Quickly getting at geometric data in a model file is often useful without having to go through the GUI, in order to quickly verify a geometry or get certain data into a file. The following command prints out all of the bond distances, including the indices of the atoms involved, from the command line:
bob@pc:~> aten data/test/methanol.inp -c 'for (Bond b = aten.model.bonds; b; ++b) printf("Distance %i-%i = %f\n", b.i.id, b.j.id, geometry(b.i,b.j)); quit();'
This will give you output along the following lines:
Autodetecting patterns for model 'Methanol'.. New pattern 'OCH4' added - startatom 1, 1 mols, 6 atoms per mol. Pattern description completed (spans 6 atoms). Done. Augmenting bonds in pattern OCH4... Distance 1-2 = 1.080000 Distance 1-3 = 1.080000 Distance 1-4 = 1.080000 Distance 1-5 = 1.080000 Distance 4-6 = 1.079999
All very good, but what about the extra information printed by Aten (such as pattern detection, etc.)? This can be inhibited by adding the
-q switch to the command.