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