This function assumes the user knows what he's doing, this is also clearly
stated in the documentation:
"RMSD of atom positions (taken blindly in the order in
which the atoms appear) in the two given views."
This check at least avoids a segfault when the number of atoms does not
match. The result would be completely wrong anyway...

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.

Changed std::vec<geom::Vec3> into geom::Vec3List.

wrong branch, big sorry

This reverts commit e77d08a6.

build superposable subsets. At least three atoms are required.
This scenario gets now checked and an error is thrown.

to 1. Exit condition of for loop is now properly set.

This solves some problems that have been discussed in the devel
mailing list. btw: the hazel nuts were awesome!

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.

they added very little benefits and were in general very slow.
The call sites of AtomsBegin have been replaced by a triple
for loop, ResiduesBegin by a double for loop. While that adds
some typing overhead, it gives a speed up compared to the old
version. It also happens to fix a problem noticed by Niklaus.

the superposition code has also been refactored to reduce
redundancy and make it easier to read.

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

Request(ICS|XCS)Editor is still available in python but marked as deprecated. Also add unit tests to check behaviour of EntityHandle.Copy() and
CreateEntityFromView()

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2123 5a81b35b-ba03-0410-adc8-b2c5c5119f08

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1933 5a81b35b-ba03-0410-adc8-b2c5c5119f08

-replaced all reinterpret_casts with manual copying over index by index

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1871 5a81b35b-ba03-0410-adc8-b2c5c5119f08

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1742 5a81b35b-ba03-0410-adc8-b2c5c5119f08