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