Implement remaining SelectionOption flags.

- If onlyAtoms() is specified, check the condition after the selections
  have been compiled.
- If onlyAtoms() is specified for all selection options, remove the
  -seltype command-line option, as it has no use.
- Removed unimplemented dynamicOnlyWhole() as the way it worked in 4.5
  is not really compatible with the current handling of selections.
  It was any way only affecting a default value, but not enforcing
  anything.

Change-Id: I0cd4ff6d425cc017bead090be12867b4f41e7783