Tools

This revision is from 2009/04/24 22:50. You can Restore it.

Cuby comes with a set of scripts helping to prepare calculations and work with the results.

Submitting cuby job to queue system

submit

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.

Analysis of the results

et_paths - search for the most probable electron transfer paths in trajectory from MD
measure

Visualization

visualize_intmatrix