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
Alright for this particular case it seems that the method is not used within biojava at all and that it duplicates the functionality of Matrix.toString(). This is the output of both for a 3x3 matrix of Math.PI:
```
Matrix.toString() :
 3.142 3.142 3.142
 3.142 3.142 3.142
 3.142 3.142 3.142

printMatrix() :
	3.141592653589793 	3.141592653589793 	3.141592653589793 
	3.141592653589793 	3.141592653589793 	3.141592653589793 
	3.141592653589793 	3.141592653589793 	3.141592653589793 
```
So I'd say the best solution is to keep the System.out.print and add a deprecate tag to the method above pointing to use instead Matrix.toString