.. biobox documentation master file, created by sphinx-quickstart on Wed Dec 28 17:34:22 2016. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. BiobOx's documentation ====================== BiobOx provides a collection of data structures and methods for loading, manipulating and analyzing atomistic and pseudo-atomistic 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 pseudoatoms * 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 include: * 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 * atomselect for molecules and assemblies of molecules * shortest physical paths between atoms on molecule using Theta* (or A*) * density map simulation .. toctree:: :maxdepth: 2 :caption: Contents: structure assembly measures examples * :ref:`genindex` * :ref:`modindex` * :ref:`search`