Default PDB chain ID back to blank. Add option to write anisotropic displacement factors to PDB file.

[drroe]

The change in default PDB chain ID (#747) resulted in several things in AmberTools breaking, most notably mmpbsa.py. This PR restores the original behavior of writing no PDB chain ID if none present in the input topology. However, if pdbres or pdbv3 are specified a default chain ID of Z will be written if none present in topology. This seems like a good middle ground.

This PR also adds a new option to PDB output, adpdata:

adpdata <set>  : Use data in <set> for anisotropic B-factors.

This can be used to write an actual PDB with the anisotropic B factors (as well as isotropic B factors via the already implemented bfacdata command), e.g.

trajin ../DPDP.nc
rms first mass
atomicfluct Heavy calcadp :2-21&!@/H
average crdset MyAvg
run
crdout MyAvg heavy.adp.pdb adpdata Heavy[ADP] bfacdata Heavy

ATOM      1 HH31 ACE     1       6.786   3.433  -4.315  1.00  0.00           H  
ATOM      2  CH3 ACE     1       6.648   3.119  -4.327  1.00  0.00           C  
ATOM      3 HH32 ACE     1       6.731   3.425  -4.668  1.00  0.00           H  
ATOM      4 HH33 ACE     1       6.468   3.344  -4.332  1.00  0.00           H  
ATOM      5  C   ACE     1       6.617   1.942  -3.870  1.00  0.00           C  
ATOM      6  O   ACE     1       6.807   1.309  -4.257  1.00  0.00           O  
ATOM      7  N   VAL     2       6.371   1.648  -3.066  1.00 20.77           N  
ANISOU    7  N   VAL     2     5328   1042   1520    244   -684    -44       N  
ATOM      8  H   VAL     2       6.208   2.226  -2.809  1.00  0.00           H  
ATOM      9  CA  VAL     2       6.316   0.541  -2.523  1.00 15.75           C  

Documentation has been updated (including an example of doing the above), and some tests have been added.

Also, the printing of formal charges in PDB files is theoretically possible now, but not yet done. The charge of 0 has been removed from ADP output.

[drroe]

So the issue seems to be that homebrew is failing:

/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- active_support/core_ext/object/blank (LoadError)
	from /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
	from /usr/local/Homebrew/Library/Homebrew/global.rb:12:in `<top (required)>'
	from /usr/local/Homebrew/Library/Homebrew/brew.rb:23:in `require_relative'
	from /usr/local/Homebrew/Library/Homebrew/brew.rb:23:in `<main>'

I'm going to try adding a brew update to see if that fixes things.

[drroe]

brew update seems to have worked. Since the previous appveyor builds passed, I'm going to merge.

[hainm]

appveyor

again? :P