Author: bugman
Date: Wed Oct 22 12:36:21 2008
New Revision: 7915
URL: http://svn.gna.org/viewcvs/relax?rev=7915&view=rev
Log:
Renamed relax_fit.read() to relax_fit.relax_time() and significantly
decreased its functionality.
Most of relax_fit.read() is now in spectrum.read_intensities() and hence this
functionality has been
axed. All that is left is the associating of a spectrum to a time point.
Modified:
branches/spectral_errors/prompt/relax_fit.py
Modified: branches/spectral_errors/prompt/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/prompt/relax_fit.py?rev=7915&r1=7914&r2=7915&view=diff
==============================================================================
--- branches/spectral_errors/prompt/relax_fit.py (original)
+++ branches/spectral_errors/prompt/relax_fit.py Wed Oct 22 12:36:21 2008
@@ -42,106 +42,43 @@
self.__relax__ = relax
- def read(self, file=None, dir=None, relax_time=0.0, format='sparky',
heteronuc='N', proton='HN', int_col=None):
- """Function for reading peak intensities from a file.
+ def relax_time(self, time=0.0, spectrum_id=None):
+ """Function for setting the relaxation time period associated with
each spectrum.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- file: The name of the file containing the sequence data.
+ time: The time, in seconds, of the relaxation period.
- dir: The directory where the file is located.
-
- relax_time: The time, in seconds, of the relaxation period.
-
- format: The type of file containing peak intensities.
-
- heteronuc: The name of the heteronucleus as specified in the peak
intensity file.
-
- proton: The name of the proton as specified in the peak intensity
file.
-
- int_col: The column containing the peak intensity data (for a
non-standard formatted file).
+ spectrum_id: The spectrum identification string.
Description
~~~~~~~~~~~
- The peak intensity can either be from peak heights or peak volumes.
-
-
- The format argument can currently be set to:
- 'sparky'
- 'xeasy'
- 'nmrview'
-
- If the 'format' argument is set to 'sparky', the file should be a
Sparky peak list saved after
- typing the command 'lt'. The default is to assume that columns 0,
1, 2, and 3 (1st, 2nd,
- 3rd, and 4th) contain the Sparky assignment, w1, w2, and peak
intensity data respectively.
- The frequency data w1 and w2 are ignored while the peak intensity
data can either be the
- peak height or volume displayed by changing the window options. If
the peak intensity data
- is not within column 3, set the argument int_col to the appropriate
value (column numbering
- starts from 0 rather than 1).
-
- If the 'format' argument is set to 'xeasy', the file should be the
saved XEasy text window
- output of the list peak entries command, 'tw' followed by 'le'. As
the columns are fixed,
- the peak intensity column is hardwired to number 10 (the 11th
column) which contains either
- the peak height or peak volume data. Because the columns are fixed,
the int_col argument
- will be ignored.
-
- If the 'format' argument is set to 'nmrview', the file should be a
NMRView peak list. The
- default is to use column 16 (which contains peak heights) for peak
intensities. To use
- use peak volumes (or evolumes), int_col must be set to 15.
-
-
- The heteronuc and proton arguments should be set respectively to the
name of the
- heteronucleus and proton in the file. Only those lines which match
these labels will be
- used.
-
-
+ Peak intensities should be loaded before calling this user function
via the
+ 'spectrum.read_intensities()' user function. The intensity values
will then be associated
+ with a spectrum identifier. To associate each spectrum identifier
with a time point in the
+ relaxation curve prior to optimisation, this user function should be
called.
"""
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "relax_fit.read("
- text = text + "file=" + `file`
- text = text + ", dir=" + `dir`
- text = text + ", relax_time=" + `relax_time`
- text = text + ", format=" + `format`
- text = text + ", heteronuc=" + `heteronuc`
- text = text + ", proton=" + `proton`
- text = text + ", int_col=" + `int_col` + ")"
+ text = sys.ps3 + "relax_fit.relax_time("
+ text = text + "time=" + `time`
+ text = text + ", spectrum_id=" + `spectrum_id` + ")"
print text
- # The file name.
- if type(file) != str:
- raise RelaxStrError, ('file name', file)
+ # The relaxation time.
+ if type(time) != int and type(time) != float:
+ raise RelaxNumError, ('relaxation time', time)
- # Directory.
- if dir != None and type(dir) != str:
- raise RelaxNoneStrError, ('directory name', dir)
-
- # The relaxation time.
- if type(relax_time) != int and type(relax_time) != float:
- raise RelaxNumError, ('relaxation time', relax_time)
-
- # The format.
- if type(format) != str:
- raise RelaxStrError, ('format', format)
-
- # The heteronucleus name.
- if type(heteronuc) != str:
- raise RelaxStrError, ('heteronucleus name', heteronuc)
-
- # The proton name.
- if type(proton) != str:
- raise RelaxStrError, ('proton name', proton)
-
- # The intensity column.
- if int_col and type(int_col) != int:
- raise RelaxNoneIntError, ('intensity column', int_col)
+ # The spectrum identification string.
+ if type(spectrum_id) != str:
+ raise RelaxStrError, ('spectrum identification string',
spectrum_id)
# Execute the functional code.
- relax_fit_obj.read(file=file, dir=dir, relax_time=relax_time,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col)
+ relax_fit_obj.relax_time(time=time, spectrum_id=spectrum_id)
def select_model(self, model='exp'):
r7915 - /branches/spectral_errors/prompt/relax_fit.py