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

Contents:

• Single Structures
  • Structure
  • Molecule
  • Convex Point Clouds
  • Density
• Assemblies
  • Assembly
  • Polyhedron
  • Multimer
• Measures
  • measuring characteristics
  • measuring distances
• Examples
  • Selecting atoms from a (multi)PDB
  • protein conformations clustering
  • protein polyhedral assemblies
  • super coarse-grain modelling
  • density map cutoff via Collision Cross Section
  • lipids density around protein
  • calculating cross-linking distance

• Index

• Module Index

• Search Page