Thanks for picking this up. If you'd like to implement the NMRView peak list support, that would free up more time for me to get Gary's multi-processor code ported and the BMRB support implemented (as well as getting Modelfree4 and Dasha running again, and cleaning up and destroying all of the remaining 1.2 line code).
Cheers, Edward On Thu, Oct 9, 2008 at 7:37 PM, <[EMAIL PROTECTED]> wrote: > Author: semor > Date: Thu Oct 9 19:37:20 2008 > New Revision: 7592 > > URL: http://svn.gna.org/viewcvs/relax?rev=7592&view=rev > Log: > Continued the implementation for the reading of a Nmrview peak list. > > > Modified: > 1.3/generic_fns/intensity.py > 1.3/prompt/noe.py > 1.3/prompt/relax_fit.py > 1.3/specific_fns/noe.py > 1.3/specific_fns/relax_fit.py > 1.3/test_suite/system_tests/nmrview.py > > Modified: 1.3/generic_fns/intensity.py > URL: > http://svn.gna.org/viewcvs/relax/1.3/generic_fns/intensity.py?rev=7592&r1=7591&r2=7592&view=diff > ============================================================================== > --- 1.3/generic_fns/intensity.py (original) > +++ 1.3/generic_fns/intensity.py Thu Oct 9 19:37:20 2008 > @@ -27,6 +27,7 @@ > # Python module imports. > from re import split > from warnings import warn > +import sys > > # relax module imports. > from generic_fns.mol_res_spin import exists_mol_res_spin_data, > generate_spin_id, return_spin > @@ -158,13 +159,32 @@ > return res_num, h_name, x_name, intensity > > > +def intensity_nmrview(line, int_col=None): > + """Function for returning relevant data from the Nmrview peak intensity > line. > + > + The residue number, heteronucleus and proton names, and peak intensity > will be returned. > + > + > + @param line: The single line of information from the intensity > file. > + @type line: list of str > + @keyword int_col: The column containing the peak intensity data (for a > non-standard formatted > + file). > + @type int_col: int > + @raises RelaxError: When the expected peak intensity is not a float. > + """ > + > + # Print some texte indicating the unavailability of this function... > + print "This function is still unavailable.\n" > + sys.exit() > + > + > def number_of_header_lines(file_data, format, int_col, intensity): > """Function for determining how many header lines are in the intensity > file. > > @param file_data: The processed results file data. > @type file_data: list of lists of str > @param format: The type of file containing peak intensities. This > can currently be one of > - 'sparky' or 'xeasy'. > + 'sparky', 'xeasy' or 'nmrview'. > @type format: str > @param int_col: The column containing the peak intensity data (for a > non-standard > formatted file). > @@ -214,7 +234,7 @@ > @keyword dir: The directory where the file is located. > @type dir: str > @keyword format: The type of file containing peak intensities. > This can currently be > - one of 'sparky' or 'xeasy'. > + one of 'sparky', 'xeasy' or 'nmrview'. > @type format: str > @keyword heteronuc: The name of the heteronucleus as specified in the > peak intensity > file. > @@ -231,7 +251,7 @@ > """ > > # Format argument. > - format_list = ['sparky', 'xeasy'] > + format_list = ['sparky', 'xeasy', 'nmrview'] > if format not in format_list: > raise RelaxArgNotInListError, ('format', format, format_list) > > @@ -253,6 +273,14 @@ > > # Set the default proton dimension. > H_dim = 'w1' > + > + # Nmrview. > + elif format == 'nmrview': > + # Print out. > + print "Nmrview formatted data file.\n" > + > + # Set the intensity reading function. > + intensity_fn = intensity_nmrview > > # Test if the current data pipe exists. > pipes.test() > > Modified: 1.3/prompt/noe.py > URL: > http://svn.gna.org/viewcvs/relax/1.3/prompt/noe.py?rev=7592&r1=7591&r2=7592&view=diff > ============================================================================== > --- 1.3/prompt/noe.py (original) > +++ 1.3/prompt/noe.py Thu Oct 9 19:37:20 2008 > @@ -128,6 +128,7 @@ > The 'format' argument can currently be set to: > 'sparky' > 'xeasy' > + 'nmrview' > > 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, > @@ -142,6 +143,8 @@ > 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 'heteronuc' and 'proton' arguments should be set respectively to > the name of the > > Modified: 1.3/prompt/relax_fit.py > URL: > http://svn.gna.org/viewcvs/relax/1.3/prompt/relax_fit.py?rev=7592&r1=7591&r2=7592&view=diff > ============================================================================== > --- 1.3/prompt/relax_fit.py (original) > +++ 1.3/prompt/relax_fit.py Thu Oct 9 19:37:20 2008 > @@ -126,6 +126,7 @@ > The format argument can currently be set to: > 'sparky' > 'xeasy' > + 'nmrview' > > 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, > @@ -140,6 +141,8 @@ > 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 heteronuc and proton arguments should be set respectively to the > name of the > > Modified: 1.3/specific_fns/noe.py > URL: > http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=7592&r1=7591&r2=7592&view=diff > ============================================================================== > --- 1.3/specific_fns/noe.py (original) > +++ 1.3/specific_fns/noe.py Thu Oct 9 19:37:20 2008 > @@ -113,7 +113,7 @@ > @keyword spectrum_type: The type of spectrum, one of 'ref' or 'sat'. > @type spectrum_type: str > @keyword format: The type of file containing peak intensities. > This can currently be > - one of 'sparky' or 'xeasy'. > + one of 'sparky', 'xeasy' or 'nmrview'. > @type format: str > @keyword heteronuc: The name of the heteronucleus as specified in > the peak intensity > file. > > Modified: 1.3/specific_fns/relax_fit.py > URL: > http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_fit.py?rev=7592&r1=7591&r2=7592&view=diff > ============================================================================== > --- 1.3/specific_fns/relax_fit.py (original) > +++ 1.3/specific_fns/relax_fit.py Thu Oct 9 19:37:20 2008 > @@ -986,7 +986,7 @@ > @keyword relax_time: The time, in seconds, of the relaxation > period. > @type relax_time: float > @keyword format: The type of file containing peak intensities. > This can currently be > - one of 'sparky' or 'xeasy'. > + one of 'sparky', 'xeasy' or 'nmrview'. > @type format: str > @keyword heteronuc: The name of the heteronucleus as specified in > the peak intensity > file. > > Modified: 1.3/test_suite/system_tests/nmrview.py > URL: > http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/nmrview.py?rev=7592&r1=7591&r2=7592&view=diff > ============================================================================== > --- 1.3/test_suite/system_tests/nmrview.py (original) > +++ 1.3/test_suite/system_tests/nmrview.py Thu Oct 9 19:37:20 2008 > @@ -57,7 +57,7 @@ > self.relax.interpreter._Spin.name(name='N') > > # Read the peak list. > - self.relax.interpreter._Relax_fit.read(file="cNTnC.xpk", > dir=sys.path[-1] + "/test_suite/shared_data/peak_lists", relax_time=0.0176) > + self.relax.interpreter._Relax_fit.read(file="cNTnC.xpk", > dir=sys.path[-1] + "/test_suite/shared_data/peak_lists", relax_time=0.0176, > format='nmrview') > > # Test the data. > self.assertEqual(cdp.mol[0].res[0].spin[0].intensities[0], > -6.88333129883) > > > _______________________________________________ > 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
