Installation

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

pip install buildamol

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

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

Optional dependencies

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

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

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

Updating BuildAMol

Warning

When updating BuildAMol 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 BuildAMol). Instead we recommend to export your data to an agnostic format before updating. BuildAMol offers quick-exports to JSON and XML formats for such purposes. Both the PDBECompounds and CHARMMTopology classes have methods to export their data to JSON and XML formats. Alternatively, to export all custom resources at once, you can use the following functions:

import buildamol as bam

bam.export_custom_resources('my_settings')

# update ...

# after updating buildamol
bam.import_custom_resources('my_settings')