Author: bugman
Date: Tue Oct 21 16:31:48 2008
New Revision: 7886
URL: http://svn.gna.org/viewcvs/relax?rev=7886&view=rev
Log:
Renamed 'spectrum_type' to the more generic 'spectrum_id'.
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=7886&r1=7885&r2=7886&view=diff
==============================================================================
--- branches/spectral_errors/prompt/spectrum.py (original)
+++ branches/spectral_errors/prompt/spectrum.py Tue Oct 21 16:31:48 2008
@@ -42,15 +42,15 @@
self.__relax__ = relax
- def error(self, error=0.0, spectrum_type=None, spin_id=None):
- """Function for setting the errors in the reference or saturated NOE
spectra.
+ def error(self, error=0.0, spectrum_id=None, spin_id=None):
+ """Function for setting the intensity error (standard deviation) in
the given spectrum.
Keyword Arguments
~~~~~~~~~~~~~~~~~
error: The error.
- spectrum_type: The type of spectrum.
+ spectrum_id: The spectrum identification string.
spin_id: The spin identification string.
@@ -58,22 +58,16 @@
Description
~~~~~~~~~~~
- The spectrum_type argument can have the following values:
- 'ref': The NOE reference spectrum.
- 'sat': The NOE spectrum with proton saturation turned on.
-
- If the 'res_num' and 'res_name' arguments are left as the defaults
of None, then the error
- value for all residues will be set to the supplied value. Otherwise
the residue number can
- be set to either an integer for selecting a single residue or a
python regular expression
- string for selecting multiple residues. The residue name argument
must be a string and can
- use regular expression as well.
+ The spectrum_id argument identifies the spectrum associated with the
error and must
+ correspond to a previously loaded set of intensities. If the
'spin_id' argument is left on
+ the default of None, then the error value for all spins will be set
to the supplied value.
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "noe.error("
text = text + "error=" + `error`
- text = text + ", spectrum_type=" + `spectrum_type`
+ text = text + ", spectrum_id=" + `spectrum_id`
text = text + ", spin_id=" + `spin_id` + ")"
print text
@@ -81,19 +75,19 @@
if type(error) != float and type(error) != int:
raise RelaxNumError, ('error', error)
- # The spectrum type.
- if type(spectrum_type) != str:
- raise RelaxStrError, ('spectrum type', spectrum_type)
+ # The spectrum identification string.
+ if type(spectrum_id) != str:
+ raise RelaxStrError, ('spectrum identification string',
spectrum_id)
# Spin identification string.
if spin_id != None and type(spin_id) != str:
raise RelaxNoneStrError, ('spin identification string', spin_id)
# Execute the functional code.
- noe_obj.set_error(error=error, spectrum_type=spectrum_type,
spin_id=spin_id)
-
-
- def read(self, file=None, dir=None, spectrum_type=None, format='sparky',
heteronuc='N', proton='HN', int_col=None):
+ noe_obj.set_error(error=error, spectrum_id=spectrum_id,
spin_id=spin_id)
+
+
+ def read(self, file=None, dir=None, spectrum_id=None, format='sparky',
heteronuc='N', proton='HN', int_col=None):
"""Function for reading peak intensities from a file for NOE
calculations.
Keyword Arguments
@@ -103,7 +97,7 @@
dir: The directory where the file is located.
- spectrum_type: The type of spectrum.
+ spectrum_id: The type of spectrum.
format: The type of file containing peak intensities.
@@ -120,7 +114,7 @@
The peak intensity can either be from peak heights or peak volumes.
- The 'spectrum_type' argument can have the following values:
+ The 'spectrum_id' argument can have the following values:
'ref': The NOE reference spectrum.
'sat': The NOE spectrum with proton saturation turned on.
@@ -160,14 +154,14 @@
To read the reference and saturated spectra peak heights from the
Sparky formatted files
'ref.list' and 'sat.list', type:
- relax> noe.read(file='ref.list', spectrum_type='ref')
- relax> noe.read(file='sat.list', spectrum_type='sat')
+ relax> noe.read(file='ref.list', spectrum_id='ref')
+ relax> noe.read(file='sat.list', spectrum_id='sat')
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_type='ref', format='xeasy')
- relax> noe.read(file='sat.text', spectrum_type='sat', format='xeasy')
+ relax> noe.read(file='ref.text', spectrum_id='ref', format='xeasy')
+ relax> noe.read(file='sat.text', spectrum_id='sat', format='xeasy')
"""
# Function intro text.
@@ -175,7 +169,7 @@
text = sys.ps3 + "noe.read("
text = text + "file=" + `file`
text = text + ", dir=" + `dir`
- text = text + ", spectrum_type=" + `spectrum_type`
+ text = text + ", spectrum_id=" + `spectrum_id`
text = text + ", format=" + `format`
text = text + ", heteronuc=" + `heteronuc`
text = text + ", proton=" + `proton`
@@ -190,9 +184,9 @@
if dir != None and type(dir) != str:
raise RelaxNoneStrError, ('directory name', dir)
- # The spectrum type.
- if type(spectrum_type) != str:
- raise RelaxStrError, ('spectrum type', spectrum_type)
+ # The spectrum identification string.
+ if type(spectrum_id) != str:
+ raise RelaxStrError, ('spectrum identification string',
spectrum_id)
# The format.
if type(format) != str:
@@ -211,4 +205,4 @@
raise RelaxNoneIntError, ('intensity column', int_col)
# Execute the functional code.
- noe_obj.read(file=file, dir=dir, spectrum_type=spectrum_type,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col)
+ noe_obj.read(file=file, dir=dir, spectrum_id=spectrum_id,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col)
r7886 - /branches/spectral_errors/prompt/spectrum.py