Re: XYZ file support. -- June 09, 2011 - 13:24

Hi Eddy,

I am following your instruction below. I failed in the point with $  
relax -s Structure.test_[han]. I generated a function called  
test_read_xyz_internal1() and I have just modified the file name and  
the directory path. But then if I run the command $ relax -s  
Structure.test_test_read_xyz_internal1, it shows the error message  
'the script file does not exist'.

Han

On Jun 6, 2011, at 10:21 AM, Edward d'Auvergne wrote:

> Hi Han,
>
> I have now created a task for adding the XYZ structure file reading
> support to relax (https://gna.org/task/index.php?7404).  To start to
> implement this, I would suggest the following small steps:
>
> - First you already have a Gna! account (https://gna.org/users/han87),
> so creating this can be skipped.
>
> - Check out a fresh copy of the xyz branch of relax "svn co
> http://svn.gna.org/svn/relax/branches/xyz";, or update an already
> checked out copy "svn up".
>
> - Find an XYZ file of a small organic molecule and attach it to the
> task.  This is for the system test, to check that the data is
> correctly read.  It should be relatively small so that the system test
> is quick, but complex enough to be a good test.  Also tell me which
> directory it should be located in, and if I need to create directories
> in 'test_suite/shared_data' for it.
>
> - Create the system test by duplicating the code of
> 'test_read_pdb_internal1()' in the file
> 'test_suite/system_tests/structure.py'.  Remember to keep the methods
> alphabetically ordered.  Modify the code for the organic molecule.
>
> - Then run the test with:
> $ relax -s Structure.test_[han]
> replacing [han] with the name of the test.
>
> - Once the test is running (but it should be failing), then type:
> $ svn diff > diff
> and attach the diff file to the task.
>
> This would be a good start, and is how one should code.  Once the
> system test passes, we will know that the XYZ reading is complete.  If
> you have any questions, please don't hesitate to ask.
>
> Cheers,
>
> Edward