Author: tlinnet Date: Thu Dec 5 22:48:13 2013 New Revision: 21798 URL: http://svn.gna.org/viewcvs/relax?rev=21798&view=rev Log: Created the back end function for the read_spins function.
Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/pipe_control/spectrum.py Modified: trunk/pipe_control/spectrum.py URL: http://svn.gna.org/viewcvs/relax/trunk/pipe_control/spectrum.py?rev=21798&r1=21797&r2=21798&view=diff ============================================================================== --- trunk/pipe_control/spectrum.py (original) +++ trunk/pipe_control/spectrum.py Thu Dec 5 22:48:13 2013 @@ -37,7 +37,7 @@ from lib.statistics import std from lib.warnings import RelaxWarning, RelaxNoSpinWarning from pipe_control import pipes -from pipe_control.mol_res_spin import check_mol_res_spin_data, generate_spin_id_unique, return_spin, spin_loop +from pipe_control.mol_res_spin import check_mol_res_spin_data, create_spin, generate_spin_id_unique, return_spin, spin_loop def __errors_height_no_repl(): @@ -609,6 +609,57 @@ write_data(out=sys.stdout, headings=["Spin_ID", "Intensity"], data=data) +def read_spins(file=None, dir=None, dim=1, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, verbose=True): + """Read the peak intensity data. + + @keyword file: The name of the file containing the peak intensities. + @type file: str + @keyword dir: The directory where the file is located. + @type dir: str + @keyword dim: The dimension of the peak list to associate the data with. + @type dim: int + @keyword spin_id_col: The column containing the spin ID strings (used by the generic intensity file format). If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none. + @type spin_id_col: int or None + @keyword mol_name_col: The column containing the molecule name information (used by the generic intensity file format). If supplied, spin_id_col must be None. + @type mol_name_col: int or None + @keyword res_name_col: The column containing the residue name information (used by the generic intensity file format). If supplied, spin_id_col must be None. + @type res_name_col: int or None + @keyword res_num_col: The column containing the residue number information (used by the generic intensity file format). If supplied, spin_id_col must be None. + @type res_num_col: int or None + @keyword spin_name_col: The column containing the spin name information (used by the generic intensity file format). If supplied, spin_id_col must be None. + @type spin_name_col: int or None + @keyword spin_num_col: The column containing the spin number information (used by the generic intensity file format). If supplied, spin_id_col must be None. + @type spin_num_col: int or None + @keyword sep: The column separator which, if None, defaults to whitespace. + @type sep: str or None + @keyword spin_id: The spin ID string used to restrict data loading to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab formatted file, the ID's are auto generated in form of Z_Ai. + @type spin_id: None or str + @keyword verbose: A flag which if True will cause all relaxation data loaded to be printed out. + @type verbose: bool + """ + + # Data checks. + pipes.test() + + # Check the file name. + if file == None: + raise RelaxError("The file name must be supplied.") + + # Read the peak list data. + peak_list = read_peak_list(file=file, dir=dir, spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col, spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep, spin_id=spin_id) + + # Loop over the peak_list. + for assign in peak_list: + mol_name = assign.mol_names[dim-1] + res_num = assign.res_nums[dim-1] + res_name = assign.res_names[dim-1] + spin_num = assign.spin_nums[dim-1] + spin_name = assign.spin_names[dim-1] + # Create the spin + create_spin(spin_num=spin_num, spin_name=spin_name, res_num=res_num, res_name=res_name, mol_name=mol_name) + + # Test that data exists. + check_mol_res_spin_data() def replicated(spectrum_ids=None): """Set which spectra are replicates. _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org 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
