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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