/System/Library/Frameworks in addition to /Library/Frameworks

starting and ending gaps penalty. good when 1 sequence is much
smaller then the other or you expect the 2 sequences just to overlap
a bit.

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.

only one EntityView, and computing the lower triangular part of the
pairwise distance matrix in that case.

Added function to extract the matrix of pairwise distances
    between the atoms in two different views

between the atoms in two different views

in view of adding PBC for non-orthogonal cells

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

fixed lddt compilation on Windows
removed DLLEXPORTS from pdbsize.cc

A circular dependency caused the gfx.Objects to be retained
forever. Breaking the circular dependency solves the problem.
As part of the bug-finding process, rewrite large parts of
the Scene Window to make it both simpler and saner

temporaly the program is in /import/bc2/home/schwede/bertoni/bin/ialign/bin/ialign.pl

While it has been possible to read/write PDb directly
from/to arbitrary streams, the stream interface is not
exposed to Python yet.

Allows to map the asa and esa values calculated by msms onto
the atoms with generic properties using the CalculateSurface
function.