r7912 - /branches/spectral_errors/prompt/spectrum.py -- October 22, 2008 - 11:56

Author: bugman
Date: Wed Oct 22 11:56:55 2008
New Revision: 7912

URL: http://svn.gna.org/viewcvs/relax?rev=7912&view=rev
Log:
Added the int_method arg to the spectrum.read_intensities() user function.


Modified:
    branches/spectral_errors/prompt/spectrum.py

Modified: branches/spectral_errors/prompt/spectrum.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/prompt/spectrum.py?rev=7912&r1=7911&r2=7912&view=diff
==============================================================================
--- branches/spectral_errors/prompt/spectrum.py (original)
+++ branches/spectral_errors/prompt/spectrum.py Wed Oct 22 11:56:55 2008
@@ -286,7 +286,7 @@
         spectrum.integration_points(N=N, spectrum_id=spectrum_id, 
spin_id=spin_id)
 
 
-    def read_intensities(self, file=None, dir=None, spectrum_id=None, 
heteronuc='N', proton='HN', int_col=None, mol_name_col=None, 
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, 
sep=None):
+    def read_intensities(self, file=None, dir=None, spectrum_id=None, 
heteronuc='N', proton='HN', int_col=None, int_method=None, mol_name_col=None, 
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, 
sep=None):
         """Function for reading peak intensities from a file for NOE 
calculations.
 
         Keyword Arguments
@@ -303,6 +303,8 @@
         proton:  The name of the proton as specified in the peak intensity 
file.
 
         int_col:  The column(s) containing the peak intensity data (for a 
non-standard format).
+
+        int_method:  The integration method.
 
         mol_name_col:  The molecule name column used by the generic 
intensity file format.
 
@@ -330,6 +332,13 @@
         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.
+
+        The 'int_method' argument is required for the subsequent error 
analysis.  When peak heights
+        are measured, this argument should be set to 'height'.  Volume 
integration methods are a bit
+        varied and hence two values are accepted.  If the volume integration 
involves pure point
+        summation, with no deconvolution algorithms or other methods 
affecting peak heights, then
+        the argument should be set to 'point sum'.  All other volume 
integration methods, e.g. line
+        shape fitting, the argument should be set to 'other'.
 
 
         File formats
@@ -432,6 +441,9 @@
                 if type(int_col[i]) != int:
                     raise RelaxListIntError, ('intensity column', int_col)
 
+        # The integration method name.
+        if type(int_method) != str:
+            raise RelaxStrError, ('integration method', int_method)
 
         # Molecule name column.
         if mol_name_col != None and type(mol_name_col) != int:
@@ -458,4 +470,4 @@
             raise RelaxNoneStrError, ('column separator', sep)
 
         # Execute the functional code.
-        spectrum.read(file=file, dir=dir, spectrum_id=spectrum_id, 
heteronuc=heteronuc, proton=proton, int_col=int_col, 
mol_name_col=mol_name_col, res_num_col=res_num_col, 
res_name_col=res_name_col, spin_num_col=spin_num_col, 
spin_name_col=spin_name_col, sep=sep)
+        spectrum.read(file=file, dir=dir, spectrum_id=spectrum_id, 
heteronuc=heteronuc, proton=proton, int_col=int_col, int_method=int_method, 
mol_name_col=mol_name_col, res_num_col=res_num_col, 
res_name_col=res_name_col, spin_num_col=spin_num_col, 
spin_name_col=spin_name_col, sep=sep)