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 >> >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
