Started work on 3D geometry estimation.

The Molecule class has a method generate3Dgeometry() which is
currently called every time Molecule.draw() is called.
Small changes to 3D geometry routines
Added note to Species class that rmg.model.Species inherits from it.

May have saved us some time.
Changed where generate3Dgeometry is called.
Trying to get generate3Dgeometry to work.

There's still confusion about rdkit atom indices and pointers.
Completed molecule generation in generate3Dgeometry

Checked the RMG bond order and added the corresponding rdkit
bond order. Now need to embed the molecule to generate the 
3D structure.
Generated 3D structure after model build.

Found the lowest energy of the optimized conformers.
Started work on the transition state 3D geometry.

Placed the function in reaction.py under the Reaction class. Called the function in model.py under generateKinetics. Gave inputs of reactants and products from the generateKinetics method.
Few edits and comments added to generate3dGeometry()

Removed some of the printing and logging done for code testing. Added comments as well.
More on generating the transition state geometry.

Finds the reaction axis only for molecules with a radical. It assumes the radical is the reaction center.
Alterations to where the transition state is called and built.

Relevant information to allow for transition state to be build for multiple types of reactions.
Merge branch 'master' into 3DCoor

Conflicts resolved:
	rmgpy/molecule.py
Changed how 3d geometries are stored in molecule.py

Added atom coordinates to atoms and rdkit mol objects to molecules.
Find the reaction axis for H_Abstraction reactions.

The reaction axis is found for each molecule and stored. Changed the conditions in makeHydrogensImplicit as the hydrogen atoms lose their coordinates.
Set up the geometry data in the array format from cantherm.geometry

Pretty useful, it sets up the data in numpy arrays which can be manipulated easily and converted to matrices when necessary.
Completed geometric manipulation for reactants in H abstraction

Translated and rotated the reactants by the origin.
Added 'transformations.py' to deal with the matrix manipulations.
Corrected small error to fix geometry rotation.
Added functions to minimize code for geometry manipulation.

Geometry sorting, translation, and rotation.
Separated rdMol building from generate3dGeometry.

RDKit::Mol can be created without embedding.