Coordinates stored on an Atom now as a numpy array.

Originally a list, however a numpy array is more flexible.
The parsed output from cclib produces these in a numpy
array, and as such the fromXYZ method also uses a numpy
array.
Make an RMG molecule from coordinates.

Takes a list of atomic numbers and the coordinates that
corresponds to each atom and guesses the connectivity
using covalent bond radii.
Method to convert all bonds to single bonds.

For molecule matching in QMTP, we do not have a reliable
way to perceive bond orders. However, we can work around
this by converting all bonds to single bonds as we are only
interested in connectivities to check the molecule.
Check molecular connectivities for QMTP after MOPAC calcs.

This has to also be done for Gaussian. Also this could be
reworked to prevent double-parsing of the log file. As
currently done, the  output is parsed to check the bonding,
then if the job was successful it is parsed again to do the
thermo calculations.
Parse the mopac output file using the parse method

Was already implemented, so just using an existing method
instead of redoing it.
Check the optimized geometry connectivity in gaussian

Previously done with mopac, now including the method
for gaussian.
Merge pull request #190 from pierrelb/checkQMGeom

Check QMTP optimized molecular geometries are the desired species.

It is possible that the geometry optimization "reacted" the species to a different isomer.
This checks that the final geometry is isomorphic with the desired molecule.
Bonds are guessed based on distances between atoms. Bond orders (single, double, etc) are not checked,
only connectivity.