[vtkusers] vtkMolecule and vtkAtom

Marcus D. Hanwell marcus.hanwell at kitware.com
Thu Sep 3 13:18:18 EDT 2015

On Thu, Sep 3, 2015 at 12:39 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> On Thu, Sep 3, 2015 at 9:36 AM, Marcus D. Hanwell
> <marcus.hanwell at kitware.com> wrote:
>> On Thu, Sep 3, 2015 at 11:22 AM, Favre  Jean <jfavre at cscs.ch> wrote:
>> >
>> > I have a C++ code building a molecule, Appending atoms, etc. No problem
>> > there.
>> >
>> > Using Python, I cannot do the same. Why aren't the AppendAtom() methods
>> > not
>> > available to a vtkMolecule object? How should one build a molecule with
>> > vtkpython?
>> I don't think they are wrapped due to limitations in the Python
>> wrapping, and the pattern we wanted to use for scalable storage of
>> molecular data. I think we could get them wrapped, or add some simpler
>> API for the Python/wrapped languages.
>> I don't think this is something we tested, or looked at very deeply.
>> Much of the code was developed in quite a short period as part of a
>> Google Summer of Code project, it would be nice to extend it to better
>> support Python.
> Marcus, don't be so pessimistic about the Python wrappers.  Jean, just tell
> cmake to wrap vtkAtom, and the AppendAtom method should work just fine.
> Change the following lines in Common/DataModel/CMakeLists.txt:

I did mean to say things may well have improved since this was
contributed, but we haven't revisited it in quite a while. I know the
vtkTuple/vtkVector style classes added many similar features.
>   set_source_files_properties(
>     ...
>     vtkAtom.h
>     )
> The problem is that WRAP_EXCLUDE includes all of the classes that Java
> and Tcl cannot wrap, and as a result, many classes are excluded from the
> Python wrapping even though Python is perfectly capable of using them.
> I should do a sweep through the cmake files to make the wrapping more
> inclusive.

That is great, the growing disparity between wrapped languages may be
an issue, but I am glad to hear things have improved so much in the
Python wrappers.

Thanks for the pointers David - can we convert to Doxygen markup in
our headers and use typed enums yet ;-)



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