Author: bugman
Date: Sun Apr 13 11:18:10 2008
New Revision: 5614
URL: http://svn.gna.org/viewcvs/relax?rev=5614&view=rev
Log:
Merged revisions 5611-5612 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r5611 | bugman | 2008-04-13 11:04:28 +0200 (Sun, 13 Apr 2008) | 6 lines
Fix for bug #11483 (https://gna.org/bugs/?11483).
The get_mf_data() method has been expanded to handle both Modelfree4 mfout
column fusion bugs. This
method should now be much more robust for parsing the mfout file.
........
r5612 | bugman | 2008-04-13 11:06:36 +0200 (Sun, 13 Apr 2008) | 3 lines
Removed some code for handling corrupt mfout files which was made redundant
by the bug fix in r5611.
........
Modified:
1.2/ (props changed)
1.2/generic_fns/palmer.py
Propchange: 1.2/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sun Apr 13 11:18:10 2008
@@ -1,1 +1,1 @@
-/1.3:1-2505,2941,2947,2950,2974,2976,2979,2984,2988,3076,3083-3084,3087,3117,3299,3309,3312,3314,3318,3345,3372,4145,4473,4476,4939,5117,5255,5396-5398,5462-5465
+/1.3:1-2505,2941,2947,2950,2974,2976,2979,2984,2988,3076,3083-3084,3087,3117,3299,3309,3312,3314,3318,3345,3372,4145,4473,4476,4939,5117,5255,5396-5398,5462-5465,5611-5612
Modified: 1.2/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/palmer.py?rev=5614&r1=5613&r2=5614&view=diff
==============================================================================
--- 1.2/generic_fns/palmer.py (original)
+++ 1.2/generic_fns/palmer.py Sun Apr 13 11:18:10 2008
@@ -23,7 +23,7 @@
from math import pi
from os import F_OK, P_WAIT, access, chdir, chmod, getcwd, listdir, remove,
system
from re import match, search
-from string import split
+from string import count, find, split
# UNIX only functions from the os module (Modelfree4 only runs under UNIX
anyway).
try:
@@ -565,13 +565,8 @@
# Get the Rex data.
if 'Rex' in data.params:
data.rex, data.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
- except TypeError:
- # Bug in Modelfree4's mfout output file (fusion of
columns).
- data.rex = None
- data_rex_err = None
+ data.rex = data.rex / (2.0 * pi * data.frq[0])**2
+ data.rex_err = data.rex_err / (2.0 * pi * data.frq[0])**2
# Get the chi-squared data.
if not sims:
@@ -587,23 +582,78 @@
def get_mf_data(self, pos):
- """Extract the model-free data from the given position of the mfout
file."""
+ """Extract the model-free data from the given position of the mfout
file.
+
+ This method is designed to catch a number of bugs in Modelfree4's
mfout file.
+
+ The first bug is the presence of a series of '*' characters causing
a fusion of two columns.
+ This is handled by splitting by the '*' char and then returning the
first element.
+
+ The second bug is when the floating point number is too big to fit
into Modelfree4's string
+ format limit of 15.3f. This results in a results line such as:
+
+ 246 10000.00019682363392.000 1 0.000 0.000
0.000 0.000
+
+ This is caught by scanning for two '.' characters in the column, and
handled by assuming
+ that every floating point number will have three decimal characters.
+
+ @param pos: The mfout line position.
+ @type pos: int
+ @return: The value and error.
+ @rtype: tuple of 2 floats
+ """
# Split the line up.
row = split(self.mfout_lines[pos])
- # Attempt to extract the value and error.
- try:
- # Catch a series of '*' joining two columns.
- val = split(row[1], '*')
- err = split(row[4], '*')
-
- # Return the value and error.
- return float(val[0]), float(err[0])
-
- # Otherwise, there is no data???
- except:
- return None, None
+ # The value and error, assuming a bug free mfout file.
+ val = row[1]
+ err = row[4]
+
+ # The Modelfree4 '*' column fusion bug.
+ if search('*', val) or search('*', err):
+ # Split by the '*' character.
+ val_row = split(val, '*')
+ err_row = split(err, '*')
+
+ # The value and error (the first elements).
+ val = val_row[0]
+ err = err_row[0]
+
+ # The Modelfree4 large float column fusion bug.
+ new_row = []
+ fused = False
+ for element in row:
+ # Count the number of '.' characters.
+ num = count(element, '.')
+
+ # Catch two or more '.' characters.
+ if num > 1:
+ # Set the fused flag.
+ fused = True
+
+ # Loop over each fused number.
+ for i in xrange(num):
+ # Find the index of the first '.'.
+ index = find(element, '.')
+
+ # The first number (index + decimal point + 3 decimal
chars).
+ new_row.append(element[0:index+4])
+
+ # Strip the first number from the element for the next
loop iteration.
+ element = element[index+4:]
+
+ # Otherwise the column element is fine.
+ else:
+ new_row.append(element)
+
+ # Bug has been caught.
+ if fused:
+ val = new_row[1]
+ err = new_row[4]
+
+ # Return the value and error, as floats.
+ return float(val), float(err)
def line_positions(self):
r5614 - in /1.2: ./ generic_fns/palmer.py