Installation

Biobuild can be directly installed via pip from the python package index:

pip install biobuild

If you want to install Biobuild from source, you can clone the repository and install it using the following command:

git clone https://github.com/NoahHenrikKleinschmidt/biobuild
cd biobuild
pip install .

Optional dependencies

Biobuild relies only on biopython for its core functions. However, many additional features may require other libraries. Especially, RDKit provides many useful features that Biobuild can use if it is installed. Apart from RDKit, Biobuild supports data exchange between Openbabel and OpenMM. If you want to install these libraries you can use the following commands:

pip install biobuild[rdkit]
pip install biobuild[openbabel]
pip install biobuild[openmm]
# or all at once
pip install biobuild[full]

We recommend to install at least biobuild[rdkit] if you want to use most features of Biobuild.

Updating biobuild

Warning

When updating biobuild to a newer version, make sure to export any custom default PDBECompounds or CHARMMTopology settings before updating, as the update will overwrite the pickle files where defaults are stored. You can re-set the custom settings after the update.

In order to export the custom data it is recommended not to pickle the objects (as a pickled object may not be compatbile with a newer version of Biobuild). Instead, you can export the data as a JSON file using the to_json method of the PDBECompounds and CHARMMTopology classes or the export_custom_resources function:

import biobuild as bb

bb.export_custom_resources('my_settings')
# after updating biobuild
bb.import_custom_resources('my_settings')