r21803 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: bugman Date: Fri Dec 6 09:07:56 2013 New Revision: 21803 URL: http://svn.gna.org/viewcvs/relax?rev=21803view=rev Log: Neutralised the negative sign of the 15N gyromagnetic ratio in the return_offset_data() method. This is to match the behaviour of Dmitry Korzhnev's cpmg_fit software. Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21803r1=21802r2=21803view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Fri Dec 6 09:07:56 2013 @@ -2581,6 +2581,11 @@ spin = spins[si] spin_id = spin_ids[si] +# The sign to multiply shifts and offsets by. +sign = 1.0 +if spin.isotope == '15N': +sign = -1.0 + # No data. shift = 0.0 if hasattr(spin, 'chemical_shift'): @@ -2613,7 +2618,7 @@ fields = return_spin_lock_nu1_single(exp_type=exp_type, frq=frq, ref_flag=False) # Convert the shift from ppm to rad/s and store it. -shifts[ei][si][mi] = frequency_to_rad_per_s(frq=shift, B0=frq, isotope=spin.isotope) +shifts[ei][si][mi] = sign * frequency_to_rad_per_s(frq=shift, B0=frq, isotope=spin.isotope) # Find a matching experiment ID. found = False @@ -2641,7 +2646,7 @@ # Store the offset in rad/s. Only once and using the first key. if offsets[ei][si][mi][oi] == None: if r1rho_flag and hasattr(cdp, 'spin_lock_offset'): -offsets[ei][si][mi][oi] = frequency_to_rad_per_s(frq=cdp.spin_lock_offset[id], B0=frq, isotope=spin.isotope) +offsets[ei][si][mi][oi] = sign * frequency_to_rad_per_s(frq=cdp.spin_lock_offset[id], B0=frq, isotope=spin.isotope) else: offsets[ei][si][mi][oi] = 0.0 ___ 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
r21805 - /trunk/user_functions/spectrum.py
Author: tlinnet Date: Fri Dec 6 09:16:21 2013 New Revision: 21805 URL: http://svn.gna.org/viewcvs/relax?rev=21805view=rev Log: Added keyword dim to frontend function for spectrum.read_spins(). Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. This is associate data with the spins of up to two dimensions. Modified: trunk/user_functions/spectrum.py Modified: trunk/user_functions/spectrum.py URL: http://svn.gna.org/viewcvs/relax/trunk/user_functions/spectrum.py?rev=21805r1=21804r2=21805view=diff == --- trunk/user_functions/spectrum.py (original) +++ trunk/user_functions/spectrum.py Fri Dec 6 09:16:21 2013 @@ -384,6 +384,14 @@ can_be_none = True ) uf.add_keyarg( +name = dim, +default = 1, +py_type = int, +min = 1, +desc_short = spectral dimension to read, +desc = Associate the data with the spins of any dimension in the peak list. This defaults to w1, the heteronucleus in HSQC type experiments. +) +uf.add_keyarg( name = spin_id_col, py_type = int, arg_type = free format, @@ -446,6 +454,9 @@ desc = The spin ID string used to restrict the loading of data to certain spin subsets., can_be_none = True ) +# Description. +uf.desc.append(Desc_container()) +uf.desc[-1].add_paragraph(The spectral dimension is used to specify if the intensity data should be loaded into the spins identified by the first dimension w1, second dimension w2, etc.) # File formats. uf.desc.append(Desc_container(File formats)) uf.desc[-1].add_paragraph(The peak list or intensity file will be automatically determined.) ___ 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
r21809 - /trunk/pipe_control/spectrum.py
Author: tlinnet Date: Fri Dec 6 09:16:36 2013 New Revision: 21809 URL: http://svn.gna.org/viewcvs/relax?rev=21809view=rev Log: Insert check if spin already exist, before creating it. 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=21809r1=21808r2=21809view=diff == --- trunk/pipe_control/spectrum.py (original) +++ trunk/pipe_control/spectrum.py Fri Dec 6 09:16:36 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, create_spin, generate_spin_id_unique, return_spin, spin_loop +from pipe_control.mol_res_spin import are_spins_named, check_mol_res_spin_data, create_spin, generate_spin_id_unique, return_spin, spin_loop def __errors_height_no_repl(): @@ -649,14 +649,21 @@ 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. +created_spins = [] 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) + +# Generate the spin_id. +spin_id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_name=spin_name) + +# Check if the spin already exist. +if not are_spins_named(spin_id=spin_id): +# Create the spin if not exist. +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() ___ 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
r21807 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet Date: Fri Dec 6 09:16:34 2013 New Revision: 21807 URL: http://svn.gna.org/viewcvs/relax?rev=21807view=rev Log: Extended reading of spin residue names from NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/nmrpipe.py Modified: trunk/lib/spectrum/nmrpipe.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21807r1=21806r2=21807view=diff == --- trunk/lib/spectrum/nmrpipe.py (original) +++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 09:16:34 2013 @@ -111,7 +111,13 @@ try: res_num = int(row1[-3]) except: -raise RelaxError(Improperly formatted NMRPipe SeriesTab file., cannot process the assignment '%s'. % line[0]) +raise RelaxError(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s'. % line[0]) + +# The residue name. +try: +res_name = row1[-4] +except: +raise RelaxError(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name. % line[0]) # Get the intensities. try: @@ -126,4 +132,4 @@ raise RelaxError(The peak intensity value %s from the line %s is invalid. % (intensity, line)) # Add the assignment to the peak list object. -peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, name2], intensity=intensities, intensity_name=spectra) +peak_list.add(res_nums=[res_num, res_num], res_names=[res_name, res_name], spin_names=[name1, name2], intensity=intensities, intensity_name=spectra) ___ 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
r21808 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet Date: Fri Dec 6 09:16:35 2013 New Revision: 21808 URL: http://svn.gna.org/viewcvs/relax?rev=21808view=rev Log: Modified NMRPipe SeriesTab to read residue numbers and name for two-dimensional list. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/nmrpipe.py Modified: trunk/lib/spectrum/nmrpipe.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21808r1=21807r2=21808view=diff == --- trunk/lib/spectrum/nmrpipe.py (original) +++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 09:16:35 2013 @@ -109,13 +109,15 @@ # Get the residue number. try: -res_num = int(row1[-3]) +res_num1 = int(row1[-3]) +res_num2 = int(row2[-3]) except: raise RelaxError(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s'. % line[0]) # The residue name. try: -res_name = row1[-4] +res_name1 = row1[-4] +res_name2 = row2[-4] except: raise RelaxError(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name. % line[0]) @@ -132,4 +134,4 @@ raise RelaxError(The peak intensity value %s from the line %s is invalid. % (intensity, line)) # Add the assignment to the peak list object. -peak_list.add(res_nums=[res_num, res_num], res_names=[res_name, res_name], spin_names=[name1, name2], intensity=intensities, intensity_name=spectra) +peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1, res_name2], spin_names=[name1, name2], intensity=intensities, intensity_name=spectra) ___ 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
r21813 - /trunk/test_suite/gui_tests/relax_disp.py
Author: tlinnet
Date: Fri Dec 6 09:57:15 2013
New Revision: 21813
URL: http://svn.gna.org/viewcvs/relax?rev=21813view=rev
Log:
Removed name from docstring in GUI test.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/test_suite/gui_tests/relax_disp.py
Modified: trunk/test_suite/gui_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/relax_disp.py?rev=21813r1=21812r2=21813view=diff
==
--- trunk/test_suite/gui_tests/relax_disp.py (original)
+++ trunk/test_suite/gui_tests/relax_disp.py Fri Dec 6 09:57:15 2013
@@ -137,7 +137,7 @@
def test_bug_21076_multi_col_peak_list(self):
-Test catching U{bug #21076https://gna.org/bugs/?21076}, loading a
multi-spectra NMRPipe seriesTab file through the GUI, Error messages occur.
Submitted by Troels E. Linnet.
+Test catching U{bug #21076https://gna.org/bugs/?21076}, loading a
multi-spectra NMRPipe seriesTab file through the GUI, Error messages occur.
