colav 0.0.4

Calculate protein structural representations (dihedral angles, CA pairwise distances, and strain analysis) for downstream analysis (e.g., PCA, t-SNE, or UMAP)

colav

colav (Conformational Landscape Visualization) provides tools for representing protein structures and mapping conformational landscapes.

colav supports calculations for dihedral angles, pairwise distances, and strain. It is built on biopandas, NumPy, and SciPy. The methods analyze .pdb files, either one-by-one or all together. The three methods currently implemented are:

Installation

You can install colav using pip:

pip install colav

Documentation

Documentation can be found here.

Examples

Examples of how to use the software can be found in scripts/.

Support

If you are having issues, please let us know. You can contact us here.

License

This code is provided under the MIT license.

Reference

If you use colav in your work, please use the following citation:
Saeed, A.A., Klureza, M.A., and Hekstra, D.R. (Forthcoming!). Mapping protein conformational ensembles using crystallographic drug fragment screens. doi