Re: [task #7404] Support for XYZ structure files. -- June 17, 2011 - 11:00

Hi,

I tried to apply the patch
https://gna.org/task/download.php?file_id=13244, but it failed with:

[edward@localhost xyz]$ patch -p0 < patch
patching file generic_fns/structure/main.py
Reversed (or previously applied) patch detected!  Assume -R? [n]

Looking at the patch, the previous commit has been reverted:

[edward@localhost xyz]$ cat patch
Index: generic_fns/structure/main.py
===================================================================
--- generic_fns/structure/main.py       (revision 13065)
+++ generic_fns/structure/main.py       (working copy)
@@ -416,7 +416,6 @@
         else:
             warn(RelaxNoPDBFileWarning(file_path))
             return
-

     # Place the  structural object into the relax data store.
     if not hasattr(cdp, 'structure'):
Index: test_suite/shared_data/structures/Indol_test.xyz
===================================================================
--- test_suite/shared_data/structures/Indol_test.xyz    (revision 13065)
+++ test_suite/shared_data/structures/Indol_test.xyz    (working copy)
@@ -1,5 +1,5 @@
 16
-1-Indolizinyl  0.000000
+1-Indolizinyl
 C  0.0784  1.9475 -0.3681
 H -0.3810  2.9138 -0.3681
 C  1.4607  1.6737 -0.3682
[edward@localhost xyz]$

Could you remake the patch without the change to 
generic_fns/structure/main.py?

Cheers,

Edward



On 17 June 2011 10:56, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Cheers, I'll add this to the commit message.
>
> Regards,
>
> Edward
>
>
> On 17 June 2011 10:53, Han Sun <hasu@xxxxxxxxxxxxxxxxx> wrote:
> > Hi,
> >
> > because this was a mistake generated by me. In a normal xyz file the second
> > line is just the molecule name. But for reading the xyz file actually it
> > does not matter whether it  has this 0.00000 or not. But I think since this
> > is a test xyz file it would be good to remove it so that it looks like a
> > normal xyz file.
> >
> > Best,
> > Han
> >
> > On Jun 17, 2011, at 10:47 AM, Edward d'Auvergne wrote:
> >
> > > Hi,
> > >
> > > Would you be able to explain why the 0.00000 was removed?
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > >
> > > On 17 June 2011 10:41, Han Sun <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> > > > Follow-up Comment #12, task #7404 (project relax):
> > > >
> > > > Modifying test_suite/shared_data/structures/Indol_test.xyz
> > > > This is Han's patch https://gna.org/task/download.php?file_id=13244
> > > > attached
> > > > to the task
> > > > http://gna.org/task/?7404.
> > > > In the test_suite/shared_data/structures/Indol_test.xyz 0.00000 after the
> > > > molecule name was removed.
> > > >
> > > >   _______________________________________________________
> > > >
> > > > Reply to this item at:
> > > >
> > > >  <http://gna.org/task/?7404>
> > > >
> > > > _______________________________________________
> > > >  Message sent via/by Gna!
> > > >  http://gna.org/