# The paths to the data files.
data_path = status.install_path + sep + 'test_suite' + sep +
'shared_data' + sep + 'dispersion' + sep + 'KTeilum_FMPoulsen_MAkke_2006' + sep
+ 'acbp_cpmg_disp_101MGuHCl_40C_041223' + sep
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r21811 - /trunk/lib/spectrum/sparky.py
Author: tlinnet Date: Fri Dec 6 09:57:13 2013 New Revision: 21811 URL: http://svn.gna.org/viewcvs/relax?rev=21811view=rev Log: Issuing a warning instead of error when loading spins from sparky list where residue names are not present. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/sparky.py Modified: trunk/lib/spectrum/sparky.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/sparky.py?rev=21811r1=21810r2=21811view=diff == --- trunk/lib/spectrum/sparky.py (original) +++ trunk/lib/spectrum/sparky.py Fri Dec 6 09:57:13 2013 @@ -134,7 +134,8 @@ try: res_name = row1[-4] except: -raise RelaxError(Improperly formatted Sparky file, cannot process the assignment '%s' for residue name. % line[0]) +raise RelaxWarning(Improperly formatted Sparky file, cannot process the assignment '%s' for residue name.\nSetting residue name to None. % line[0]) +res_name = None # Chemical shifts. w1 = None ___ 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
r21814 - in /trunk: lib/spectrum/sparky.py test_suite/gui_tests/relax_disp.py user_functions/spectrum.py
Author: tlinnet Date: Fri Dec 6 09:57:17 2013 New Revision: 21814 URL: http://svn.gna.org/viewcvs/relax?rev=21814view=rev Log: Added name to Copyrights header of modified files. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/sparky.py trunk/test_suite/gui_tests/relax_disp.py trunk/user_functions/spectrum.py Modified: trunk/lib/spectrum/sparky.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/sparky.py?rev=21814r1=21813r2=21814view=diff == --- trunk/lib/spectrum/sparky.py (original) +++ trunk/lib/spectrum/sparky.py Fri Dec 6 09:57:17 2013 @@ -2,6 +2,7 @@ # # # Copyright (C) 2004-2013 Edward d'Auvergne # # Copyright (C) 2008 Sebastien Morin # +# Copyright (C) 2013 Troels E. Linnet # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # Modified: trunk/test_suite/gui_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/relax_disp.py?rev=21814r1=21813r2=21814view=diff == --- trunk/test_suite/gui_tests/relax_disp.py (original) +++ trunk/test_suite/gui_tests/relax_disp.py Fri Dec 6 09:57:17 2013 @@ -1,6 +1,7 @@ ### # # # Copyright (C) 2013 Edward d'Auvergne# +# Copyright (C) 2013 Troels E. Linnet # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # Modified: trunk/user_functions/spectrum.py URL: http://svn.gna.org/viewcvs/relax/trunk/user_functions/spectrum.py?rev=21814r1=21813r2=21814view=diff == --- trunk/user_functions/spectrum.py (original) +++ trunk/user_functions/spectrum.py Fri Dec 6 09:57:17 2013 @@ -1,6 +1,7 @@ ### # # # Copyright (C) 2004-2013 Edward d'Auvergne # +# Copyright (C) 2004-2013 Troels E. Linnet# # # # This file is part of the program relax (http://www.nmr-relax.com). # # # ___ 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
r21815 - /trunk/pipe_control/spectrum.py
Author: tlinnet Date: Fri Dec 6 09:57:18 2013 New Revision: 21815 URL: http://svn.gna.org/viewcvs/relax?rev=21815view=rev Log: Changed to use return_spin for testing presence of spin. 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=21815r1=21814r2=21815view=diff == --- trunk/pipe_control/spectrum.py (original) +++ trunk/pipe_control/spectrum.py Fri Dec 6 09:57:18 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 are_spins_named, check_mol_res_spin_data, create_spin, 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(): @@ -661,7 +661,7 @@ spin_id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_name=spin_name) # Check if the spin already exist. -if not are_spins_named(spin_id=spin_id): +if return_spin(spin_id=spin_id) == None: # Create the spin if not exist. create_spin(spin_num=spin_num, spin_name=spin_name, res_num=res_num, res_name=res_name, mol_name=mol_name) ___ 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
r21812 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet Date: Fri Dec 6 09:57:14 2013 New Revision: 21812 URL: http://svn.gna.org/viewcvs/relax?rev=21812view=rev Log: Issued a warning instead of error, when loadning spin residue names from a NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/nmrpipe.py Modified: trunk/lib/spectrum/nmrpipe.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21812r1=21811r2=21812view=diff == --- trunk/lib/spectrum/nmrpipe.py (original) +++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 09:57:14 2013 @@ -114,12 +114,19 @@ except: raise RelaxError(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s'. % line[0]) -# The residue name. +# The residue name for dimension 1. try: res_name1 = row1[-4] +except: +raise RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 1.\nSetting residue name to None. % line[0]) +res_name1 = None + +# The residue name for dimension 2. +try: res_name2 = row2[-4] except: -raise RelaxError(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name. % line[0]) +raise RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 2.\nSetting residue name to None. % line[0]) +res_name2 = None # Get the intensities. try: ___ 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
r21810 - /trunk/test_suite/gui_tests/relax_disp.py
Author: tlinnet
Date: Fri Dec 6 09:57:11 2013
New Revision: 21810
URL: http://svn.gna.org/viewcvs/relax?rev=21810view=rev
Log:
Fix for proper spacing and comments in GUI test.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/test_suite/gui_tests/relax_disp.py
Modified: trunk/test_suite/gui_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/relax_disp.py?rev=21810r1=21809r2=21810view=diff
==
--- trunk/test_suite/gui_tests/relax_disp.py (original)
+++ trunk/test_suite/gui_tests/relax_disp.py Fri Dec 6 09:57:11 2013
@@ -178,7 +178,7 @@
analysis.peak_wizard_launch(None)
wizard = analysis.peak_wizard
-# The spectrum, use Keyword auto.
+# The spectrum, where the use of Keyword auto will auto-assign spectra
Z_A{i}.
page = wizard.get_page(wizard.page_indices['read'])
page.uf_args['file'].SetValue(str_to_gui(%sfolded_sparky_corr_final_max_standard_trunc.ser
% data_path))
page.uf_args['spectrum_id'].SetValue(['auto'])
@@ -191,11 +191,16 @@
# Get ID from RMSD window.
page = wizard.get_page(wizard.page_indices['rmsd'])
+
# Flush all wx events (to allow the spectrum list GUI element to
populate all its rows).
wx.Yield()
-# Get the ID
+
+# Get the first ID from list.
cur_id = page.uf_args['spectrum_id'].GetValue()
+
+# Now check that the first is set to 'Z_A0', since the keyword 'auto'
was used for spectrum_id.
self.assertEqual(cur_id, 'Z_A0')
+
def test_hansen_trunc_data(self):
Test the GUI analysis with Flemming Hansen's CPMG data truncated to
residues 70 and 71.
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r21819 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 11:09:21 2013 New Revision: 21819 URL: http://svn.gna.org/viewcvs/relax?rev=21819view=rev Log: Implemented system test for reading spin ID's from NMRView formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21819r1=21818r2=21819view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 11:09:21 2013 @@ -139,6 +139,37 @@ # Check the values. for i in range(len(times)): self.assertEqual(spin.intensities[names[i]], heights[index][i]) + + +def test_read_spins_peak_list_nmrview(self): +Test the reading of an NMRView peak list. + +# Read the peak list. +self.interpreter.spectrum.read_spins(file=cNTnC.xpk, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) +self.interpreter.spectrum.read_spins(file=cNTnC.xpk, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 2) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 70) +self.assertEqual(cdp.mol[0].res[0].name, None) +self.assertEqual(len(cdp.mol[0].res[0].spin), 2) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HN') + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 72) +self.assertEqual(cdp.mol[0].res[1].name, None) +self.assertEqual(len(cdp.mol[0].res[1].spin), 2) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[1].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'HN') def test_read_spins_peak_list_NMRPipe_seriesTab(self): ___ 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
r21820 - /trunk/lib/spectrum/nmrview.py
Author: tlinnet
Date: Fri Dec 6 11:09:22 2013
New Revision: 21820
URL: http://svn.gna.org/viewcvs/relax?rev=21820view=rev
Log:
Made reading of NMRView formatted file return the residue number as integer
instead of string.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/lib/spectrum/nmrview.py
Modified: trunk/lib/spectrum/nmrview.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrview.py?rev=21820r1=21819r2=21820view=diff
==
--- trunk/lib/spectrum/nmrview.py (original)
+++ trunk/lib/spectrum/nmrview.py Fri Dec 6 11:09:22 2013
@@ -80,7 +80,7 @@
res_num = line[1].strip('{')
res_num = res_num.strip('}')
res_num = res_num.split('.')
