Re: XYZ file support. -- June 09, 2011 - 17:31

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