The bindings module contains functions and classes that interface with command-line programs commonly used in bioinformatics.
If you would like to write your own wrapper, consult Using External Programs within OpenStructure.
So far, the binding module includes:
dssp- Secondary structure assignment
blast- Search related sequences in databases
hhblits- Search related sequences in databases
msms– Calculating Molecular Surfaces
tmtools- Structural superposition
clustalw- Perform multiple sequence alignment
hbplus- Perform hydrogen bond analysis
kclust- Perform fast and sensitive clustering
naccess- Calculate accessible area of a molecule
lga- Find 3D similarities in protein structures
cadscore- Compare protein structures by difference between physical contacts