add a props dict as an attribute to Species

this allows the user to store user-defined, and arbitrary
key-value pairs of his/her choice.

Conflicts:[RESOLVED]

	rmgpy/species.py
add props attribute in constructor as parameter and default to empty dict

this is more flexible than setting it in the constructor to an empty dict.
This way, one can also transfer a properties dict from elsewhere.

Conflicts:[resolved]

	rmgpy/species.py
add props parameter when calling constructor of species.Species

Conflicts:[RESOLVED]

	rmgpy/rmg/model.py
add cythonized props dict in species.pxd
add documentation in rmgpy/species.Species on props attribute
added test in speciesTest for props dictionary attribute of Species.

testing if props attribute is a dictionary, and if dictionary entries
are properly stored.
Merge pull request #278 from nickvandewiele/props_species_refactor

Add props dictionary attribute to the Species class for storing various user-defined properties.
test checking multiplicity parsing of group
Correct the new testFromAdjacencyList_multiplicity unit test.

Written by a java dev :-)
Fix bug in parsing group adjacency list multiplicities.

Also added comments for the somewhat complicated reg-ex.
Thanks for finding the bug, Nick.
Added another unit test for parsing multiplicity lists in group adjacency lists.
Merge pull request #281 from rwest/multiplicity-regex-bug

Multiplicity regex bug
Exclude temporarily tetra-valent nitrogen from QM in Gaussian

Previously done for MOPAC in b67b2c232f6939f0f64e41ebc3911c30469c1836

Done because RDKit cannot recognize tetra-valent nitrogen
Consistent logging and source comments

For mopac and gaussian. Depending on the QM package used,
we were logging different lines and storing different source
formats. Not a good thing long term. This should help.

The sourcing will become important as we also load thermo files
created from previous calculations. If the job requests PM6 and the
previous file is a PM3 calculation, we currently use the old file.
Later commits will address this problem.
Modify qm/main to store files in method subfolders

Also includes some default values for other options.
The tests have been updated to match the modified
QMCalculator settings.