Hi,
Sorry for not getting back to this message earlier, I've had a few
deadlines lately. Please see below for more.
On Wed, Feb 4, 2009 at 9:16 PM, Sébastien Morin
<sebastien.mori...@ulaval.ca> wrote:
> Hi Ed,
>
> I tried what you proposed...
>
> ========================
> from generic_fns.mol_res_spin import spin_loop
> pipe.create()
> sequence.read()
> structure.read_pdb()
> structure.vectors()
> for spin, spin_id in spin_loop(return_id=True):
> print "%s %s" % (spin_id, spin.xh_vect)
> ========================
>
> However, there is something quite annoying (but predictable)... If the
> sequence used contains residues for which the N-H vector does not exist
> (e.g. N-terminal residue, or proline), the spin loop will produce an
> error message such as:
>
> ========================
> for spin, spin_id in spin_loop(return_id=True):
> print "%s %s" % (spin_id, spin.xh_vect)
>
> Traceback (most recent call last):
> File "<console>", line 2, in <module>
> AttributeError: 'SpinContainer' object has no attribute 'xh_vect'
> ========================
This can be solved using the hasattr() function. So in the spin loop have:
if not hasattr(spin, 'xh_vect'):
continue
This will skip all spins with no XH vectors. You can make the output
a bit fancier if you set the spin_loop() argument full_info to True as
this will then return the molecule name, residue name, residue number,
and the spin container which contains the atom name and number.
Regards,
Edward
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