biobox on Pypi

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

Biobox requires Python3.x and the following packages:

install with: python setup.py install and make sure the folder where Biobox is located is in your PYTHONPATH.

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)

Documentation:

Tutorial:

A Jupyter notebook presenting Biobox's main functionalities is available at https://github.com/degiacom/biobox_notebook
The notebook can be run directly in a browser via Binder: https://mybinder.org/v2/gh/degiacom/biobox_notebook/HEAD

A publication is currently in preparation. If you use Biobox in your work, please cite this repository.