--view

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.