-res_num = res_num[0]
+res_num = int(res_num[0])
except ValueError:
raise RelaxError(The peak list is invalid.)
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r21818 - /trunk/lib/spectrum/sparky.py
Author: tlinnet Date: Fri Dec 6 11:09:19 2013 New Revision: 21818 URL: http://svn.gna.org/viewcvs/relax?rev=21818view=rev Log: Fix for issuing a warning when reading spins from a sparky formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/sparky.py Modified: trunk/lib/spectrum/sparky.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/sparky.py?rev=21818r1=21817r2=21818view=diff == --- trunk/lib/spectrum/sparky.py (original) +++ trunk/lib/spectrum/sparky.py Fri Dec 6 11:09:19 2013 @@ -27,10 +27,12 @@ # Python module imports. from re import split +from warnings import warn # relax module imports. from lib.errors import RelaxError from lib.io import open_write_file, strip +from lib.warnings import RelaxWarning def read_list(peak_list=None, file_data=None): @@ -135,7 +137,7 @@ try: res_name = row1[-4] except: -raise RelaxWarning(Improperly formatted Sparky file, cannot process the assignment '%s' for residue name.\nSetting residue name to None. % line[0]) +raise warn(RelaxWarning(Improperly formatted Sparky file, cannot process the assignment '%s' for residue name.\nSetting residue name to None. % line[0])) res_name = None # Chemical shifts. ___ 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
r21817 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet Date: Fri Dec 6 11:09:17 2013 New Revision: 21817 URL: http://svn.gna.org/viewcvs/relax?rev=21817view=rev Log: Fix for issuing a warning in reading spins from a NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/nmrpipe.py Modified: trunk/lib/spectrum/nmrpipe.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21817r1=21816r2=21817view=diff == --- trunk/lib/spectrum/nmrpipe.py (original) +++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 11:09:17 2013 @@ -25,10 +25,12 @@ # Python module imports. import re +from warnings import warn # relax module imports. from lib.errors import RelaxError from lib.io import open_write_file, strip +from lib.warnings import RelaxWarning def read_seriestab(peak_list=None, file_data=None, int_col=None): @@ -118,14 +120,14 @@ try: res_name1 = row1[-4] except: -raise RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 1.\nSetting residue name to None. % line[0]) +raise warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 1.\nSetting residue name to None. % line[0])) res_name1 = None # The residue name for dimension 2. try: res_name2 = row2[-4] except: -raise RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 2.\nSetting residue name to None. % line[0]) +raise warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 2.\nSetting residue name to None. % line[0])) res_name2 = None # Get the intensities. ___ 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
r21816 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 11:09:16 2013 New Revision: 21816 URL: http://svn.gna.org/viewcvs/relax?rev=21816view=rev Log: Implemented another system test for reading NMRPipe SeriesTab files. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21816r1=21815r2=21816view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 11:09:16 2013 @@ -139,6 +139,46 @@ # Check the values. for i in range(len(times)): self.assertEqual(spin.intensities[names[i]], heights[index][i]) + + +def test_read_spins_peak_list_NMRPipe_seriesTab(self): +Test the reading of an NMRPipe seriesTab peak list. + +# Read the peak list. +self.interpreter.spectrum.read_spins(file=seriesTab.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) +self.interpreter.spectrum.read_spins(file=seriesTab.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 3) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 62) +self.assertEqual(cdp.mol[0].res[0].name, 'W') +self.assertEqual(len(cdp.mol[0].res[0].spin), 2) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'NE1') +self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HE1') + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 10) +self.assertEqual(cdp.mol[0].res[1].name, 'L') +self.assertEqual(len(cdp.mol[0].res[1].spin), 2) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[1].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'HN') + +# 3rd residue. +self.assertEqual(cdp.mol[0].res[2].num, 6) +self.assertEqual(cdp.mol[0].res[2].name, 'V') +self.assertEqual(len(cdp.mol[0].res[2].spin), 2) +self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[2].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'HN') def test_read_spins_peak_list_NMRPipe_seriesTab_multi(self): ___ 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
r21821 - in /trunk/lib/spectrum: nmrpipe.py sparky.py
Author: tlinnet Date: Fri Dec 6 11:26:35 2013 New Revision: 21821 URL: http://svn.gna.org/viewcvs/relax?rev=21821view=rev Log: Fix for calling the warn() function. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/nmrpipe.py trunk/lib/spectrum/sparky.py Modified: trunk/lib/spectrum/nmrpipe.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21821r1=21820r2=21821view=diff == --- trunk/lib/spectrum/nmrpipe.py (original) +++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 11:26:35 2013 @@ -120,7 +120,7 @@ try: res_name1 = row1[-4] except: -raise warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 1.\nSetting residue name to None. % line[0])) +warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the assignment '%s' for residue name dimension 1. Setting residue name to None. % line[0])) res_name1 = None # The residue name for dimension 2. Modified: trunk/lib/spectrum/sparky.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/sparky.py?rev=21821r1=21820r2=21821view=diff == --- trunk/lib/spectrum/sparky.py (original) +++ trunk/lib/spectrum/sparky.py Fri Dec 6 11:26:35 2013 @@ -137,7 +137,7 @@ try: res_name = row1[-4] except: -raise warn(RelaxWarning(Improperly formatted Sparky file, cannot process the assignment '%s' for residue name.\nSetting residue name to None. % line[0])) +warn(RelaxWarning(Improperly formatted Sparky file, cannot process the assignment '%s' for residue name. Setting residue name to None. % line[0])) res_name = None # Chemical shifts. ___ 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
r21822 - /trunk/lib/spectrum/nmrview.py
Author: tlinnet
Date: Fri Dec 6 11:31:10 2013
New Revision: 21822
URL: http://svn.gna.org/viewcvs/relax?rev=21822view=rev
Log:
Extended the error description for reading NMRView files.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/lib/spectrum/nmrview.py
Modified: trunk/lib/spectrum/nmrview.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrview.py?rev=21822r1=21821r2=21822view=diff
==
--- trunk/lib/spectrum/nmrview.py (original)
+++ trunk/lib/spectrum/nmrview.py Fri Dec 6 11:31:10 2013
@@ -82,7 +82,7 @@
res_num = res_num.split('.')
res_num = int(res_num[0])
except ValueError:
-raise RelaxError(The peak list is invalid.)
