Fix bytes vs unicode error when missing DTD
Update Seq.py

Fix the docstring of Seq().count() and MutableSeq().count().
More updated NCBI DTD files.

Adding http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/bookdoc_140101.dtd
and http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_140101.dtd
and http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_140101.dtd

Reported by email.
Remove unused import
Rename 'homology' in SearchIO aln_annotation attributes to 'similarity'
Note down 'homology' -> 'similarity' rename in NEWS
Remove last remnants of Seq.tostring and deprecate it
Remove redundant str(...) in print statements
Make these full Biopython deprecation warnings, not just pending.

Also remove duplicate imports
PEP8 tweaks, print functions
Remove deprecated Bio.HotRand module
Remove deprecated Bio.Search module
Remove deprecated class InterlacedSequenceIterator from SeqIO
Now testing under Python 3.4

We'll have this on the buildbot server shortly, while
Python 3.4 support on Travis-CI.org is expected soon.
Remove deprecated legacy BLAST functions blastall, blastpgp, rpsblast
Remove deprecated legacy BLAST wrappers from Bio.BLAST.Applications
Remove deprecated Bio.UniGene.UniGene module (HTML parser)
Deprecate function quick_FASTA_reader
Use assertEqual in unit test, not assert statement.

Also remove unused variable.

This test is failing for me with Python 3.4 on Windows XP (32 bit),
likely due to some global warning filter issue and/or new core
warning.
Bugfix for DNA/RNA masses; enhanced molecular_weight function

In Bio.Data.IUPACData:
- corrected masses for monophosphate nucleotides in unambiguous_dna_weights and unambiguous_rna_weights (most values where too high by a mass of 16 Da)
- added two dictionaries with monoisotopic masses for monophosphate nucleotides (monoisotopic_unambiguous_dna_weights and monoisotopic_unambiguous_rna_weights)
- added average and monisotopic masses for selenocysteine and pyrrolysine in protein_weights and monoisotopic_protein_weights

Rewrote method molecular_weight to:
- correct the calculation (sum masses of sequence elements and substract 18 Da for each formed bond)
- allow mass calculation for RNA and protein sequences
- allow mass calculation for double stranded nucleic acids
- use  more precise masses for water

Updated test_ProtParam.py with new results due to changed masses in IUPACData

Also now using Python 3 print style for docstrings