convert some AtomPlacer metohds to static methods and fixup their invocations

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
remove debug log statements in AtomPlacer.java

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
add new MolecularFormulaManipulator.getElementCount static methods that take (formula, IIsotope) and (formula, String)
Including JavaDoc for new methods. Would also be better to use Elements from a symbol, currently the method is case sensitive.