+raise RelaxError(Improperly formatted NMRView file, cannot
process the assignment '%s'. % line[0])
# Nuclei names.
name2 = ''
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r21823 - /trunk/lib/spectrum/nmrview.py
Author: tlinnet
Date: Fri Dec 6 11:32:27 2013
New Revision: 21823
URL: http://svn.gna.org/viewcvs/relax?rev=21823view=rev
Log:
Fix for print statement.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/lib/spectrum/nmrview.py
Modified: trunk/lib/spectrum/nmrview.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrview.py?rev=21823r1=21822r2=21823view=diff
==
--- trunk/lib/spectrum/nmrview.py (original)
+++ trunk/lib/spectrum/nmrview.py Fri Dec 6 11:32:27 2013
@@ -82,7 +82,7 @@
res_num = res_num.split('.')
res_num = int(res_num[0])
except ValueError:
-raise RelaxError(Improperly formatted NMRView file, cannot
process the assignment '%s'. % line[0])
+raise RelaxError(Improperly formatted NMRView file, cannot
process the assignment '%s'. % line[1])
# Nuclei names.
name2 = ''
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r21824 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 12:09:54 2013 New Revision: 21824 URL: http://svn.gna.org/viewcvs/relax?rev=21824view=rev Log: Implemented system test for reading spins from a NMRPipe SeriesTab formatted file, where the assignments for second dimension is missing. This will be a typically export from SPARKY, converted to NMRPipe format, and proÂcessed with SeriesTab. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21824r1=21823r2=21824view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 12:09:54 2013 @@ -253,6 +253,33 @@ self.assertEqual(len(cdp.mol[0].res[3].spin), 1) self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') + + +def test_read_spins_peak_list_NMRPipe_seriesTab_multi_no_2dim(self): +Test the reading of an NMRPipe seriesTab peak list, with no assignment for second dimension. + +# Read the peak list. + self.interpreter.spectrum.read_spins(file=folded_sparky_corr_final_max_standard_trunc.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+'acbp_cpmg_disp_101MGuHCl_40C_041223', dim=1) + self.interpreter.spectrum.read_spins(file=folded_sparky_corr_final_max_standard_trunc.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+'acbp_cpmg_disp_101MGuHCl_40C_041223', dim=2) + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 2) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 61) +self.assertEqual(cdp.mol[0].res[0].name, 'L') +self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') + +# 2nd residue, which is a None residue. +self.assertEqual(cdp.mol[0].res[1].num, None) +self.assertEqual(cdp.mol[0].res[1].name, None) +self.assertEqual(len(cdp.mol[0].res[1].spin), 1) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'HN') def test_read_spins_peak_list_sparky(self): ___ 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
r21825 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet
Date: Fri Dec 6 12:09:56 2013
New Revision: 21825
URL: http://svn.gna.org/viewcvs/relax?rev=21825view=rev
Log:
Fixed for reading spins from a NMRPipe SeriesTab formatted file, where
dimension 2 misses residue number and residue name.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/lib/spectrum/nmrpipe.py
Modified: trunk/lib/spectrum/nmrpipe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21825r1=21824r2=21825view=diff
==
--- trunk/lib/spectrum/nmrpipe.py (original)
+++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 12:09:56 2013
@@ -109,25 +109,32 @@
row2 = re.split('([a-zA-Z]+)', assign2)
name2 = row2[-2] + row2[-1]
-# Get the residue number.
+# Get the residue number for dimension 1.
try:
res_num1 = int(row1[-3])
+except:
+raise RelaxError(Improperly formatted NMRPipe SeriesTab file,
cannot process the residue number for dimension 1 in assignment: %s. % line[0])
+
+# Get the residue number for dimension 2.
+try:
res_num2 = int(row2[-3])
except:
-raise RelaxError(Improperly formatted NMRPipe SeriesTab file,
cannot process the assignment '%s'. % line[0])
+# We cannot always expect dimension 2 to have residue number.
+warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file,
cannot process the residue number for dimension 2 in assignment: %s. Setting
residue number to None. % line[0]))
+res_num2 = None
# The residue name for dimension 1.
try:
res_name1 = row1[-4]
except:
-warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file,
cannot process the assignment '%s' for residue name dimension 1. Setting
residue name to None. % line[0]))
+warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file,
cannot process the residue name for dimension 1 in assignment: %s. % line[0]))
res_name1 = None
# The residue name for dimension 2.
try:
res_name2 = row2[-4]
except:
-raise warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab
file, cannot process the assignment '%s' for residue name dimension 2.\nSetting
residue name to None. % line[0]))
+warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file,
cannot process the residue name for dimension 2 in assignment: %s. Setting
residue name to None. % line[0]))
res_name2 = None
# Get the intensities.
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r21826 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet Date: Fri Dec 6 12:12:43 2013 New Revision: 21826 URL: http://svn.gna.org/viewcvs/relax?rev=21826view=rev Log: Expanded the warning message for a systemtest. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/nmrpipe.py Modified: trunk/lib/spectrum/nmrpipe.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21826r1=21825r2=21826view=diff == --- trunk/lib/spectrum/nmrpipe.py (original) +++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 12:12:43 2013 @@ -127,7 +127,7 @@ try: res_name1 = row1[-4] except: -warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue name for dimension 1 in assignment: %s. % line[0])) +warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue name for dimension 1 in assignment: %s. Setting residue name to None. % line[0])) res_name1 = None # The residue name for dimension 2. ___ 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
r21828 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet Date: Fri Dec 6 13:20:23 2013 New Revision: 21828 URL: http://svn.gna.org/viewcvs/relax?rev=21828view=rev Log: If dimension 2 in a SeriesTab formatted file does not contain residue number+name, it defaults to the dimension 1. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/nmrpipe.py Modified: trunk/lib/spectrum/nmrpipe.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21828r1=21827r2=21828view=diff == --- trunk/lib/spectrum/nmrpipe.py (original) +++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 13:20:23 2013 @@ -110,9 +110,11 @@ name2 = row2[-2] + row2[-1] # Get the residue number for dimension 1. +got_res_num1 = True try: res_num1 = int(row1[-3]) except: +got_res_num1 = False raise RelaxError(Improperly formatted NMRPipe SeriesTab file, cannot process the residue number for dimension 1 in assignment: %s. % line[0]) # Get the residue number for dimension 2. @@ -120,22 +122,31 @@ res_num2 = int(row2[-3]) except: # We cannot always expect dimension 2 to have residue number. -warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue number for dimension 2 in assignment: %s. Setting residue number to None. % line[0])) -res_num2 = None +if got_res_num1: +res_num2 = res_num1 +else: +res_num2 = None +warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue number for dimension 2 in assignment: %s. Setting residue number to %s. % (line[0], res_num2))) # The residue name for dimension 1. +got_res_name1 = True try: res_name1 = row1[-4] except: -warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue name for dimension 1 in assignment: %s. Setting residue name to None. % line[0])) +got_res_name1 = False res_name1 = None +warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue name for dimension 1 in assignment: %s. Setting residue name to %s. % (line[0], res_name1))) # The residue name for dimension 2. try: res_name2 = row2[-4] except: -warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue name for dimension 2 in assignment: %s. Setting residue name to None. % line[0])) -res_name2 = None +# We cannot always expect dimension 2 to have residue name. +if got_res_name1: +res_name2 = res_name1 +else: +res_name2 = None +warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab file, cannot process the residue name for dimension 2 in assignment: %s. Setting residue name to %s. % (line[0], res_name2))) # Get the intensities. try: ___ 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
