conda install -c conda-forge c-compiler

ValueError when importing Biotite

When importing one of Biotite’s subpackages one of the following errors might occur:

ValueError: numpy.ufunc size changed, may indicate binary incompatibility.
ValueError: numpy.ndarray size changed, may indicate binary incompatibility.

The reason for this error is, that Biotite was built against a NumPy version other than the one installed. This happens for example when NumPy is updated, but Biotite is already installed. Try updating NumPy and Biotite to solve this issue.