Installation

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

pip install glycosylator

Optional dependencies

Glycosylator relies on BuildAMol for its core functionality. BuildAMol itself has some optional but highly useful dependencies such as RDKit and Openbabel. If you want to install these libraries you can use the following commands:

pip install glycosylator[rdkit]
pip install glycosylator[openbabel]

Glycosylator can use GlycoWork to draw glycans in SNFG format (Matplotlib-based native SNFG drawing is also available). To install GlycoWork together with Glycosylator use:

# this is also included in full
pip install glycosylator[glycowork]

We recommend to install at least glycosylator[rdkit] if you want to use most features of Glycosylator. Or install everything with:

pip install glycosylator[full]

Updating Glycosylator

Warning

When updating Glycosylator 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, you can export the data as a JSON or XML file using the to_json or to_xml methods of the PDBECompounds and CHARMMTopology classes or the export_custom_resources function:

import glycosylator as gl

gl.export_custom_resources('my_settings')

# ... update glycosylator

# after updating glycosylator
gl.import_custom_resources('my_settings')