Re: [task #7404] Support for XYZ structure files. -- June 16, 2011 - 11:53

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()'.
>
>
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