Seb, This might be a change worth noting! I will be adding some code to the generic_fns.intensities module to auto-detect the peak list or intensity file format. This should be easy enough to detect from the peak list header, and simplifies relax for the user.
Regards, Edward On Tue, Oct 21, 2008 at 4:45 PM, <[EMAIL PROTECTED]> wrote: > 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) > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-commits mailing list > [EMAIL PROTECTED] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
