Calculated some addition beta scissions for the JP10Betascission library. Intra diels alder are ON in the families.txt.
Added some new species to the JP10 thermo lib.
Added hydrogen abstraction reactions with allene and propargyl to the H abstraction family tree.
Updated the Diels-Alder additions to include additions of triple bonds to dienes. Calculated two rates for this and corrected on older value.
Merge branch 'master' of https://github.com/GreenGroup/RMG-Java

Conflicts:
	databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt
Introduced new reaction family for H shifts in cyclopentadiene type rings. 1 rate was taken from H shift in ethyleneCPD.
Merge branch 'master' of https://github.com/GreenGroup/RMG-Java
Test to exclude constraint intra H abstractions and intra disproportionation reactions in cyclics.
Merge branch 'master' of https://github.com/GreenGroup/RMG-Java
Debugging R_Add_Multibond by Naths script.
- 2 Ct ligands were wrongly named Cd
- redefined SJ (in older version Level 1 and Level 2 were identical)
Merge branch 'master' of https://github.com/GreenGroup/RMG-Java
Additional hard coded constrains for Intra_Diels_alder2
Before reacting the code will see how many bicyclic nodes are made in the reactants and forbid the reaction if this value is larger than 2.
Changing rank values for Intra_R_Add_Endocyclic and Intra_R_Add_Exocyclic
family.

Previously everything was set to rank 0, for now I am changing them to
rank 5. I am unclear about interpretation of rank 0, my memory says it
disallows averaging down the tree while exact hits will use the rule value and
other will fall up.

RMG-Py comment by @jwallen states that rank 0 would mean we have so little
trust in it that we disregard the rule and instead fill it up by averaging
Merge branch 'master' of github.com:agvandeputte/RMG-Java
Added a new resonance function that should avoid dubble counting of aromatics (e.g. napthalene) and other rings that are characterized by the
following bond structure single-double-single-double... with number of single bonds = number of double bonds
Few modifications:
1. Instead of printi rates for forbidden reactions, just omit the reaction
2. Hard coded double counting of some intra H abstractions
Merge branch 'master' of https://github.com/GreenGroup/RMG-Java

Conflicts:
	source/RMG/jing/chemUtil/Graph.java
	source/RMG/jing/rxn/ReactionTemplate.java
 Flagged out part of the code that didnt do what it was supposed to do
 It tried to find 2 adjacent radical sites and make a double bond between them
 However, there is no cycling over the different resonance isomers
 and nodes are not updated after they have been changed making the new graph identical to the first graph
 A working code doing the same has been written long before in the generateResonanceIsomersFromRadicalCenter() subroutine
 but was flagged out due to wrong thermo for birads and unwanted reactions
Skip checking for the stablest resonance isomer once thermo for initial graph
is obtained from a thermo library.
Bug-fix: resonance isomers always include the original molecule when they exist and only then
This made the new conjugated ring code to add various similar species, as in this case only the resonance isomer
was added to the resonance isomer vector.

This also relates to previous commit: when resonance isomers existed, it was checking all of them for lowest thermo
unrelated to the fact if the original thermo was obtained from a library.
New change that might speed up the code a little bit in cases a lot of non-resonating radicals are present.

Old code always added the radical to a new resonance vector, while now this is only done when a first resonance isomer is found.
This can help bypassing some checks if(resonanceIsomers = null) speeding up the code and requiring less mem.