Adding subtree 'R5-SD-DD' in 'R5-SD' group to fix degeneracy calculation error, RMG-Py issue#69!
Add Cdd atom type to *3 in Intra-R-Add-Endocyclic reaction family.

Some of these have been added already in recent commits.
Now, we went through systematically and added them all.
Removed a node we recently added.
Added some comments to the longDesc fields.
Jobs crashed with this error message:
"ValueError: invalid literal for int() with base 10"
Fixing the error with deleting spaces in the braces.
Merge remote-tracking branch 'fariba/master'