Updates to structure project, conversion to slf4j and minor bug fixes

Conversion of org.biojava.bio.structure package (main) in biojava3-structure project to slf4j.  Minor bug fixes including printing array contents instead of address, handling potential null pointer exception
We'll have to be careful about converting all System.out.println() to logger.info. I'd say here the intention of the printMatrix method can really be printing to std out. There's a further problem here: the output won't look like a matrix anymore as the new lines are not placed correctly anymore.