Package prompt :: Module noe :: Class Noe
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Class Noe

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Instance Methods [hide private]
 
__init__(self, relax) source code
 
error(self, run=None, error=0.0, spectrum_type=None, res_num=None, res_name=None)
Function for setting the errors in the reference or saturated NOE spectra.
source code
 
read(self, run=None, file=None, dir=None, spectrum_type=None, format='sparky', heteronuc='N', proton='HN', int_col=None)
Function for reading peak intensities from a file for NOE calculations.
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Method Details [hide private]

error(self, run=None, error=0.0, spectrum_type=None, res_num=None, res_name=None)

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Function for setting the errors in the reference or saturated NOE spectra.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run.

error:  The error.

spectrum_type:  The type of spectrum.

res_num:  The residue number.

res_name:  The residue name.


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.

read(self, run=None, file=None, dir=None, spectrum_type=None, format='sparky', heteronuc='N', proton='HN', int_col=None)

source code 
Function for reading peak intensities from a file for NOE calculations.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run.

file:  The name of the file containing the sequence data.

dir:  The directory where the file is located.

spectrum_type:  The type of spectrum.

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).


Description
~~~~~~~~~~~

The peak intensity can either be from peak heights or peak volumes.


The 'spectrum_type' argument can have the following values:
    'ref':  The NOE reference spectrum.
    'sat':  The NOE spectrum with proton saturation turned on.


The 'format' argument can currently be set to:
    'sparky'
    'xeasy'

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.


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.


Examples
~~~~~~~~

To read the reference and saturated spectra peak heights from the Sparky formatted files
'ref.list' and 'sat.list' to the run 'noe', type:

relax> noe.read('noe', file='ref.list', spectrum_type='ref')
relax> noe.read('noe', file='sat.list', spectrum_type='sat')

To read the reference and saturated spectra peak heights from the XEasy formatted files
'ref.text' and 'sat.text' to the run 'noe', type:

relax> noe.read('noe', file='ref.text', spectrum_type='ref', format='xeasy')
relax> noe.read('noe', file='sat.text', spectrum_type='sat', format='xeasy')