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
- Single Structures