Add occupied fraction and PDB output to g_ana select.

Add occupied fraction and PDB output to g_ana select.

- Add output option -of to write out the occupied fraction.
- Add output option -ofpdb to write the same information into a PDB
  file. Option -pdbatoms can be used to control which atoms to write
  out.
- Reorganize error checking for options that only work with a single
  selection or only make sense with dynamic selections.

Supporting changes:
- Add PDB file type to FileNameOption.
- Make write_trxframe_indexed() take the index as a const array.
- Add ConstArrayRef::data() following std::vector::data() from C++11.

The PDB output can also be used to more easily check what is selected by
a selection.

Change-Id: Icabab4b2c88cc21e4d5ebb672a1471c254acb05e