The --view option will run the specified software on the resulting geometry. It uses a Python command:
os.system("%s elbow.LIG.pdb" % options.view)
is equivalent to typing the passed option and the filename at the command line. Note that the appropriate filename is used.
For example:
elbow.builder --smiles --view molden
will result in:
molden elbow.LIG.pdb
being run on completion.
While the viewing program is active, the elbow builder is paused. A file name fixed.pdb (or fixed.xyz) written to the current directory will be read by the builder and used as the geometry for the next step.