Tools
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Cuby comes with a set of scripts helping to prepare calculations and work with the results.
Submitting cuby job to queue system
Geometry format conversion
- geometry2xyz - Format conversion: to .xyz
- geometry2pdb - Format conversion: to PDB file
Geometry manipulation
- 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
- geometry_reorder
Analysis of the results
- et_paths - search for the most probable electron transfer paths in trajectory from MD
- measure - geometric measurements in MD trajectory
Visualization
Other tools
- optimize_parameters - universal optimizer of externally provided function