r21827 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 13:20:22 2013 New Revision: 21827 URL: http://svn.gna.org/viewcvs/relax?rev=21827view=rev Log: Modified system test for reading an assignment, where the second dimension is missing. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21827r1=21826r2=21827view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 13:20:22 2013 @@ -265,21 +265,16 @@ # Test some of the sequence. self.assertEqual(len(cdp.mol), 1) self.assertEqual(cdp.mol[0].name, None) -self.assertEqual(len(cdp.mol[0].res), 2) +self.assertEqual(len(cdp.mol[0].res), 1) # 1st residue. self.assertEqual(cdp.mol[0].res[0].num, 61) self.assertEqual(cdp.mol[0].res[0].name, 'L') -self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(len(cdp.mol[0].res[0].spin), 2) self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') - -# 2nd residue, which is a None residue. -self.assertEqual(cdp.mol[0].res[1].num, None) -self.assertEqual(cdp.mol[0].res[1].name, None) -self.assertEqual(len(cdp.mol[0].res[1].spin), 1) -self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) -self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'HN') +self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HN') def test_read_spins_peak_list_sparky(self): ___ 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
r21830 - /trunk/lib/spectrum/xeasy.py
Author: tlinnet Date: Fri Dec 6 13:23:30 2013 New Revision: 21830 URL: http://svn.gna.org/viewcvs/relax?rev=21830view=rev Log: Modified xeasy reading function to pass residue names back. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/xeasy.py Modified: trunk/lib/spectrum/xeasy.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/xeasy.py?rev=21830r1=21829r2=21830view=diff == --- trunk/lib/spectrum/xeasy.py (original) +++ trunk/lib/spectrum/xeasy.py Fri Dec 6 13:23:30 2013 @@ -2,6 +2,7 @@ # # # Copyright (C) 2004-2013 Edward d'Auvergne # # Copyright (C) 2008 Sebastien Morin # +# Copyright (C) 2013 Troels E. Linnet # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -24,9 +25,13 @@ Module containing functions for handling XEasy files. +# Python module imports. +from warnings import warn + # relax module imports. from lib.errors import RelaxError from lib.io import strip +from lib.warnings import RelaxWarning def read_list(peak_list=None, file_data=None, int_col=None): @@ -46,6 +51,8 @@ w2_col = 2 ass_w1_col = 7 ass_w2_col = 4 +res_name1_col = 9 +res_name2_col = 5 if int_col == None: int_col = 10 @@ -75,15 +82,26 @@ if line[ass_w1_col] == 'inv.' or line[ass_w2_col] == 'inv.': continue -# The residue number. +# The residue number for dimension 1. try: -res_num = int(line[5]) +res_num1 = int(line[8]) except: -raise RelaxError(Improperly formatted XEasy file, cannot read the line %s. % line) +raise RelaxError(Improperly formatted XEasy file, cannot process the residue number for dimension 1 in assignment: %s. % line) + +# The residue number for dimension 2. +try: +res_num2 = int(line[5]) +except: +warn(RelaxWarning(Improperly formatted XEasy file, cannot process the residue number for dimension 2 in assignment: %s. Setting residue number to None. % line)) +res_num2 = None # Nuclei names. name1 = line[ass_w1_col] name2 = line[ass_w2_col] + +# Residue names. +res_name1 = line[res_name1_col] +res_name2 = line[res_name2_col] # Chemical shifts. try: @@ -102,4 +120,4 @@ raise RelaxError(The peak intensity value from the line %s is invalid. % line) # Add the assignment to the peak list object. -peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity) +peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1, res_name2], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity) ___ 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
r21829 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 13:23:29 2013 New Revision: 21829 URL: http://svn.gna.org/viewcvs/relax?rev=21829view=rev Log: Implemented system test for reading spins from an xeasy file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21829r1=21828r2=21829view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 13:23:29 2013 @@ -331,6 +331,49 @@ self.assertEqual(len(cdp.mol[0].res[5].spin), 1) self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') + + +def test_read_spins_peak_list_xeasy(self): +Test the reading of spins from an XEasy peak list. + +# Read the peak list. +self.interpreter.spectrum.read_spins(file=xeasy_r1_20ms.text, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 21) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 21) +self.assertEqual(cdp.mol[0].res[0].name, 'LEU') +self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 79) +self.assertEqual(cdp.mol[0].res[1].name, 'TRP') +self.assertEqual(len(cdp.mol[0].res[1].spin), 1) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'NE1') + +# 3rd residue. +self.assertEqual(cdp.mol[0].res[2].num, 110) +self.assertEqual(cdp.mol[0].res[2].name, 'PHE') +self.assertEqual(len(cdp.mol[0].res[2].spin), 1) +self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') + +# 10th residue. +self.assertEqual(cdp.mol[0].res[9].num, 107) +self.assertEqual(cdp.mol[0].res[9].name, 'TRP') +self.assertEqual(len(cdp.mol[0].res[9].spin), 2) +self.assertEqual(cdp.mol[0].res[9].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[9].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[9].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[9].spin[1].name, 'C') + def test_read_peak_list_generic(self): Test the reading of a generic peak intensity list. ___ 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
r21831 - /trunk/test_suite/shared_data/peak_lists/sparky2dim.list
Author: tlinnet Date: Fri Dec 6 14:08:34 2013 New Revision: 21831 URL: http://svn.gna.org/viewcvs/relax?rev=21831view=rev Log: Copyied SeriesTab file for implementation of double assignment in sparky files. Added: trunk/test_suite/shared_data/peak_lists/sparky2dim.list - copied unchanged from r21830, trunk/test_suite/shared_data/peak_lists/seriesTab.ser ___ 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
r21832 - in /trunk: specific_analyses/relax_disp/ target_functions/
Author: bugman Date: Fri Dec 6 14:52:31 2013 New Revision: 21832 URL: http://svn.gna.org/viewcvs/relax?rev=21832view=rev Log: Redesign of the CPMG frequency and spin-lock field strength data structures. These now have an extra dimension for the offset so that the values are now experiment, magnetic field strength and offset dependent. If many offsets are present but are variable for each dispersion point, then this saves a lot of calculation time. This mainly affects R1rho-type data. To better handle this, all of the specific_analyses.relax_disp.disp_data.loop_*() functions have been modified to accept data values rather than indices. Modified: trunk/specific_analyses/relax_disp/catia.py trunk/specific_analyses/relax_disp/disp_data.py trunk/specific_analyses/relax_disp/optimisation.py trunk/specific_analyses/relax_disp/sherekhan.py trunk/target_functions/relax_disp.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/specific_analyses/relax_disp/catia.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/catia.py?rev=21832r1=21831r2=21832view=diff Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21832r1=21831r2=21832view=diff Modified: trunk/specific_analyses/relax_disp/optimisation.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=21832r1=21831r2=21832view=diff Modified: trunk/specific_analyses/relax_disp/sherekhan.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/sherekhan.py?rev=21832r1=21831r2=21832view=diff Modified: trunk/target_functions/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=21832r1=21831r2=21832view=diff ___ 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
