Re: r5607 - /1.3/generic_fns/palmer.py -- April 12, 2008 - 23:21

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 = ""
 +        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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