Add Molecule::perceiveBondsSimple() method

This adds a new method to the Molecule class which perceives
bonds in a molecule based on the 3D coordinates.

Change-Id: I122f749ac6e6b5c0a0651ae62cbb6ae624db7b61
Merge topic 'perceive-bonds' into master

99a89b4b Add Molecule::perceiveBondsSimple() method