Biobox provides a collection of data structures and methods for loading, manipulating and analyzing atomistic and pseudoatomistic structures.
Biobox main features:
- importing of PDB, PQR and GRO files, possibly containing multiple conformations (e.g. multi-PDB, gro trajectory)
- generation of coarse grain shapes composed of specific arrangements of pseudo-atoms
- loading and manipulation of density maps, including their transformation into a solid object upon isovalue definition
- assemblies of any points arrangement can be produced (i.e. densities converted in solid and geometric shapes can be equally treated).
Allowed operations on structures incude:
- generation of assemblies according to custom symmetries
- rototranslation and alignment on principal axes
- on ensembles: RMSD, RMSF, PCA and clustering
- calculation of CCS, SAXS, SASA, convex hull, s2 (for molecules), mass and volume estimation (for densities)
- atomselect for molecules and assemblies of molecules
- shortest solvent accessible path between atoms on molecule (using lazy Theta* or A*)
- density map simulation.
INSTALLATION AND REQUIREMENTS
The best way to install Biobox is via Anaconda
conda install biobox -c conda-forge
Biobox can be also installed via pip
pip install biobox
Biobox can otherwise be installed manually typing the followin command in the Biobox folder: python setup.py build_ext --inplace followed by python setup.py install. Please make sure the folder where Biobox is located is in your PYTHONPATH.
Biobox requires Python3.x and the following packages:
- numpy
- scipy
- pandas
- scikit-learn
- cython
Optional external software:
- CCS calculation relies on a call to IMPACT (requires definition of IMPACTPATH environment variable)
- SAXS simulations rely on a call to crysol, from ATSAS suite (requires definition of ATSASPATH environment variable)
USAGE
Documentation:
- Biobox's API is available at https://Degiacomi-Lab.github.io/biobox/
Tutorial:
- A Jupyter notebook presenting Biobox's main functionalities is available at https://github.com/Degiacomi-Lab/biobox_notebook
- The notebook can be run directly in a browser via Binder: https://mybinder.org/v2/gh/degiacom/biobox_notebook/HEAD
CITATION
When using Biobox in your work, please cite: L. S. P. Rudden, S. C. Musson, J. L. P. Benesch, M. T. Degiacomi (2021). Biobox: a toolbox for biomolecular modelling, Bioinformatics