Hi Ed, Auto-detection is a very good idea and I completely agree that headers should allow this easily.
Regards, Séb Edward d'Auvergne wrote: > 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 > > _______________________________________________ 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
