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GlyContact: 3D Analysis of Glycan Structures

GlyContact is a Python package for retrieving, processing, and analyzing 3D glycan structures from GlycoShape, molecular dynamics, NMR, or X-ray crystallography.

The package is organized into the following main modules:

  • process: utilities for parsing and analyzing 3D glycan structures
  • visualize: functions for plotting contact maps and glycan features
  • learning: functions for training and using machine learning models


GlyContact provides a comprehensive toolkit that enables researchers to:

  • Visualize complex glycan structures with 3D-SNFG symbols
  • Quantify structural properties such as SASA and flexibility
  • Analyze conformational preferences and structure variability
  • Compare different glycan structures
  • Generate structural features for machine learning applications

These capabilities help bridge the gap between glycan sequence and function by revealing the critical spatial arrangements that determine molecular recognition.



Install

GlyContact can be cloned from GitHub or directly installed using pip.

All modules in GlyContact, except for ml, can be run on any machine. For most parts of ml, however, a GPU is needed to load and run torch_geometric.


Requirements

We recommend using at least the following Python and packages versions to ensure similar functionalities and performances as described in the publication:

  • Python ≥ 3.12.6
  • glycowork ≥ 1.6
  • scipy ≥ 1.11


Installation using pip

If you are using pip, all the required Python packages will be automatically installed with GlyContact.

pip install git+https://github.com/lthomes/glycontact.git


An optional [ml] install is available for machine learning features:

pip install -e git+https://github.com/lthomes/glycontact.git#egg=glycontact[ml]


Getting started with GlyContact

When you try GlyContact for the first time, you may encounter the following FileNotFoundError message: 

You need to equip GlyContact with GlycoShape structures. Download them from https://glycoshape.org/downloads and place the zipped folder into your GlyContact folder, then run it again.

GlyContact requires, at least, a folder with PDB files collected from GlycoShape. Below are the steps you must follow to get them:

  1. Download the GlycoShape.zip file from https://glycoshape.org/downloads

  2. If you have installed GlyContact using the pip install command, place the GlycoShape.zip file directly in the GlyContact package folder. The package location is indicated when you first pip install GlyContact. If, instead, you have git cloned GlyContact, place the GlycoShape.zip file in the glycontact/glycontact/ folder.

  3. Retry the import of the package. If you see the following lines, it works!

Identified zipped GlycoShape structures. Starting extraction.
Processing glycan structures: 100%|██████████| 639/639 [00:06<00:00, 100.13it/s]
Extraction succeeded. You should be good to go.

If after following these steps you still encounter an error message, feel free to open an issue.



Contributing

Contributions to GlyContact are welcome! Please feel free to submit a Pull Request.



Citation

If you use GlyContact in your research, please cite:

[Citation information will be added upon publication]



Licence

This project is licensed under the MIT License—see the LICENSE file for details.