fix master CMakeLists.txt to only add -Wno-attributes for newer compilers (not all older compilers have that option)

After an initial superposition, subsets get built using a distance
threshold. These subsets get superposed iteratively until a maximum
number of iterations is reached or the transformation matrix
between two superposition steps converges to the identity matrix.
This procedure usually converges to the largest group of superposable
atoms and is usefull for flexible domains. An example is the
superposition of 1AKE and 4AKE.

since the ost startup script lives in the same directory as the
top-level ost modules (python{version}/site-packages/ost), the
directory got automatically added to sys.path. That's bad for
several reasons I don't want to go in right now (see discussion
on the mailing list). Instead of passing the script as a script
name to execute, we now use execfile with the startup script.
This circumvents addition of the directory to the path and
makes Gabriel smile again.

the ownership semantics of sip/PyQt changed between versions. Object
which were previously staying in memory are now garbage collected.
Event handlers associated with these objects were then removed.
The fix presented in this patch is rather ugly. We store references to
the objects inside the _Init* functions. Ideally, these types of hacks
would not be required, but I could not find another way to approach
the problem.

- replaced boundary check in operator[] with assert
- replaced int data array with int variables (x,y,z)
- moved some methods to header to allow inlining
- used boost operator for operator implementations
- exported x,y,z members to python

instead of per-residue base in mol::alg::structure_analysis::WrapEntityInPeriodicCell

Documentation for the new versions of the FliterClashes and CheckStereoChemistry functions. Changed some method name in the Info classes

violation data

The previous function was hard to understand. Every specified column gets
plotted at one position in the plot. If there are several rows, several
row indices are passed as argument respectively, the values of the
resulting column get plotted in parallel at this position. Note, that
the number off rows is limited to 7.

e.g. direct comparison of a value from a column of type bool with
a value from a column with type string raises an error. NaN and None
handling has also been improved.

conversion

Moved printed messages out of the FilterClashes and CheckStereoChemistry
functions. Breaks those two functions

for large radii, the number of buckets that have to be looked at
when doing a HasWithin starts to dominate query performance. To
work around these cases we now do the following two things:

  -  store the bounding box for the buckets and intersect the cube
     of buckets which have to be traversed with the bounding box.
  -  when the number of buckets which have to be traversed gets
     larger than the total number of buckets in the organizer,
     loop over all buckets instead of looping over the cube.