Re: r5607 - /1.3/generic_fns/palmer.py -- April 13, 2008 - 00:21

Hi,

No, no, this is the old bug with many *'s in a column, specifically
for Rex, that I described here
(https://mail.gna.org/public/relax-users/2008-04/msg00020.html,
Message-id: <7f080ed10804090112m437f001ar81399aa9f79cae9c@xxxxxxxxxxxxxx>).
 This will not catch this other column fusion Modelfree bug.

Regards,

Edward


On Sat, Apr 12, 2008 at 11:20 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
>  Hi Ed,
>
>  Nice that you found this one.
>
>  So you say that this will catch the ModelFree fused column bug ?
>
>  Ciao !
>
>
>  Séb
>
>
>
>  Edward d'Auvergne wrote:
>
>  Hi,
>
> I've found one bug below. Note though that this is an ancient bug I
> introduced many, many years ago and affects the code for catching the
> Modelfree fused column bug
> (https://mail.gna.org/public/relax-users/2008-04/msg00018.html,
> Message-id: <47FB8D12.8090502@xxxxxxxxx>).
>
>
>
> On Sat, Apr 12, 2008 at 10:39 PM, <sebastien.morin.1@xxxxxxxxx> wrote:
>
>
>  Author: semor
>  Date: Sat Apr 12 22:39:33 2008
>  New Revision: 5607
>
>  URL: http://svn.gna.org/viewcvs/relax?rev=5607&view=rev
>  Log:
>  Corrected more of the bugs introduced in former revisions as part of the
> move to the new design.
>
>  These were spotted by Edward d'Auvergne in a post at:
>  https://mail.gna.org/public/relax-devel/2008-04/msg00056.html (#
> Message-id:
>  <1208030368.8064.47.camel@localhost>)
>
>
>  Modified:
>  1.3/generic_fns/palmer.py
>
>  Modified: 1.3/generic_fns/palmer.py
>  URL:
> http://svn.gna.org/viewcvs/relax/1.3/generic_fns/palmer.py?rev=5607&r1=5606&r2=5607&view=diff
>
> ==============================================================================
>  --- 1.3/generic_fns/palmer.py (original)
>  +++ 1.3/generic_fns/palmer.py Sat Apr 12 22:39:33 2008
>  @@ -505,7 +505,7 @@
>  chdir(orig_dir)
>
>
>  - def extract(self, dir):
>  + def extract(self, dir, spin_id=None):
>  """Function for extracting the Modelfree4 results out of the 'mfout'
> file."""
>
>  # Alias the current data pipe.
>  @@ -545,65 +545,63 @@
>
>  # Loop over the sequence.
>  pos = 0
>  - for i in xrange(len(cdp.res)):
>  - # Reassign the data structure.
>  - data = cdp.res[i]
>  + for spin in spin_loop(spin_id):
>
>  # Skip unselected residues.
>  - if not data.select:
>  + if not spin.select:
>  continue
>
>  # Missing data sets.
>  - if not hasattr(data, 'model'):
>  + if not hasattr(spin, 'model'):
>  continue
>
>  # No relaxation data.
>  - if not hasattr(data, 'num_frq'):
>  + if not hasattr(spin, 'num_frq'):
>  continue
>
>  # Get the S2 data.
>  - if 'S2' in data.params:
>  - data.s2, data.s2_err = self.get_mf_data(self.mfout_S2_pos + pos)
>  + if 'S2' in spin.params:
>  + spin.s2, spin.s2_err = self.get_mf_data(self.mfout_S2_pos + pos)
>
>  # Get the S2f data.
>  - if 'S2f' in data.params or 'S2s' in data.params:
>  - data.s2f, data.s2f_err = self.get_mf_data(self.mfout_S2f_pos + pos)
>  + if 'S2f' in spin.params or 'S2s' in spin.params:
>  + spin.s2f, spin.s2f_err = self.get_mf_data(self.mfout_S2f_pos + pos)
>
>  # Get the S2s data.
>  - if 'S2f' in data.params or 'S2s' in data.params:
>  - data.s2s, data.s2s_err = self.get_mf_data(self.mfout_S2s_pos + pos)
>  + if 'S2f' in spin.params or 'S2s' in spin.params:
>  + spin.s2s, spin.s2s_err = self.get_mf_data(self.mfout_S2s_pos + pos)
>
>  # Get the te data.
>  - if 'te' in data.params:
>  - data.te, data.te_err = self.get_mf_data(self.mfout_te_pos + pos)
>  - data.te = data.te / 1e12
>  - data.te_err = data.te_err / 1e12
>  + if 'te' in spin.params:
>  + spin.te, spin.te_err = self.get_mf_data(self.mfout_te_pos + pos)
>  + spin.te = spin.te / 1e12
>  + spin.te_err = spin.te_err / 1e12
>
>  # Get the ts data.
>  - if 'ts' in data.params:
>  - data.ts, data.ts_err = self.get_mf_data(self.mfout_te_pos + pos)
>  - data.ts = data.ts / 1e12
>  - data.ts_err = data.ts_err / 1e12
>  + if 'ts' in spin.params:
>  + spin.ts, spin.ts_err = self.get_mf_data(self.mfout_te_pos + pos)
>  + spin.ts = spin.ts / 1e12
>  + spin.ts_err = spin.ts_err / 1e12
>
>  # Get the Rex data.
>  - if 'Rex' in data.params:
>  - data.rex, data.rex_err = self.get_mf_data(self.mfout_Rex_pos + pos)
>  + if 'Rex' in spin.params:
>  + spin.rex, spin.rex_err = self.get_mf_data(self.mfout_Rex_pos + pos)
>  try:
>  - data.rex = data.rex / (2.0 * pi * data.frq[0])**2
>  - data.rex_err = data.rex_err / (2.0 * pi * data.frq[0])**2
>  + spin.rex = spin.rex / (2.0 * pi * spin.frq[0])**2
>  + spin.rex_err = spin.rex_err / (2.0 * pi * spin.frq[0])**2
>  except TypeError:
>  # Bug in Modelfree4's mfout output file (fusion of columns).
>  - data.rex = None
>  - data_rex_err = None
>  + spin.rex = None
>  + spin_rex_err = None
>
>  Here is my bug. The last line should read 'spin.rex_eror = None'
> rather than 'spin_res_error'. I'll fix this bug in both the 1.2 and
> 1.3 lines.
>
> Cheers,
>
> Edward
>
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