Issue a warning when translating partial codons

See mailing list dicussion. Some felt this was useful functionality
and perhaps worthy of another optional argument to the translate
functions/methods, but they are already quite complicated. Using
a warning for now, and an exception later is to help migrate old
code which may be using this (e.g. ORF finding code).

This will requires explicitly padding/trimming the sequence to be
a multiple of three before translation.
Avoid new translation warning in unittests
Ensure ORF finder translates no partial codons.

This is to avoid the new warning message if translating
a partial codon.
Avoid warning from partial codon translation
Truncate test sequences to avoid partial codon translation warning
Avoid partial codons and new warning
Make the new warning fixed text for ease of filtering.

Old version include the sequence length, making a simple
filter based on the message and warning type impossible.
More progress on the Bio.PDB chapter
some further progress on the Bio.PDB documentation. Not donen yet, though
Finished merging the Bio.PDB chapter in the Tutorial with the Bio.PDB FAQ