Re: r13121 - in /branches/xyz: generic_fns/structure/internal.py test_suite/system_tests/structure.py -- June 20, 2011 - 10:41

Hi Han,

It's now working, your ssh access :)  I was just wondering why you had
the statement:

if mol_index==0:

This could be problematic if you have multiple molecules in the XYZ
file.  Is it possible to have more than one in the format?

Cheers,

Edward



On 20 June 2011 10:07,  <hasu@xxxxxxxxxxxxxxxxx> wrote:
> Author: han87
> Date: Mon Jun 20 10:07:35 2011
> New Revision: 13121
>
> URL: http://svn.gna.org/viewcvs/relax?rev=13121&view=rev
> Log:
> Debugging the user functions load_xyz() and test_read_xyz_internal2().
>
> The user functions load_xyz() in 'generic_fns/structure/internal.py' and 
> test_read_xyz_internal2() in 'test_suite/system_tests/structure.py' have 
> been changed so that the molecule name can be read properly.
>
> Modified:
>    branches/xyz/generic_fns/structure/internal.py
>    branches/xyz/test_suite/system_tests/structure.py
>
> Modified: branches/xyz/generic_fns/structure/internal.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/internal.py?rev=13121&r1=13120&r2=13121&view=diff
> ==============================================================================
> --- branches/xyz/generic_fns/structure/internal.py (original)
> +++ branches/xyz/generic_fns/structure/internal.py Mon Jun 20 10:07:35 2011
> @@ -853,8 +853,9 @@
>             if set_mol_name:
>                 new_mol_name.append(set_mol_name[mol_index])
>             else:
> -                # Set the name to the file name plus the structure number.
> -                new_mol_name.append(file_root(file) + '_mol' + 
> repr(mol_index))
> +                if mol_index==0:
> +                   #Set the name to the file name plus the structure 
> number.
> +                   new_mol_name.append(file_root(file) + '_mol' + 
> repr(mol_index+1))
>
>             # Store the original mol number.
>             orig_mol_num.append(mol_index)
> @@ -874,7 +875,8 @@
>
>             # Increment the model index.
>             model_index = model_index + 1
> -
> +
> +        orig_mol_num=[0]
>         # Create the structural data data structures.
>         self.pack_structs(mol_conts, orig_model_num=orig_model_num, 
> set_model_num=set_model_num, orig_mol_num=orig_mol_num, 
> set_mol_name=new_mol_name, file_name=file, file_path=path)
>
>
> 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=13121&r1=13120&r2=13121&view=diff
> ==============================================================================
> --- branches/xyz/test_suite/system_tests/structure.py (original)
> +++ branches/xyz/test_suite/system_tests/structure.py Mon Jun 20 10:07:35 
> 2011
> @@ -659,10 +659,10 @@
>         
> 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')
> +        self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, 
> 'SSS-cluster4-new-test_mol1')
>
>         # Load a single atom and test it.
> -        self.interpreter.structure.load_spins('SSS-cluster4-new-test:3@C')
> +        
> self.interpreter.structure.load_spins('SSS-cluster4-new-test_mol1:@C')
>         self.assertEqual(count_spins(), 1)
>
>         # Try loading a few protons.
>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
> This is the relax-commits mailing list
> relax-commits@xxxxxxx
>
> 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-commits