When searching for polycyclic ring correction, select correction covering most atoms

Polycylic correction should use the largest possible ring correction found.
Overrides previous usage which was to find the deepest stack, which then gave
reproducibility errors when there are two group values of the same depth and
RMG chooses the first one it finds (random).
When searching for polycyclic ring correction, select correction covering most atoms

Polycylic correction should use the largest possible ring correction found.
Overrides previous usage which was to find the deepest stack, which then gave
reproducibility errors when there are two group values of the same depth and
RMG chooses the first one it finds (random).
New JP10 library JP10calculated = older JP10seedmech + JP10
Merge branch 'aaron' of https://github.com/agvandeputte/RMG-Java into jp10
Fix printing of thermo comments in output files.
Flagged out one of the older cycloaddition rate rules.
Added one rate coefficient to JP10BetaScission Library. JR5BS2
Updating rate rules for intra H migration from alkoxy radical

Rate rules derived from following reactions at BMK/cbsb7 level

CH2OH = CH3O,

CH2CH2CH2OH = CH2CH2CH2O
Updating rate rules for beta scission of alpha-Hydroxyethyl
Correcting rate rules which were incorrectly assigned when the tree was
restructured

Because we merged in Aaron's tree it caused butanol rate coefficients were
now assigned to butene system instead. SSM had used website to figure out
where rate rules should go and had defined it in a more general definition
instead I should have made a more specific node in the first place to avoid
confusion and errors like these.
Small corrections to database, adding some reactions from the JP10rxnlib to JP10calculated
Changes in database to account for O and O2 addition to double
Keto enol reaction family
Cyclic ether formation updated
B-scission in birads
H_Abstraction prepared for merging with AG Vandeputte database
Small changes to databases:
- recalculated one of the polyring corrections
- R_Addition_Multiple bond got rid of O=O
Intra_H_migration same approach as for other intramolecular reactions (thermodynamic consistency)
Reversed some changes made priorly:
- recognition of Cb bonds (problems with radical sites that did not loose their free electron when converted to Cb)
- QM on polycyclics: we recently added a feature to do QM on bicyclics (even when rings are not fused) but results indicate
that in particular for saturated rings, QM underestimate the enthalpy of formation with ~10 kcal/mol
Merge branch 'aaron' of github.com:agvandeputte/RMG-Java

Conflicts:
	databases/RMG_database/kinetics_groups/H_Abstraction/dictionary.txt
	databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt
	databases/RMG_database/kinetics_groups/H_Abstraction/tree.txt
	databases/RMG_database/kinetics_groups/Intra_R_Add_Endocyclic/rateLibrary.txt
	databases/RMG_database/kinetics_groups/R_Addition_MultipleBond/rateLibrary.txt
	databases/RMG_database/kinetics_groups/R_Addition_MultipleBond/tree.txt
	databases/RMG_database/kinetics_groups/families.txt
	databases/RMG_database/kinetics_groups/intra_H_migration/rateLibrary.txt
	databases/RMG_database/kinetics_libraries/JP10BetaScission/reactions.txt
	databases/RMG_database/kinetics_libraries/JP10calculated/species.txt
	databases/RMG_database/thermo_libraries/JP10/Dictionary.txt
	databases/RMG_database/thermo_libraries/JP10/Library.txt
	source/RMG/jing/chemUtil/Graph.java
Fixed some errors in database

One of the kinetics libraries had a strange format for the line breaks, using
only carriage returns (CR) and no line feeds (LF). This doesn't cause any
errors in Java, but it does when trying to import into python. I know there is
at least one more instance of this, but I'm leaving it in for further
testing I will do soon.

The other errors were adjacency list typos in some of the thermo groups,
that made the adjacency list self-inconsistent or otherwise invalid. RMG runs
even though these errors were present, which is worrisome.
HO2 elimination I defined R2OO_1H wrongly, should be R2OO_0H
Translated the Shamel groups to our current groups (got rid of InChI codes)
Also kicked a few of his rate coefficients out as parents and childs were assigned the same value (this must be checked)
Commented out a printline in graph.java
Cyclics in 1,4_Cyclic_birad_scission had wrong connectivity.
Merge branch 'master' of https://github.com/GreenGroup/RMG-Java