Modified deep copy of low level objects.
Modified name of 'ABCParticlesContainer' and 'ParticlesContainer' to 'ABCParticleContainer and 'ParticleContainer' due to another developer request
Changed 'x', 'y', 'z' attributes of Particle for a 'coordinates' attribute.
Fixed equal operator for particles and bonds, and removed the others since we dont need them for now. Added a property in the base class 'ElementsCommon' for the id making it read-only for the moment.
Added more info in exceptions and errors.