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
# Get the chi-squared data.
if not sims:
row = split(self.mfout_lines[self.mfout_chi2_pos + pos])
- data.chi2 = float(row[1])
+ spin.chi2 = float(row[1])
else:
# The mfout chi2 position (with no sims) plus 2 (for the
extra XML) plus the residue position times 22 (because of the simulated SSE
rows).
row = split(self.mfout_lines[self.mfout_chi2_pos + 2 +
22*pos])
- data.chi2 = float(row[1])
+ spin.chi2 = float(row[1])
# Increment the residue position.
pos = pos + 1
r5607 - /1.3/generic_fns/palmer.py