Re: [h5md-user] Molecular viewer for H5MD/Mosaic trajectories

[Pierre de Buyl]

Hi Konrad,

On Tue, Nov 19, 2013 at 10:01:04AM +0100, Konrad Hinsen wrote:
> Pierre de Buyl writes:
>  > No luck for me:
>  > __main__.MolecularViewerError: The file u'/home/pierre/Downloads/2ONX.xml' 
> could
>  > not be loaded.
> 
> Strange. I just installed everything on a fresh virtual machine and it
> works as expected.
> 
> Could you please try to open the file from the command line:
> 
>    python MolecularViewer.py /home/pierre/Downloads/2ONX.xml
> 
> You should get a more useful error message then. GUI error messages
> still need a lot of work.

Here's the log for the three files available at
https://bitbucket.org/molsim/mosaic/downloads

address@hidden:~/tmp-soft/mosaic-viewer$ python MolecularViewer.py 
/home/pierre/Downloads/SPCE_water_500.h5 
Traceback (most recent call last):
  File "MolecularViewer.py", line 987, in <module>
    configurations = load_HDF5(filename)
  File "MolecularViewer.py", line 956, in load_HDF5
    for path, data_item in mosaic.hdf5.HDF5Store(filename).recursive_iterator():

    yield name, self.retrieve(node)
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/hdf5.py", line 181, in 
retrieve
    data = handler(self, node)
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/hdf5.py", line 390, in 
_retrieve_universe
    py_str(node['convention'][...]))
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/array_model.py", line 
179, in from_arrays
    assert atom_array.dtype == atom_array_dtype
AssertionError
address@hidden:~/tmp-soft/mosaic-viewer$ python MolecularViewer.py 
/home/pierre/Downloads/2ONX.xml 
Traceback (most recent call last):
  File "MolecularViewer.py", line 985, in <module>
    configurations = load_XML(filename)
  File "MolecularViewer.py", line 937, in load_XML
    for xml_id, data_item in mosaic.xml_io.XMLReader(xml_file):
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/xml_io.py", line 384, in 
__iter__
    data = handler(self, el)
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/xml_io.py", line 446, in 
_read_configuration
    pos = self._property((3,), dtype, el_pos.text)
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/xml_io.py", line 510, in 
_property
    data = IN.array([dtype(s) for s in text.split()])
ValueError: invalid literal for float(): 0.04300000146|0.03950000182
address@hidden:~/tmp-soft/mosaic-viewer$ python MolecularViewer.py 
/home/pierre/Downloads/1AZS.h5 
Traceback (most recent call last):
  File "MolecularViewer.py", line 987, in <module>
    configurations = load_HDF5(filename)
  File "MolecularViewer.py", line 956, in load_HDF5
    for path, data_item in mosaic.hdf5.HDF5Store(filename).recursive_iterator():
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/hdf5.py", line 210, in 
recursive_iterator
    yield name, self.retrieve(node)
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/hdf5.py", line 181, in 
retrieve
    data = handler(self, node)
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/hdf5.py", line 390, in 
_retrieve_universe
    py_str(node['convention'][...]))
  File "/opt/mosaic/lib/python2.7/site-packages/mosaic/array_model.py", line 
179, in from_arrays
    assert atom_array.dtype == atom_array_dtype
AssertionError

Maybe I can post those error messages instead to your project's issue tracker?

Cheers,

Pierre