Author: bugman
Date: Fri Oct 24 15:40:05 2008
New Revision: 7964
URL: http://svn.gna.org/viewcvs/relax?rev=7964&view=rev
Log:
Renamed and converted the read() method to relax_time().
The method now simply creates a structure in the relax data store matching
cdp.spectrum_ids and
storing the associated relaxation time periods.
Modified:
branches/spectral_errors/specific_fns/relax_fit.py
Modified: branches/spectral_errors/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/specific_fns/relax_fit.py?rev=7964&r1=7963&r2=7964&view=diff
==============================================================================
--- branches/spectral_errors/specific_fns/relax_fit.py (original)
+++ branches/spectral_errors/specific_fns/relax_fit.py Fri Oct 24 15:40:05
2008
@@ -943,66 +943,41 @@
continue
- def read(self, file=None, dir=None, relax_time=0.0, format=None,
heteronuc=None, proton=None, int_col=None):
- """Read in the peak intensity data.
-
- This method sets up the global data structures in the current data
pipe and then calls
- intensity.read().
-
-
- @keyword file: The name of the file containing the peak
intensities.
- @type file: str
- @keyword dir: The directory where the file is located.
- @type dir: str
- @keyword relax_time: The time, in seconds, of the relaxation
period.
- @type relax_time: float
- @keyword format: The type of file containing peak
intensities. This can currently be
- one of 'sparky', 'xeasy' or 'nmrview'.
- @type format: str
- @keyword heteronuc: The name of the heteronucleus as specified
in the peak intensity
- file.
- @type heteronuc: str
- @keyword proton: The name of the proton as specified in the
peak intensity file.
- @type proton: str
- @keyword int_col: The column containing the peak intensity
data (for a non-standard
- formatted file).
- @type int_col: int
+ def relax_time(self, time=0.0, spectrum_id=None):
+ """Set the relaxation time period associated with a given spectrum.
+
+ @keyword time: The time, in seconds, of the relaxation
period.
+ @type time: float
+ @keyword spectrum_id: The spectrum identification string.
+ @type spectrum_id: str
"""
# Alias the current data pipe.
cdp = pipes.get_pipe()
+ # Test if the spectrum id exists.
+ if spectrum_id not in cdp.spectrum_ids:
+ raise RelaxError, "The peak heights corresponding to spectrum id
'%s' have not been loaded." % spectrum_id
+
# Store the relaxation time in the class instance.
- self.__relax_time = float(relax_time)
-
- # Global relaxation time data structure.
+ self.__relax_time = float(time)
+
+ # The index.
+ index = cdp.spectrum_ids.index(spectrum_id)
+
+ # Initialise the global relaxation time data structure if needed.
if not hasattr(cdp, 'relax_times'):
- cdp.relax_times = []
-
- # Number of spectra.
- if not hasattr(cdp, 'num_spectra'):
- cdp.num_spectra = []
-
- # Determine if the relaxation time already exists for the residue
(duplicated spectra).
- index = None
- for i in xrange(len(cdp.relax_times)):
- if relax_time == cdp.relax_times[i]:
- index = i
-
- # A new relaxation time.
- if index == None:
- # Add the time.
- cdp.relax_times.append(relax_time)
-
- # First spectrum.
- cdp.num_spectra.append(1)
-
- # Duplicated spectra.
- else:
- cdp.num_spectra[index] = cdp.num_spectra[index] + 1
-
- # Generic intensity function.
- intensity.read(file=file, dir=dir, format=format,
heteronuc=heteronuc, proton=proton, int_col=int_col,
assign_func=self.assign_function)
+ cdp.relax_times = [None] * len(cdp.spectrum_ids)
+
+ # Index not present in the global relaxation time data structure.
+ while 1:
+ if index > len(cdp.relax_times) - 1:
+ cdp.relax_times.append(None)
+ else:
+ break
+
+ # Add the time at the correct position.
+ cdp.relax_times[index] = time
def return_data(self, spin):
r7964 - /branches/spectral_errors/specific_fns/relax_fit.py