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
Don't saturate groups read from adjacency lists

- groups do not have to be complete and can contain only part of the
neighboring, bonded atoms
Update unit test transportDataTest for new style adjacency list format
Add check for file system to locate symmetry executable
remove saturateH for fromAdjacencyList in Group

- label saturateH not defined in Group implementation of
fromAdjacencyList
Add atom types for He, Ne, Cl, and Ar

- this prevents receiving noce instead of atomType
- lateron it will could useful to distinguish ions
Use RDKit to generate geometries foe tri-valent nitrogen

- relax limitation on all nitrogen to penta-valent only, that way we can
make use of RDKit's advantages for cyclic compunds with tri-valent
nitrogen
- openBabel will now only be use for penta-valent nitrogen species
- improving the handling of the carbon monoxide exception introduced in
c7ca1ba0c02f29eb65d32068dc4d02dc56febd89 because it could lead in some
cases to wrong drawings by confusing the order of the atom labels during
rendering
Change TransportData __repr__ function and fix pdep/network#_#.py files.

@enochd pointed out in a comment to commit 
8a6d32441007649807e3137ba7da0e6c2dab9f6d
that RMG-py was creating cantherm/measure input files
(eg. pdep/network23_1.py) that were malformed.

This should fix it, I hope.