Re: [task #7404] Support for XYZ structure files. -- June 16, 2011 - 13:44

Hi,

I haven't applied these changes to the repository version.  I would
suggest you check out a new, clean copy, and make your changes step by
step in the new copy.  You can remove all your changes with:

$ svn revert -R .

But be warned, you will loose all your changes.  Therefore I would
recommend getting a new copy, or copying the current version and using
this svn revert command on the copies.

Regards,

Edward



On 16 June 2011 12:23, Han Sun <hasu@xxxxxxxxxxxxxxxxx> wrote:
> Hi,
>
> Could you resume the old internal.py file so that I can added my new change
> step by step?
>
> Thanks!
> Han
>
> On Jun 16, 2011, at 11:53 AM, Edward d'Auvergne wrote:
>
> > Hi,
> >
> > I have applied the patch, but there are too many unrelated changes
> > grouped together.  So unfortunately I cannot apply it.  I can see that
> > there are three new functions in the internal structural reader:
> >
> > __parse_models_xyz()
> > __parse_mols_xyz()
> > load_xyz()
> >
> > This could go in one patch, but they should be described.  There is
> > also a lot of debugging print outs, it would be useful to mention
> > this.
> >
> > Then there is the new class MolContainer_xyz.  This is not needed as
> > MolContainer is a generic class with a few PDB specific methods.
> > These specific methods could have '_pdb' added to the end, and then
> > these are duplicated and changed to *_xyz().  But I would put these as
> > a separate patch.  The original MolContainer should be preserved as
> > this defines the internal structure object.
> >
> > Then generic_fns/structure/main.py has a single empty line removed, so
> > this can be a single patch.  And the modification to the file
> > test_suite/shared_data/structures/Indol_test.xyz should be in a
> > separate patch, with a commit message explaining this change.
> > Finally, the test_read_xyz_internal1() system test has been modified
> > for the new SSS-cluster4-new-test.xyz file.  I would suggest that this
> > is done differently.  The current test can be duplicated and called
> > test_read_xyz_internal2().  The first test if for the Indol_test.xyz
> > file, the second is for the multi-model SSS-cluster4-new-test.xyz
> > file.
> >
> > Cheers,
> >
> > Edward
> >
> >
> > On 16 June 2011 11:33, Han Sun <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> > > Follow-up Comment #9, task #7404 (project relax):
> > >
> > > Generating new user function 'load_xyz()'.
> > > This is Han's patch https://gna.org/task/download.php?file_id=13226
> > > attached
> > > to the task
> > > http://gna.org/task/?7404.
> > > The user function 'load_xyz()' was generated and modified in the
> > > generic_fns/structure/internal.py based on the function 'load_pdb()'.
> > >
> > >
> > >   _______________________________________________________
> > >
> > > Reply to this item at:
> > >
> > >  <http://gna.org/task/?7404>
> > >
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