Fixes to group Intra_R_Add_Endocyclic definitions
Added missing rate rules for several families.

The rate rules were missing because they came from rules that shared an
index with a later rule in the same family. This was caused mainly by the
sulfur rules, many of which overlap with non-sulfur rules. In the long
term we should give each rule a unique index, but this works for now.
Fixes to group Intra_R_Add_Endocyclic
Merge remote-tracking branch 'fariba/master'
Fix to OCOO rule in HO2_Elimination_from_PeroxyRadical.

For some reason this rule was not properly imported from the RMG-Java
database before.
Changed definition of OJ in Substitution_O to allow adjacent biradical.

This avoids an error where the Substitution_O family could only identify
a reaction in one direction (this family is its own reverse, so you
should be able to identify it in both directions).
Imported polycyclic thermo groups from RMG-Java.
Merge branch 'master' of github.com:GreenGroup/RMG-database
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' to fix Intra_R_Add_Endocyclic

This hopefully fixes all the remaining bugs in Intra_R_Add_Endocyclic
that were due to Cdd atom types being excluded from the list of
carbons with double bonds (Remember Cd means C with only one double bond.)

We also added some comments to the longDesc fields to help explain the tree.
Added Polycyclic stuff to output/RMG_database/thermo_groups

I copied these files straight from the RMG-Java database.
Perhaps they should be exported from this RMG-database project 
to make them formatted prettily. Or perhaps something else.
All I know is that without these, the ".loadOld" methods fail.
Added drawings of reaction families in ChemBioDraw format.

These are useful for visualizing what the various reaction families
represent.
Fixed bug in reading indices of rate rule entries.