Hi Ed, I can try to implement the NMRView peak list support...
Regards, Séb Edward d'Auvergne wrote: > 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 > > _______________________________________________ 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
