Great! I'll get to work on Modelfree4 and Dasha then. Cheers,
Edward On Sat, Oct 11, 2008 at 5:46 PM, Sébastien Morin <[EMAIL PROTECTED]> wrote: > 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
