Author: bugman
Date: Tue Oct 21 16:45:27 2008
New Revision: 7889
URL: http://svn.gna.org/viewcvs/relax?rev=7889&view=rev
Log:
Deletion of the format argument from the spectrum.read_intensities() user
function.
To compensate for this, relax will be modified to auto-detect the file format.
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=7889&r1=7888&r2=7889&view=diff
==============================================================================
--- branches/spectral_errors/prompt/spectrum.py (original)
+++ branches/spectral_errors/prompt/spectrum.py Tue Oct 21 16:45:27 2008
@@ -87,7 +87,7 @@
noe_obj.set_error(error=error, spectrum_id=spectrum_id,
spin_id=spin_id)
- def read_intensities(self, file=None, dir=None, spectrum_id=None,
format='sparky', heteronuc='N', proton='HN', int_col=None):
+ def read_intensities(self, file=None, dir=None, spectrum_id=None,
heteronuc='N', proton='HN', int_col=None):
"""Function for reading peak intensities from a file for NOE
calculations.
Keyword Arguments
@@ -98,8 +98,6 @@
dir: The directory where the file is located.
spectrum_id: The spectrum identification string.
-
- format: The type of file containing peak intensities.
heteronuc: The name of the heteronucleus as specified in the peak
intensity file.
@@ -118,28 +116,24 @@
This is a unique identifier, so the label must not already exist.
- The 'format' argument can currently be set to:
- 'sparky'
- 'xeasy'
- 'nmrview'
+ The peak list or intensity file will be automatically determined.
- 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).
+ Sparky peak list: 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.
+ XEasy peak list: 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.
+ 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
@@ -159,8 +153,8 @@
To read the reference and saturated spectra peak heights from the
XEasy formatted files
'ref.text' and 'sat.text', type:
- relax> noe.read(file='ref.text', spectrum_id='ref', format='xeasy')
- relax> noe.read(file='sat.text', spectrum_id='sat', format='xeasy')
+ relax> noe.read(file='ref.text', spectrum_id='ref')
+ relax> noe.read(file='sat.text', spectrum_id='sat')
"""
# Function intro text.
@@ -169,7 +163,6 @@
text = text + "file=" + `file`
text = text + ", dir=" + `dir`
text = text + ", spectrum_id=" + `spectrum_id`
- text = text + ", format=" + `format`
text = text + ", heteronuc=" + `heteronuc`
text = text + ", proton=" + `proton`
text = text + ", int_col=" + `int_col` + ")"
@@ -187,10 +180,6 @@
if type(spectrum_id) != str:
raise RelaxStrError, ('spectrum identification string',
spectrum_id)
- # The format.
- if type(format) != str:
- raise RelaxStrError, ('format', format)
-
# The heteronucleus name.
if type(heteronuc) != str:
raise RelaxStrError, ('heteronucleus name', heteronuc)
@@ -204,4 +193,4 @@
raise RelaxNoneIntError, ('intensity column', int_col)
# Execute the functional code.
- noe_obj.read(file=file, dir=dir, spectrum_id=spectrum_id,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col)
+ noe_obj.read(file=file, dir=dir, spectrum_id=spectrum_id,
heteronuc=heteronuc, proton=proton, int_col=int_col)
r7889 - /branches/spectral_errors/prompt/spectrum.py