Fix the drawing of some molecules with the incorrect aspect ratio.

Also update the comments in the rdkit drawing code.
Closes #139
Signed-off-by: Richard West <r.west@neu.edu>
Tweak the logic node parsing.

I think this is correct. It may have been OK before, but I made this change on
another branch. One change or the other is needed to make it cope with node names
containing "OR".
Match truncated InChI from MOPAC logfiles due to MOPAC2012 bug.

MOPAC2012 deletes 81st character from InChI string in input file, leading
to some mismatches.  Use only up to the first 80 characters to match to
the InChI (at least until they fix this bug.)

See https://github.com/GreenGroup/RMG-Py/issues/137 for more details.
Added parsing of Molepro files to cantherm

Currently can only parse energy from CCSD(T)-f12 moleprol
jobs. Syntax for use is based off the of GaussianLog class
and can be seen in the ethene example.
Hopefully remove redundant spin states when generating reaction templates.

When you removed two radical electrons from an atom type in a functional group
that was {2S,2T} it would create an atom type that was {0,0}.
Hopefully this commit will make it only 0. 

Also, I think it removes a bug whereby previously if you removed 1 radical
electron from something that was 2S, it would become something with a 
single free radical, but a multiplicity of zero! (instead of two).

This should remove the {0,0} part of the RMG-database exporting issue
GreenGroup/RMG-database#18
https://github.com/GreenGroup/RMG-database/issues/18
Slight speed tweaks for applying actions to atoms.

To do with local scoping - avoid looking up action[0] and converting
it to an upper case string every time you want to compare it 
with something,  and avoid checking to see if self has 
an attribute called radicalElectrons every time you want 
to compare it with an integer.
Tweaks for writing old RMG-Java style database.

1) Replace '{2S,2T}' with '2' when saving group adjacency lists in a dictionary,

2) Save temperature ranges on every entry in a family's rate library.
   (If the rate was entered without a range - tss tss - then we put 1-9999 K.)

3) make a puneHeteroatoms() method on thermo databases so you can delete species
   from the thermo libraries that Java would not like (things containing Nitrogen)

Deals in part with issue GreenGroup/RMG-database#18
https://github.com/GreenGroup/RMG-database/issues/18
Revamp the way ScalarQuantities store and process uncertainties.

In commit 851b2ba42b60488e38267a0b8f231e6ee34cceff it was changed so that
Quantitiy.value and Quantity.uncertainty were now in customizable units,
and Quantitiy.value_si was the SI value. However, there was no uncertainty_si.

Now the uncertainty is also stored in SI units, like the value, and converted
to output units on demand. This change should be transparent, i.e. not change 
anything that was correct before, but it does create a new Quantity.uncertainty_si 
property, which is what we should have been using instead of .uncertainty in 
various places. i.e. we now need to go around using this to fix other bugs,
such as @GreenGroup/RMG-database#21 https://github.com/GreenGroup/RMG-database/issues/21

Also to do: do the same thing for the ArrayQuantity class.
Use the new uncertainty_si property to fix units bug in saving old database rules.

This should close @GreenGroup/RMG-database#21 https://github.com/GreenGroup/RMG-database/issues/21
But there are probably other places the same bug exists (i.e. foo.uncertainty should be replaced
with foo.uncertainty_si)

Also, why don't any of the Quantity unit tests check uncertainties at all? Hmm...
Tweaks to layout of rate rules when exporting the RMG-Java style database.
Don't save unnecessary items in the dictionary when exporting old RMG-Java database.

The database entries list in RMG-Py contains the reverse template, and potentially 
other unused nodes. These can cause problems when trying to read the dictionary in to RMG-Java.
See @GreenGroup/RMG-database#22. 

This commit makes it so anything that is not referred to in the tree, is commented out
when you save the database. The difficulty is that some nodes are not explicitly mentioned
in the tree, but are needed to fully define some logic node that IS in the tree.
It ends up a little complicated recursing through these cases, but it seems to work.

Closes @GreenGroup/RMG-database#22.
Saving old database creates kinetics_groups/families.txt file.

By default all families are listed and turned on.
This should make the 'as saved' database more nearly ready for
running straight in RMG-Java
Updated atom energies for CCSD(T)-F12 jobs

Previous bond energies were calculated using
the F12b method,updated them to now use the F12a energies.

These energies have been provided by Caleb Class
and Beat Buesser.
Add corrections for various model chem in cantherm

All these values are still a work-in-prgress obtained from Beat.
However, the recent updates for cantherm made by Shamel and I are a bit
incomplete without these.

Atomic energy corrections are provided for:
CCSD(T)-F12/cc-pVDZ-F12_H-TZ
CCSD(T)-F12/cc-pVDZ-F12
CCSD(T)-F12/cc-pCVDZ-F12
CCSD(T)-F12/aug-cc-pVDZ
B-CCSD(T)-F12/cc-pVDZ-F12
B-CCSD(T)-F12/cc-pCVDZ-F12
B-CCSD(T)-F12/aug-cc-pVDZ
DFT_ks_b3lyp
MP2_rmp2_pVDZ
MP2_rmp2_pVTZ
MP2_rmp2_pVQZ
CCSD_DZ
CCSD_TZ
CCSD_QZ
CCSD_core_DZ

Bond energy corrections were added for CCSD(T)-F12/cc-pVDZ-F12

Additionally, there were bug fixes and additional unit tests for the
Molepro parser.
Tidy up thermo comments in chemkin files.

-Removed unecessary declaration line '! Thermo Comments:'
-Added 'Thermo library:' label to thermo originating from thermo libraries.
-Removed the NASA fitting to Wilhoit comments because they clutter up the comments
Tidy up kinetics comments in chemkin files.

-Removed unecessary declation of '! Kinetics comments:'
-Fixed labeling of exact rate rule matches (was falsely labeling some kinetics
as estimates when they were actually exact matches)
-Removed extra line with reaction string using original names.  The chemkin
reaction string should be sufficient.
-Removed line commenting on flux pairs (generates clutter and not super useful)

Concern:
- When merging RMG models together, a lot of comments will be duplicated.
This should be fixed later.
Added Chlorine to allowed atoms for Cantherm.
Fixed transcription error for Sulfur experimental enthalpy of formation at 0K.

Now matches http://www.gaussian.com/g_whitepap/thermo.htm
Cantherm: added energy corrections for Chlorine for CBS-QB3 methods.
Added BAC for H-Cl bond for CBS-QB3 method.