r21833 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: bugman Date: Fri Dec 6 15:03:48 2013 New Revision: 21833 URL: http://svn.gna.org/viewcvs/relax?rev=21833view=rev Log: Fix for a bug introduced in the last commit (r21832). Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21833r1=21832r2=21833view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Fri Dec 6 15:03:48 2013 @@ -3008,9 +3008,9 @@ # Convert to numpy arrays. relax_times = array(relax_times, float64) -for ei in range(exp_num): +for exp_type, ei in loop_exp(return_indices=True): for si in range(spin_num): -for mi in range(field_count): +for frq, mi in loop_frq(return_indices=True): for offset, oi in loop_offset(exp_type=exp_type, frq=frq, return_indices=True): values[ei][si][mi][oi] = array(values[ei][si][mi][oi], float64) errors[ei][si][mi][oi] = array(errors[ei][si][mi][oi], float64) ___ 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
r21834 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: bugman Date: Fri Dec 6 15:06:18 2013 New Revision: 21834 URL: http://svn.gna.org/viewcvs/relax?rev=21834view=rev Log: Reverted r21803 as this change was rubbish. The command used was: svn merge -r21803:r21802 . . r21803 | bugman | 2013-12-06 09:07:56 +0100 (Fri, 06 Dec 2013) | 5 lines Changed paths: M /trunk/specific_analyses/relax_disp/disp_data.py Neutralised the negative sign of the 15N gyromagnetic ratio in the return_offset_data() method. This is to match the behaviour of Dmitry Korzhnev's cpmg_fit software. . Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21834r1=21833r2=21834view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Fri Dec 6 15:06:18 2013 @@ -2636,11 +2636,6 @@ spin = spins[si] spin_id = spin_ids[si] -# The sign to multiply shifts and offsets by. -sign = 1.0 -if spin.isotope == '15N': -sign = -1.0 - # No data. shift = 0.0 if hasattr(spin, 'chemical_shift'): @@ -2673,7 +2668,7 @@ fields = return_spin_lock_nu1_single(exp_type=exp_type, frq=frq, offset=offset, ref_flag=False) # Convert the shift from ppm to rad/s and store it. -shifts[ei][si][mi] = sign * frequency_to_rad_per_s(frq=shift, B0=frq, isotope=spin.isotope) +shifts[ei][si][mi] = frequency_to_rad_per_s(frq=shift, B0=frq, isotope=spin.isotope) # Find a matching experiment ID. found = False @@ -2701,7 +2696,7 @@ # Store the offset in rad/s. Only once and using the first key. if offsets[ei][si][mi][oi] == None: if r1rho_flag and hasattr(cdp, 'spin_lock_offset'): -offsets[ei][si][mi][oi] = sign * frequency_to_rad_per_s(frq=cdp.spin_lock_offset[id], B0=frq, isotope=spin.isotope) +offsets[ei][si][mi][oi] = frequency_to_rad_per_s(frq=cdp.spin_lock_offset[id], B0=frq, isotope=spin.isotope) else: offsets[ei][si][mi][oi] = 0.0 ___ 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
r21835 - /trunk/specific_analyses/relax_disp/disp_data.py
Author: bugman Date: Fri Dec 6 15:09:48 2013 New Revision: 21835 URL: http://svn.gna.org/viewcvs/relax?rev=21835view=rev Log: Improved the printout of the relax_disp.r2eff_read_spin user function for the R2eff keys. Modified: trunk/specific_analyses/relax_disp/disp_data.py Modified: trunk/specific_analyses/relax_disp/disp_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21835r1=21834r2=21835view=diff == --- trunk/specific_analyses/relax_disp/disp_data.py (original) +++ trunk/specific_analyses/relax_disp/disp_data.py Fri Dec 6 15:09:48 2013 @@ -2189,9 +2189,9 @@ # Append the data for printout. if disp_point_col != None: -data.append([%20.15f % disp_point, %20.15f % value, %20.15f % error]) +data.append([%-40s % point_key, %20.15f % disp_point, %20.15f % value, %20.15f % error]) else: -data.append([%20.15f % offset, %20.15f % value, %20.15f % error, point_key]) +data.append([%-40s % point_key, %20.15f % offset, %20.15f % value, %20.15f % error]) # Data added. data_flag = True @@ -2203,9 +2203,9 @@ # Print out. print(The following R2eff/R1rho data has been loaded into the relax data store:\n) if disp_point_col != None: -write_data(out=sys.stdout, headings=[Disp_point, R2eff, R2eff_error], data=data) +write_data(out=sys.stdout, headings=[R2eff_key, Disp_point, R2eff, R2eff_error], data=data) else: -write_data(out=sys.stdout, headings=[Offset (ppm), R2eff, R2eff_error, key], data=data) +write_data(out=sys.stdout, headings=[R2eff_key, Offset (ppm), R2eff, R2eff_error], data=data) def randomise_R1(spin=None, ri_id=None, N=None): ___ 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
r21837 - /trunk/test_suite/shared_data/peak_lists/sparky2dim.list
Author: tlinnet Date: Fri Dec 6 15:35:07 2013 New Revision: 21837 URL: http://svn.gna.org/viewcvs/relax?rev=21837view=rev Log: Modified sparky peak list for two dimensional assignment example. This will typically be the export from CcpNmr Analysis. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/shared_data/peak_lists/sparky2dim.list Modified: trunk/test_suite/shared_data/peak_lists/sparky2dim.list URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/peak_lists/sparky2dim.list?rev=21837r1=21836r2=21837view=diff == --- trunk/test_suite/shared_data/peak_lists/sparky2dim.list (original) +++ trunk/test_suite/shared_data/peak_lists/sparky2dim.list Fri Dec 6 15:35:07 2013 @@ -1,16 +1,9 @@ -REMARK SeriesTab Input: ../peaks.dat Output: ../peaks_0.ser -REMARK Mode: Summation Dimensions: 2 -REMARK Input Region:X +/- 1 X-ZF: 3 -REMARK Analysis Region: X +/- 1 -REMARK Input Region:Y +/- 1 Y-ZF: 3 -REMARK Analysis Region: Y +/- 1 + Assignment w1 w2 Data Height -VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0 -FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s %7.4f - -NULLVALUE -666 -NULLSTRING * - -1 246.65818.2689.932 128.374 +1.851056e+06 W62NE1-W62HE1 1. -2 321.69830.9949.419 127.066 +3.224387e+05 L10N-L10HN 1. -3 320.08955.7379.430 124.523 +1.479366e+06 V6N-V6HN 1. + W62NE1-W62HE1128.374 9.932 +1.851056e+06 + L10N-L10HN127.066 9.419 +3.224387e+05 +V6N-V6HN124.523 9.430 +1.479366e+06 +T2N-T2HN115.994 8.521 +1.179448e+06 +K3N-T2HN125.899 8.695 +4.407306e+06 +A4N-T2HN123.001 9.123 +3.480382e+06 +V5N-T2HN120.839 9.444 +4.306408e+06 ___ 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
r21839 - /trunk/lib/spectrum/sparky.py
Author: tlinnet
Date: Fri Dec 6 15:35:10 2013
New Revision: 21839
URL: http://svn.gna.org/viewcvs/relax?rev=21839view=rev
Log:
Extended reading of spins from sparky files for up to two dimensional
assignments.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/lib/spectrum/sparky.py
Modified: trunk/lib/spectrum/sparky.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/sparky.py?rev=21839r1=21838r2=21839view=diff
==
--- trunk/lib/spectrum/sparky.py (original)
+++ trunk/lib/spectrum/sparky.py Fri Dec 6 15:35:10 2013
@@ -127,18 +127,44 @@
row4 = split('([a-zA-Z]+)', assign4)
name4 = row4[-2] + row4[-1]
-# The residue number.
-try:
-res_num = int(row1[-3])
-except:
-raise RelaxError(Improperly formatted Sparky file, cannot process
the assignment '%s'. % line[0])
-
-# The residue name.
-try:
-res_name = row1[-4]
-except:
-warn(RelaxWarning(Improperly formatted Sparky file, cannot
process the assignment '%s' for residue name. Setting residue name to None. %
line[0]))
-res_name = None
+# Get the residue number for dimension 1.
+got_res_num1 = True
+try:
+res_num1 = int(row1[-3])
+except:
+got_res_num1 = False
+raise RelaxError(Improperly formatted Sparky file, cannot process
the residue number for dimension 1 in assignment: %s. % line[0])
+
+# Get the residue number for dimension 2.
+try:
+res_num2 = int(row2[-3])
+except:
+# We cannot always expect dimension 2 to have residue number.
+if got_res_num1:
+res_num2 = res_num1
+else:
+res_num2 = None
+warn(RelaxWarning(Improperly formatted Sparky file, cannot
process the residue number for dimension 2 in assignment: %s. Setting residue
number to %s. % (line[0], res_num2)))
+
+# The residue name for dimension 1.
+got_res_name1 = True
+try:
+res_name1 = row1[-4]
+except:
+got_res_name1 = False
+res_name1 = None
+warn(RelaxWarning(Improperly formatted Sparky file, cannot
process the residue name for dimension 1 in assignment: %s. Setting residue
name to %s. % (line[0], res_name1)))
+
+# The residue name for dimension 2.
+try:
+res_name2 = row2[-4]
+except:
+# We cannot always expect dimension 2 to have residue name.
+if got_res_name1:
+res_name2 = res_name1
+else:
+res_name2 = None
+warn(RelaxWarning(Improperly formatted NMRPipe SeriesTab
file, cannot process the residue name for dimension 2 in assignment: %s.
