Updating rate rule for CO2 elimination from methyl esters

Rate calculations for CO2 + C3H8 = methyl propanoate
by Aaron using BMK/CBSB7 without hindered rotors
Fixing typo in 1,3 CO2 insertion

Ea = 118.0 kcal/mol
Clossing aromaticity perception for generation of reactions

To allow species like cyclohexadienyl radical to go to benzene
we need the aromatic species to be represented by single-double
bonds.

However to get the correct thermo and transport properties we still
should convert it back to Cb representation. Currently we will just make
a copy of the graph and percive aromaticity on it to get the correct
thermo and transport properties.

Done with help of Aaron Vandeputte
Updating aromatic perception

Updated Sandeep`s algoritm to sample an additional time through all rings when an aromatic ring is recognized
solves naphtalene problems (checked for benzene, naphtalene, anthracene, corene and C7H8)

Conflicts:

	source/RMG/jing/chem/ChemGraph.java
Debugging to account for phenyl radical

C in ring with 2 adjacent neighbours breaks aromaticity
this commit will not recognize benzyne as being aromatic, need to correct with ring corrections
Fixed bug in checking aromaticity of phenyl radical
More bug fixes for aromaticity perception

No of pi electrons have to be more than two
Earlier code would break for fused aromatic ring with radical

If one of the resonance isomers has fused rings with
one ring classified as aromatic and the second as
non aromatic then a shared C can have a B bond and
a D bond C {*,B} {*,B} {*,D}
causing the valency check to fail.

To avoid this we now have additional checks
which convert the other ring to be classified as non-aromatic.

This is for academic interest only :) .... since Aaron thinks
the most stable isomers will have both rings classified as
aromatic.
Aarons update for aromaticity perception in fused rings

Earlier bug fixes did not classify anthracene as aromatic anymore.
The algorithim is now modified such that the second aromaticity check
updates a new list which is sent for reclassification by Sandeep's
aromaticity algorithim. This ensures that when one ring classification
is changed from aromatic to non-aromatic we recheck all the other rings
to see if their classification has changed. This a recurssive and
converges when the aromatic List and updated aromatic List match.
Only then we convert the aromatic species to B bonds.

This change was almost entirely written by Aaron Vandeputte .. I have
just made it more streamlined and cleaned up the code a bit.
Commenting print lines used for debugging
Populatereactions module does not read in rate coefficients
from Reaction Libraries

It seems we forgot to set the LibraryReactionGenerator before
trying to call the model enlarger to fill in the networks
partially. Hopefully this should fix it.
tabase additions and changes to group notation

Merged in changes from AGVandeputte's branch from working on JP10.

-Many additional rules for R_Multiple_Bond_Addition and H_Abstraction

-New kinetic familes: 1,4_Cyclic_birad_scission,
1,4_Linear_birad_scission, and Intra_Diels_alder

-Allows using 'X' as the radical number on group definitions in
dictionary.txt of the kinetic families

-Allows use of bracket notation for unions of bond types in group
definitions. i.e It is now acceptable to write {2,{S,D}} in adjcency lists
instead of having to to make two separate groups.

-made check so that polycyclics with 2 rings or more always goes to QMTP
unless ring correction is found

-Automatic kukalization of aromatics from libraries and seed mechanisms