in the structure_analysis.py module.

This is used to make functions written at the CoordFrame level
accesible to analyze both entities and trajectories.

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.

this is getting embarassing

This function returns a geom::Vec3List containing the positions
of all the atoms in the entity.

For selections that do not explicitely state a QueryFlag option, a default
query flag is used instead of 0. This is an extension to current behavior
and should have zero impact on existing code.

The cause for this is actually a bug in Boost.Python that triggers when
arg("arg")... is used in the export and the number of arg("") arguments
doesn't match the number of argument of the function. When one then uses
a wrong kwarg, the program crashes. I'll submit a bug report to the
Boost.Python on this issue. I fear that there are many more cases in
the pymod export where we are using arg("") as we did for the query.

The cause for this is actually a bug in Boost.Python that triggers when
arg("arg")... is used in the export and the number of arg("") arguments
doesn't match the number of argument of the function. When one then uses
a wrong kwarg, the program crashes. I'll submit a bug report to the
Boost.Python on this issue. I fear that there are many more cases in
the pymod export where we are using arg("") as we did for the query.

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

Instead of only checking for the validity of the impl class, the view
classes now also check if the view data is valid. This improves debugging in
cases (when the trying to access, for example, an AtomView whose EntityView has
been deleted.

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()

GetGeometricStart()/GetGeometricEnd() has been deprecated and
will be removed sooner or later.

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