Changes to N5s atomtype.  Decrement bond to N3s.  Form bond to N5s.

We expect when N5s breaks a bond for resonance to appear, making
the atomtype N3s.
cantherm examples input files fixed

input files had old LennardJones tranport attribute which now crashes
cantherm. also fixed typo in cantherm/input.py
Reverting back the change made by Enoch

RMG-Py naming convention is
Attributes are camelBack
Class is CamelCaps
Rename to correct spelling of Bozzelli in ch3no2 example input file.
Remove memory profiling from generateReactions.py

Not really necessary for generateReactions script.
Add generateReactions example to the examples folder.
Return no product structures if reaction recipe action fails somewhere.

Prior to this, the molecule C1=CCC=C1 attempted to use the
1,4_Cyclic_birad_scission family in the reverse direction to
find a reaction.  There was no check that FORM_BOND should raise
an InvalidActionError if there is an existing bond between the
two atoms.  Therefore we were producing a nonsensical reaction
between [CH]1C[CH]CC1 = C1=CCC=C1

It turns out that many reactions prevent things like this from
happening by using forbidden groups (see Birad_recombination),
but it might be better to return no product structures when we
see the recipe application fail, since it is difficult to
come up with all forbidden groups beforehand.
Change entry.depository from dictionary to list

It seems like it was orginally meant to be a dictionary with some
functions written for it as such, but was changed to a list later. Changed
its usage in a function and the comments.
Update newStyleAdjMatcher for adjacency lists with molecule labels
update adjlist.py

- remove duplicated code segment
- activate lone pairs for groups
Add Ot atom type and update atom type actions

- Ot is the the atom type of an oxygen atom with one triple bond, as far
as we can see we will encounter it only in carbon monoxide (C#O)

- update atom type actions for Ot, Od, and Ct
Check for exceptions first in draw.py

- That way we might be checking the if conditions more often but we can
avoid problems with RDKit and carbon monoxide with triple bond (C#O)
because of changing valency of the oxygen atom.
Split the _known_smiles dictionary into two, for molecules and radicals

- This allows us to add a few more smiles and is a simple solution to
the SMILES confusions with carbon monoxide with triple bond and CO
biradicals
Recreate the folder for optional saving of edge species

- prevents from mixing with drawings of previous runs
- folder name: species_edge
Add correct path to optionally draw edge species
Rename the functional element N2d to N1d 

- to be consistent with the definition of N3 and N5
- N1d is a nitrogen atom that has one single bond and provides one
electron to bonding

e.g.: H2NN

1 H 0 0 {3,S}
2 H 0 0 {3,S}
3 N5d 0 0 {1,S} {2,S} {4,D}
4 N1d 0 2 {3,D}
Correct adjacency list of He in molecule.py
Update unit test moleculeTest for new adjacency list style
Remove atom type N2d
Extend unit test atomtypeTest for nitrogen atoms