changes:

-GetPrincipalAxes in Vec3List
 Results with Eigen3 have been verified with 10 randomly picked pdb structures.
 Differences only occur with changing signs of the vectors.

-CalcPrincipalAxis in BoundingBox
 No difference in algorithm, the SelfAdjointEigenSolver no lives in
 Eigenvalues. Does in principal the same thing as the function above,
 just using different functionality.

-SVD superposer
 Unit tests still run through with the changes introduced for Eigen3
 and also manual testing seems to work well.

-CartoonRenderer
 Principal axes calculation for rendering helices as cylinders had to be
 adapted. Rendering looks exactly the same...

-SuperposeFrames
 Not yet tested...

ToDo:
numeric.h and levenberg_marquardt.h in the img/alg module have to be
ported. This will be done in the next few days.

wrong branch, big sorry

This reverts commit e77d08a6.

removed ost::PairToTupleConverter from export_vec3.cc as it creates cyclical dependency in the build system

of the fitted cylinder. The input was also changed from taking both a direction
and center as initial guess to just the direction. The center is guessed from
the geometrical center of the atoms and fitted during the optimization
procedure.

in view of adding PBC for non-orthogonal cells

The function to calculate the unit cell vectors was added to geom

and in Rotation3.SetRotationMatrix(Mat3)

Vec3 from two Vec3List that are closest.

On some old versions of Boost.Python, std::out_of_range
is not properly converted to IndexError. Instead, a
RuntimeError is raised. For these versions, we overwrite
the IndexError type with the type of the exception
raised by geom.Vec2()[3].

fixed BOOST_TEST_DYNLINK define for some unit tests

against floating point errors

Some compilers (including gcc 4.2) seem to have difficulties to inline
functions with exceptions, even though it would be possible to know at
compile-time that the exceptions never get thrown.

The boundary checked versions for item access for Vec/Mat classes are
available as the VecX/MatX::At methods. The Python export has been
adapted to use the At methods, so guarantee we never crash from Python.

the internal representation of a transformation for EntityImpl was changed from Mat4 to Transform
in preparation for adding transformations to entity views; this impacts quite a few higher-level routines
that used the transformation matrix, which now can use the more elegant Transform::Apply method instead;

GetTransformationMatrix and IsTransformationIdentity methods in the EntityHandle interface are marked
as deprecated; use GetTransform and HasTransform instead. In addition, there is a ClearTransform method
which ensures that the internal has_transform flag gets set to false

geom::Transform was extended to offer ApplyInverse, and matrix inversion exceptions are handled internally

constructing a Vec3 from a Vec4 no longer throws a DivideByZero error when w is close to zero, instead it
is silently assumed that this is not a true homogeneous coordinate conversion

as an additional comment (and note to self), atom->GetPos always returns transformed positions; however,
GetAltPos returns original positions, and original positions are also stored in the AtomGroup on the
Impl level. Both the mol unit test as well as the PDB writer expect this behavior; the PDB writer applies
the transform after calling GetAltPos. Commented code is in place now to change this behavior, i.e. have
GetAltPos return transformed positions, making it consistent with GetPos, should this be desired.

fixed Transform SetMatrix behaviour
fixed Transform unit tests
fixed mol.Transform proxy
added Transform.Apply(Transform)

The Transform class was moved from the mol module to the geom module. A typedef
was put into the mol namespace in C++, and a similar alias was put into the
mol python module, with an added deprecation warning.

fixed some DLLEXPORTs for exceptions
based ost:Error on std::runtime_error (avoids string member in ost::Error)

added cmake option to set hidden visibility for gcc compiles; fixed several missing visibility declarations

Closes again BZDNG-344