structure subpackage

Going 3D - The structure subpackage

biotite.structure is a Biotite subpackage for handling molecular structures. This subpackage enables efficient and easy handling of protein structure data by representing atom attributes in NumPy ndarray objects. These atom attributes include so called annotations (polypetide chain id, residue name, atom name, element, charge etc.) and the atom coordinates.

The package contains three central types: Atom, AtomArray and AtomArrayStack. An Atom contains data for a single atom, an AtomArray stores data for an entire model and AtomArrayStack stores data for multiple models, where each model contains the same atoms but differs in the atom coordinates. Both, AtomArray and AtomArrayStack, store the attributes in NumPy*` arrays. This approach has multiple advantages:

• Convenient selection of atoms in a structure by using NumPy style indexing

• Fast calculations on structures using C-accelerated ndarray operations

• Simple implementation of custom calculations

Based on the implementation using ndarray objects, this package also contains functions for structure analysis and manipulation.

Note

The universal length unit in Biotite is Å. This includes coordinates, distances, surface areas, etc.