Hi,
So the next is to keep following where the system test fails:
======================================================================
ERROR: Load the 'Indol_test.xyz' XYZ file (using the internal
structural object XYZ reader).
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> structure.read_xyz(file='Indol_test.xyz',
dir='/data/relax/branches/xyz/test_suite/shared_data/structures',
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None)
Traceback (most recent call last):
File "test_suite/system_tests/structure.py", line 636, in
test_read_xyz_internal1
self.interpreter.structure.read_xyz(file='Indol_test.xyz', dir=path)
File "prompt/structure.py", line 571, in read_xyz
generic_fns.structure.main.read_xyz(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num)
AttributeError: 'module' object has no attribute 'read_xyz'
----------------------------------------------------------------------
As you can see, the function generic_fns.structure.main.read_xyz() is
missing, so this can be duplicated from
generic_fns.structure.main.read_pdb(). This is more complicated, so
if you have any questions, don't hesitate to ask.
Regards,
Edward
On 10 June 2011 10:41, Edward d'Auvergne <[email protected]> wrote:
> Hi,
>
> For the next step in making the system test
>
> $ relax -s Structure.test_read_xyz_internal1
>
> operational would be to make the front end of the user function. That
> will require modifying code in the 'prompt' directory, again
> duplicating the load_pdb() code by modifying it for the XYZ format.
>
> Regards,
>
> Edward
>
>
> On 9 June 2011 17:34, Edward d'Auvergne <[email protected]> wrote:
>> Hi,
>>
>> Could you attach the file to the task instead? Cheers. Email systems
>> destroys the file format, so copying and pasting the text does not
>> work and causes the "patch" program to fail :( Could you also add a
>> quick commit message as a comment to the attached file?
>>
>> Cheers,
>>
>> Edward
>>
>>
>> On 9 June 2011 17:32, Han Sun <[email protected]> wrote:
>>> The function of the test_read_xyz_internal1() is generated.
>>>
>>> Following is the patch after running svn diff > patch.
>>>
>>> Index: structure.py
>>> ===================================================================
>>> --- structure.py (revision 12899)
>>> +++ structure.py (working copy)
>>> @@ -633,3 +633,31 @@
>>> self.assertEqual(mol.file_path, paths[i][j])
>>> self.assertEqual(mol.file_model, models[i][j])
>>> self.assertEqual(mol.file_mol_num, 1)
>>> +
>>> +
>>> + def test_read_xyz_internal1(self):
>>> + """Load the 'Indol_test.xyz' XYZ file (using the internal
>>> structural object XYZ reader)."""
>>> +
>>> + # Path of the files.
>>> + path = status.install_path +
>>> sep+'test_suite'+sep+'shared_data'+sep+'structures'
>>> +
>>> + # Read the PDB.
>>> + self.interpreter.structure.read_pdb(file='Indol_test.xyz',
>>> dir=path, parser='internal')
>>> +
>>> + # Test the molecule name.
>>> + self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name,
>>> '1F35_N_H_molmol_mol1')
>>> +
>>> + # Load a single atom and test it.
>>> + self.interpreter.structure.load_spins('#1F35_N_H_molmol_mol1:3@N')
>>> + self.assertEqual(count_spins(), 1)
>>> +
>>> + # Try loading a few protons.
>>> + self.interpreter.structure.load_spins('@*H*')
>>> +
>>> + # And now all the rest of the atoms.
>>> + self.interpreter.structure.load_spins()
>>> +
>>> + # Extract a N-Ca vector.
>>> + self.interpreter.structure.vectors('CA',
>>> spin_id='#1F35_N_H_molmol_mol1:3@N')
>>> + print((cdp.mol[0].res[0].spin[0]))
>>> + self.assert_(hasattr(cdp.mol[0].res[0].spin[0], 'bond_vect'))
>>> ~
>>> ~
>>> ~
>>>
>>> Best,
>>> Han
>>>
>>>
>>> On Jun 9, 2011, at 5:25 PM, Edward d'Auvergne wrote:
>>>
>>>> Cheers. I have added the file to the repository. And I have performed
>>>> an:
>>>>
>>>> $ svnmerge.py merge
>>>>
>>>> on your branch, so it should be up to date.
>>>>
>>>> Regards,
>>>>
>>>> Edward
>>>>
>>>>
>>>> On 9 June 2011 17:15, Han Sun <[email protected]> wrote:
>>>>>
>>>>> Hi,
>>>>> the test xyz-file 'Indol_test.xyz' will be in the directory:
>>>>> xyz/test_suite/shared_data/structures.
>>>>> Han
>>>
>>>
>>
>
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