Re: XYZ file support. -- June 09, 2011 - 17:35

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 <hasu@xxxxxxxxxxxxxxxxx> 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 <hasu@xxxxxxxxxxxxxxxxx> wrote:
> > > Hi,
> > > the test xyz-file 'Indol_test.xyz' will be in the directory:
> > > xyz/test_suite/shared_data/structures.
> > > Han