Revert "Use SeqUtils.seq1() instead of SCOP.to_one_letter_code()."

This reverts commit ca7762e8247dbcd6b3cbc6d0a7082eaf36dceb46.

It was causing test failure in some of the PDB code due to not
handling all the 'odd' three letter codes for modified amino
acids. I was too hasty in checking this in... opps.