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