Highlighted atoms in material visualizer

Merged Jose Pizarro requested to merge 1373-highlighted-atoms-in-material-visualizer into develop

@himanel1 would you mind reviewing these changes?

I am not sure what is the best procedure about [showBonds, setShowBonds]. I added a line to check whether the method is 'parser/hightlight', but there might be a better option.

Closes #1373 (closed)

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