read(self,
run=None,
file=None,
dir=None,
relax_time=0.0,
fit_type='exp',
format='sparky',
heteronuc='N',
proton='HN',
int_col=None)
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Function for reading peak intensities from a file.
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.
relax_time: The time, in seconds, of the relaxation period.
fit_type: The type of relaxation curve to fit.
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 supported relaxation experiments include the default two parameter exponential fit,
selected by setting the 'fit_type' argument to 'exp', and the three parameter inversion
recovery experiment in which the peak intensity limit is a non-zero value, selected by
setting the argument to 'inv'.
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.
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