Re: r13180 - in /branches/xyz: generic_fns/structure/main.py test_suite/system_tests/structure.py -- June 23, 2011 - 15:24

Hi Edward,

I added the residue check as you suggested. A new problem was coming  
out. Firstly, a single atom 2 can be loaded properly. But if all  
atoms are loaded, then it complains that the second atom exists and a  
new spin with the same name can not be generated again. I guess the  
code can not check properly that the atom 2 has been loaded, but I  
could not find the problem in the code. Could you help me with that?

Best,
Han


On Jun 23, 2011, at 3:19 PM, hasu@xxxxxxxxxxxxxxxxx wrote:

> Author: han87
> Date: Thu Jun 23 15:19:45 2011
> New Revision: 13180
>
> URL: http://svn.gna.org/viewcvs/relax?rev=13180&view=rev
> Log:
> Debugging the user function load_spins() and changing the system  
> test test_read_xyz_internal2().
>
> In the user function load_spins() in generic_fns/structure/main.py  
> a check whether the residue name exists or not has been included.  
> The code is similiar to the molecule check. Also see email: https:// 
> mail.gna.org/public/relax-devel/2011-06/msg00226.html. And in the  
> system test 'test_read_xyz_internal2()' all models were loaded  
> instead of 2 and the line for loading proton was removed.
>
> Modified:
>     branches/xyz/generic_fns/structure/main.py
>     branches/xyz/test_suite/system_tests/structure.py
>
> Modified: branches/xyz/generic_fns/structure/main.py
> URL: http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/ 
> structure/main.py?rev=13180&r1=13179&r2=13180&view=diff
> ====================================================================== 
> ========
> --- branches/xyz/generic_fns/structure/main.py (original)
> +++ branches/xyz/generic_fns/structure/main.py Thu Jun 23 15:19:45  
> 2011
> @@ -236,11 +236,26 @@
>
>          # Add the residue if it doesn't exist.
>          if res_cont == None:
> -            # Add the residue.
> -            mol_cont.res.add_item(res_name=res_name, res_num=res_num)
> -
> -            # Get the container.
> -            res_cont = mol_cont.res[-1]
> +            # Get the unnamed residue, assuming there is only one:
> +            res_cont = return_residue()
> +
> +            # Got something!
> +            if res_cont != None:
> +                # Rename the residue name if the res name is given  
> and the sole container is unnamed.
> +                if res_cont.name == None and res_name:
> +                    # Print out.
> +                    print(("Renaming the unnamed sole residue  
> container to '%s'." % res_name))
> +
> +                    # Get the name.
> +                    res_cont.name = res_name
> +
> +            # Nothing exists yet.
> +            else:
> +                # Add the residue.
> +                mol_cont.res.add_item(res_name=res_name,  
> res_num=res_num)
> +
> +                # Get the container.
> +                res_cont = mol_cont.res[-1]
>
>          # Add the atom number to the ID string (atom name is  
> ignored because only the number is unique).
>          id = id + '@' + repr(atom_num)
>
> Modified: branches/xyz/test_suite/system_tests/structure.py
> URL: http://svn.gna.org/viewcvs/relax/branches/xyz/test_suite/ 
> system_tests/structure.py?rev=13180&r1=13179&r2=13180&view=diff
> ====================================================================== 
> ========
> --- branches/xyz/test_suite/system_tests/structure.py (original)
> +++ branches/xyz/test_suite/system_tests/structure.py Thu Jun 23  
> 15:19:45 2011
> @@ -656,7 +656,7 @@
>          path = status.install_path + sep+'test_suite'+sep 
> +'shared_data'+sep+'structures'
>
>          # Read the xyz.
> -        self.interpreter.structure.read_xyz(file='SSS-cluster4-new- 
> test.xyz', dir=path, read_model=[1,3])
> +        self.interpreter.structure.read_xyz(file='SSS-cluster4-new- 
> test.xyz', dir=path)
>
>          # Test the molecule name.
>          self.assertEqual(cdp.structure.structural_data[0].mol 
> [0].mol_name, 'SSS-cluster4-new-test_mol1')
> @@ -666,8 +666,8 @@
>          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()
> -
> +        #self.interpreter.structure.load_spins('@H')
> +
> +        # And now all the rest of the atoms.
> +        self.interpreter.structure.load_spins()
> +
>
>
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