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Re: [h5md-user] Molecular viewer for H5MD/Mosaic trajectories
From: |
Pierre de Buyl |
Subject: |
Re: [h5md-user] Molecular viewer for H5MD/Mosaic trajectories |
Date: |
Tue, 19 Nov 2013 10:49:30 +0100 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
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