add test data for disulphides part of and #1 closes #6

this is a simple test molecule with a disulphide bond and good geometry

ACAGGACA
 |    |
 ------
 
the data includes a script to create the molecule using xplor
[build.sh], a pdb with good geometry, a psf, a driver script for
calculating shifts with camshift [calc.sh], and shifts calculated by
camshift 1.35.

to run the scripts you would have to change some paths
add test data for the disluphide bridge subpotential

add code to create a set of test disulphide chemical shifts for the
molecule acaggaca using camshift 1.35. This includes scripts that
will create a python test file.

this closes #7
add acagaca.py to the test directory
disulphide extractor has running serialize method and test ticket #13
add table skipping, extractors can now decide to skip certain tables


this cose #15
add a command line filter to select only one sub-potential for output

this closes #16
add code to make a data table for a disulphide chemical shift patch

this closes #12 #13
Merge branch 'master' into ss-hbond-cs
remove unintentional  dependence on python 2.7
disulphide patch was wrongly named base  when it should be cys
remove misplaced ;
correct file name
correct bad comment string referring to xtra not disu
rename disulpide patch file to be a base file
remove a spurious line produced while creating the file
add a disulphide table manager and shifts
update the table manager to be able to load disulphide tables

this closes #14
add enough to create & test the components for the disulphide potential

part of #11
add shift calculation for acaggaca and tests

part of #11
add complete test that shift calculations work for acaggaca

specific notes: 

a  number of corrections needed to be made, specifically

camshift includes HG1 atoms in its structures and adds them if they are
missing. The side-chain chemical shift calculations expect HG1 atoms to
be present an give erroneous results if they aren't. Disulphide shift
corrections are then added for cytines with SG1's that are closer than
9A.

in xcamshift the disulphide shift corrections is applied when a
disulphide patch is present and there is an -SG-SG- bond. This means
that the chemical shifts for the side chain give incorrect results as
the shifts due to the HG---HB are not present and so the disulphide
shift correction has to be corrected to allow for this.

It should also be noted that the lack of a HG1 atom also affects the non
boned term so (small) corrections have to be made between the shifts
calculated by xcamshift and those in the camshift test data set.

Finally hydrogen bonds are not currently implemented so these have to be
corrected for when using the test data. These corrections will be
removed when the hydrogen bond potential is complete.


this closes #11 and #1