Setting residue name to %s. % (line[0], res_name2)))
# Chemical shifts.
w1 = None
@@ -175,13 +201,13 @@
# Add the assignment to the peak list object.
if dim == 1:
-peak_list.add(res_nums=[res_num], res_names=[res_name],
spin_names=[name1], shifts=[w1], intensity=intensity)
+peak_list.add(res_nums=[res_num1], res_names=[res_name1],
spin_names=[name1], shifts=[w1], intensity=intensity)
elif dim == 2:
-peak_list.add(res_nums=[res_num, res_num], res_names=[res_name,
res_name], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity)
+peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1,
res_name2], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity)
elif dim == 3:
-peak_list.add(res_nums=[res_num, res_num, res_num],
res_names=[res_name, res_name, res_name], spin_names=[name1, name2, name3],
shifts=[w1, w2, w3], intensity=intensity)
+peak_list.add(res_nums=[res_num1, res_num2, res_num1],
res_names=[res_name1, res_name2, res_name1], spin_names=[name1, name2, name3],
shifts=[w1, w2, w3], intensity=intensity)
elif dim == 4:
-peak_list.add(res_nums=[res_num, res_num, res_num, res_num],
res_names=[res_name, res_name, res_name, res_name], spin_names=[name1, name2,
name3, name4], shifts=[w1, w2, w3, w4], intensity=intensity)
+peak_list.add(res_nums=[res_num1, res_num2, res_num1, res_num1],
res_names=[res_name1, res_name2, res_name1, res_name1], spin_names=[name1,
name2, name3, name4], shifts=[w1, w2, w3, w4], intensity=intensity)
def write_list(file_prefix=None, dir=None, res_names=None, res_nums=None,
atom1_names=None, atom2_names=None, w1=None, w2=None, data_height=None,
force=True):
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r21838 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 15:35:08 2013 New Revision: 21838 URL: http://svn.gna.org/viewcvs/relax?rev=21838view=rev Log: Implemented system test for using double assignments in sparky formatted files. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21838r1=21837r2=21838view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 15:35:08 2013 @@ -334,6 +334,76 @@ self.assertEqual(len(cdp.mol[0].res[5].spin), 2) self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') + + +def test_read_spins_peak_list_sparky_with_2dim_ass(self): +Test the reading of spins from a Sparky peak list with two dimensional assignment + +# Read the spins from peak list. +self.interpreter.spectrum.read_spins(file=sparky2dim.list, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) +self.interpreter.spectrum.read_spins(file=sparky2dim.list, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 7) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 62) +self.assertEqual(cdp.mol[0].res[0].name, 'W') +self.assertEqual(len(cdp.mol[0].res[0].spin), 2) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'NE1') +self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HE1') + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 10) +self.assertEqual(cdp.mol[0].res[1].name, 'L') +self.assertEqual(len(cdp.mol[0].res[1].spin), 2) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[1].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'HN') + +# 3rd residue. +self.assertEqual(cdp.mol[0].res[2].num, 6) +self.assertEqual(cdp.mol[0].res[2].name, 'V') +self.assertEqual(len(cdp.mol[0].res[2].spin), 2) +self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[2].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[1].name, 'HN') + +# 4th residue. +self.assertEqual(cdp.mol[0].res[3].num, 2) +self.assertEqual(cdp.mol[0].res[3].name, 'T') +self.assertEqual(len(cdp.mol[0].res[3].spin), 2) +self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[3].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[3].spin[1].name, 'HN') + +# 5th residue. +self.assertEqual(cdp.mol[0].res[4].num, 3) +self.assertEqual(cdp.mol[0].res[4].name, 'K') +self.assertEqual(len(cdp.mol[0].res[4].spin), 1) +self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') + +# 6th residue. +self.assertEqual(cdp.mol[0].res[5].num, 4) +self.assertEqual(cdp.mol[0].res[5].name, 'A') +self.assertEqual(len(cdp.mol[0].res[5].spin), 1) +self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') + +# 7th residue. +self.assertEqual(cdp.mol[0].res[6].num, 5) +self.assertEqual(cdp.mol[0].res[6].name, 'V') +self.assertEqual(len(cdp.mol[0].res[6].spin), 1) +self.assertEqual(cdp.mol[0].res[6].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[6].spin[0].name, 'N') def test_read_spins_peak_list_xeasy(self): ___ 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
r21836 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 15:35:06 2013 New Revision: 21836 URL: http://svn.gna.org/viewcvs/relax?rev=21836view=rev Log: Extended system test for reading spins from SPARKY files with empty residue name+number second dimension assignment. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21836r1=21835r2=21836view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 15:35:06 2013 @@ -281,7 +281,8 @@ Test the reading of spins from a Sparky peak list. # Read the spins from peak list. -self.interpreter.spectrum.read_spins(file=ref_ave.list, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') +self.interpreter.spectrum.read_spins(file=ref_ave.list, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) +self.interpreter.spectrum.read_spins(file=ref_ave.list, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=2) # Test some of the sequence. self.assertEqual(len(cdp.mol), 1) @@ -291,35 +292,37 @@ # 1st residue. self.assertEqual(cdp.mol[0].res[0].num, 3) self.assertEqual(cdp.mol[0].res[0].name, 'LEU') -self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(len(cdp.mol[0].res[0].spin), 2) self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') +self.assertEqual(cdp.mol[0].res[0].spin[1].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'HN') # 2nd residue. self.assertEqual(cdp.mol[0].res[1].num, 4) self.assertEqual(cdp.mol[0].res[1].name, 'GLY') -self.assertEqual(len(cdp.mol[0].res[1].spin), 1) +self.assertEqual(len(cdp.mol[0].res[1].spin), 2) self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') # 3rd residue. self.assertEqual(cdp.mol[0].res[2].num, 5) self.assertEqual(cdp.mol[0].res[2].name, 'SER') -self.assertEqual(len(cdp.mol[0].res[2].spin), 1) +self.assertEqual(len(cdp.mol[0].res[2].spin), 2) self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') # 4th residue. self.assertEqual(cdp.mol[0].res[3].num, 6) self.assertEqual(cdp.mol[0].res[3].name, 'MET') -self.assertEqual(len(cdp.mol[0].res[3].spin), 1) +self.assertEqual(len(cdp.mol[0].res[3].spin), 2) self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) self.assertEqual(cdp.mol[0].res[3].spin[0].name, 'N') # 5th residue. self.assertEqual(cdp.mol[0].res[4].num, 40) self.assertEqual(cdp.mol[0].res[4].name, 'TRP') -self.assertEqual(len(cdp.mol[0].res[4].spin), 2) +self.assertEqual(len(cdp.mol[0].res[4].spin), 4) self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) self.assertEqual(cdp.mol[0].res[4].spin[0].name, 'N') self.assertEqual(cdp.mol[0].res[4].spin[1].num, None) @@ -328,7 +331,7 @@ # 6th residue. self.assertEqual(cdp.mol[0].res[5].num, 55) self.assertEqual(cdp.mol[0].res[5].name, 'ASN') -self.assertEqual(len(cdp.mol[0].res[5].spin), 1) +self.assertEqual(len(cdp.mol[0].res[5].spin), 2) self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') ___ 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
r21841 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 16:46:38 2013 New Revision: 21841 URL: http://svn.gna.org/viewcvs/relax?rev=21841view=rev Log: Added system test for reading CcpNmr Analysis exported sparky file Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21841r1=21840r2=21841view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 16:46:38 2013 @@ -334,6 +334,47 @@ self.assertEqual(len(cdp.mol[0].res[5].spin), 2) self.assertEqual(cdp.mol[0].res[5].spin[0].num, None) self.assertEqual(cdp.mol[0].res[5].spin[0].name, 'N') + + +def test_read_spins_peak_list_sparky_export_ccpnmr_analysis(self): +Test the reading of spins from a Sparky peak list exported from CcpNmr Analysis. + +# Read the spins from peak list. + self.interpreter.spectrum.read_spins(file=peak_list_ccpnmr_analysis.list, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 3) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 76) +self.assertEqual(cdp.mol[0].res[0].name, 'L') +self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 74) +self.assertEqual(cdp.mol[0].res[1].name, 'T') +self.assertEqual(len(cdp.mol[0].res[1].spin), 1) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') + +# 3rd residue. +self.assertEqual(cdp.mol[0].res[2].num, 31) +self.assertEqual(cdp.mol[0].res[2].name, 'T') +self.assertEqual(len(cdp.mol[0].res[2].spin), 1) +self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[0].name, 'N') + +# Read the peak list intensity. + self.interpreter.spectrum.read_intensities(file=peak_list_ccpnmr_analysis.list, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='test', int_method='height') + +# Test the data. + self.assertEqual(list(cdp.mol[0].res[0].spin[0].intensities.values())[0], 2.32E+05) + self.assertEqual(list(cdp.mol[0].res[1].spin[0].intensities.values())[0], 2.01E+05) + self.assertEqual(list(cdp.mol[0].res[2].spin[0].intensities.values())[0], 2.08E+05) def test_read_spins_peak_list_sparky_with_2dim_ass(self): ___ 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
