Additional API to support color in cylinders

It is often useful to be able to render cylinders with two colors, also
took the opportunity to  update the documentation.

Change-Id: I484be02df2e8bec0f95e42c4c4b8fa6f5303de91
Updated ball and stick to use colored cylinders

We need to add configuration dialogs soon so that options can be added.
For now this defaults to imparting the color of the atom on each on of
the bond to the cylinder.

Change-Id: I60469e398144da52cd6bbfad307e395f4e4b35b7
Merge topic 'colorful-cylinders' into master

4fecd4b5 Updated ball and stick to use colored cylinders
e37bcfbb Additional API to support color in cylinders