Cuby comes with a set of scripts helping to prepare calculations and work with the results.
- geometry - basic operations with geometry
- geometry_pdbtools - operations specific to PDB files
- geometry_fragmentation - script handling multiple tasks useful when preparing fragmented calculation.
- geometry_scan - generate series of geometries by varying internal coordinates
- et_paths - search for the most probable electron transfer paths in trajectory from MD
- measure - geometric measurements in MD trajectory
- optimize_parameters - universal optimizer of externally provided function