import_array() must be called when the numpy C-API is called.
This is a macro that in our case defined a return value that makes
the compiler complain. The added #define statement enforces no return value

wrong branch, big sorry

This reverts commit e77d08a6.

Fixes BZDNG-416

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.

behaviour in GaussianSmooth function in table class

to the editor. still messy and no unit tests...

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

added option to rotate all atoms of a torsion or just specified one; removed legacy Set/RotateAngle from TorsionHandle which is in ICSEditor

Fixed bug BZDNG-212 (RenameResidue(ResidueHandle, new_name) is missing in EditorBase), added documentation for Rename[Atom|Chain|Residue] functions as well as unit tests. Made some tests compatible with Python 2.4.

various related cleanups and optimizations:
 - removed superfluous sort in load_dcd
 - added explicit *TransformedPos() methods to complement *Pos() methods
   (XCSEditor, AtomHandle, AtomImpl)
 - changed getter/setter logic for AtomImpl Name, TransformedPos
   and OriginalPos to direct access, deprecated GetName and removed
   Get*Pos and Set*Pos

This finishes changes started in the mem-optimize branch to
remove the AtomProp class from the public interface.

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()

added QueryFlags handling to mol::QueryViewWrapper
fixed empty pov output (caused by multiple renderer problem in gfx::Entity impl)
removed GLEW_VERSION_2_0 tokens
various tiny gfx tweaks
added stereo toggling key to gui ('=')
added residue reordering to mol::EntityEditor

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2106 5a81b35b-ba03-0410-adc8-b2c5c5119f08

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