r21842 - /trunk/lib/spectrum/sparky.py
Author: tlinnet Date: Fri Dec 6 16:46:39 2013 New Revision: 21842 URL: http://svn.gna.org/viewcvs/relax?rev=21842view=rev Log: Modified reading of sparky files, when exported from CcpNmr Analysis. The keyword 'Data' is not present here. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/sparky.py Modified: trunk/lib/spectrum/sparky.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/sparky.py?rev=21842r1=21841r2=21842view=diff == --- trunk/lib/spectrum/sparky.py (original) +++ trunk/lib/spectrum/sparky.py Fri Dec 6 16:46:39 2013 @@ -71,8 +71,13 @@ w4_col = i # The peak height. -elif file_data[0][i] == 'Data' and file_data[0][i+1] == 'Height': +elif file_data[0][i] == 'Height': +# The peak height when exported from CcpNmr Analysis export without 'Data'. int_col = i + +# The peak height when exported from Sparky. +if file_data[0][i-1] == 'Data' and file_data[0][i] == 'Height': +int_col = i-1 # The peak volume. elif file_data[0][i] == 'Intensity': ___ 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
r21840 - /trunk/test_suite/shared_data/peak_lists/peak_list_ccpnmr_analysis.list
Author: tlinnet Date: Fri Dec 6 16:46:37 2013 New Revision: 21840 URL: http://svn.gna.org/viewcvs/relax?rev=21840view=rev Log: Added example of CcpNmr analysis exported Sparky file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Added: trunk/test_suite/shared_data/peak_lists/peak_list_ccpnmr_analysis.list Added: trunk/test_suite/shared_data/peak_lists/peak_list_ccpnmr_analysis.list URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/peak_lists/peak_list_ccpnmr_analysis.list?rev=21840view=auto == --- trunk/test_suite/shared_data/peak_lists/peak_list_ccpnmr_analysis.list (added) +++ trunk/test_suite/shared_data/peak_lists/peak_list_ccpnmr_analysis.list Fri Dec 6 16:46:37 2013 @@ -1,0 +1,4 @@ + Assignment w1 w2 Height Volume + L76N-L76HN115.052 8.406 2.32E+05 1.09E+06 bx + T74N-T74HN114.602 8.082 2.01E+05 9.87E+05 bx + T31N-T31HN114.568 8.174 2.08E+05 1.04E+06 bx ___ 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
r21845 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 18:11:32 2013 New Revision: 21845 URL: http://svn.gna.org/viewcvs/relax?rev=21845view=rev Log: Added another systemtest for returning spins from a generic file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21845r1=21844r2=21845view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 18:11:32 2013 @@ -186,6 +186,32 @@ self.assertEqual(len(cdp.mol[0].res[4].spin), 1) self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) self.assertEqual(cdp.mol[0].res[4].spin[0].name, None) + + +def test_read_spins_peak_list_generic_with_spin_name(self): +Test the reading of spins with spin name in columns from a generic peak intensity list. + +# Read the peak spins. +self.interpreter.spectrum.read_spins(file='test.seq', dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5) + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, 'protein') +self.assertEqual(len(cdp.mol[0].res), 10) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 10) +self.assertEqual(cdp.mol[0].res[0].name, 'L') +self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, 10) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N') + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 6) +self.assertEqual(cdp.mol[0].res[1].name, 'V') +self.assertEqual(len(cdp.mol[0].res[1].spin), 1) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, 6) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N') def test_read_spins_peak_list_nmrview(self): ___ 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
r21844 - /trunk/lib/spectrum/peak_list.py
Author: tlinnet Date: Fri Dec 6 18:11:30 2013 New Revision: 21844 URL: http://svn.gna.org/viewcvs/relax?rev=21844view=rev Log: Modified the generic list to also return spin information when intensity is not present. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/lib/spectrum/peak_list.py Modified: trunk/lib/spectrum/peak_list.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/peak_list.py?rev=21844r1=21843r2=21844view=diff == --- trunk/lib/spectrum/peak_list.py (original) +++ trunk/lib/spectrum/peak_list.py Fri Dec 6 18:11:30 2013 @@ -96,12 +96,14 @@ @raises RelaxError: When the expected peak intensity is not a float. -# Check the intensity column argument. -if data_col == None: -raise RelaxError(The data column argument has not been supplied.) - # Strip the data. file_data = strip(file_data) + +# Check the intensity column argument. +data_present = True +if data_col == None: +warn(RelaxWarning(The data column argument has not been supplied, and function will only return spin data.)) +data_present = False # Convert the the data_col argument to a list if needed. if not isinstance(data_col, list): @@ -115,14 +117,21 @@ # Extract the data for the single line (loop of a single element). for values in read_spin_data(file_data=[line], 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, data_col=data_col[i], sep=sep, spin_id=spin_id): # Check the values. -if len(values) != 6: +if len(values) != 6 and data_present: raise RelaxError(The molecule name, residue number and name, spin number and name, and value columns could not be found in the data %s. % repr(values)) -# Unpack. -mol_name, res_num, res_name, spin_num, spin_name, value = values - -# Store the intensity. -intensity.append(value) +# Unpack when peak data is present +elif data_present: +# Unpack. +mol_name, res_num, res_name, spin_num, spin_name, value = values + +# Store the intensity. +intensity.append(value) + +# Unpack when peak data is not present. +elif not data_present: +# Unpack. +mol_name, res_num, res_name, spin_num, spin_name = values # Add the assignment to the peak list object. peak_list.add(mol_names=[mol_name, mol_name], res_nums=[res_num, res_num], res_names=[res_name, res_name], spin_nums=[spin_num, spin_num], spin_names=[spin_name, spin_name], intensity=intensity) ___ 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
r21843 - /trunk/test_suite/system_tests/peak_lists.py
Author: tlinnet Date: Fri Dec 6 18:11:29 2013 New Revision: 21843 URL: http://svn.gna.org/viewcvs/relax?rev=21843view=rev Log: Added system for using generic file for reading spins. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/peak_lists.py Modified: trunk/test_suite/system_tests/peak_lists.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/peak_lists.py?rev=21843r1=21842r2=21843view=diff == --- trunk/test_suite/system_tests/peak_lists.py (original) +++ trunk/test_suite/system_tests/peak_lists.py Fri Dec 6 18:11:29 2013 @@ -139,6 +139,53 @@ # Check the values. for i in range(len(times)): self.assertEqual(spin.intensities[names[i]], heights[index][i]) + + +def test_read_spins_peak_list_generic(self): +Test the reading of spins from a generic peak intensity list. + + # Read the peak spins. +self.interpreter.spectrum.read_spins(file=generic_intensity.txt, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', res_num_col=1, res_name_col=2) + +# Test some of the sequence. +self.assertEqual(len(cdp.mol), 1) +self.assertEqual(cdp.mol[0].name, None) +self.assertEqual(len(cdp.mol[0].res), 5) + +# 1st residue. +self.assertEqual(cdp.mol[0].res[0].num, 20) +self.assertEqual(cdp.mol[0].res[0].name, 'GLY') +self.assertEqual(len(cdp.mol[0].res[0].spin), 1) +self.assertEqual(cdp.mol[0].res[0].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[0].spin[0].name, None) + +# 2nd residue. +self.assertEqual(cdp.mol[0].res[1].num, 23) +self.assertEqual(cdp.mol[0].res[1].name, 'ALA') +self.assertEqual(len(cdp.mol[0].res[1].spin), 1) +self.assertEqual(cdp.mol[0].res[1].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[1].spin[0].name, None) + +# 3rd residue. +self.assertEqual(cdp.mol[0].res[2].num, 34) +self.assertEqual(cdp.mol[0].res[2].name, 'CYS') +self.assertEqual(len(cdp.mol[0].res[2].spin), 1) +self.assertEqual(cdp.mol[0].res[2].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[2].spin[0].name, None) + +# 4th residue. +self.assertEqual(cdp.mol[0].res[3].num, 35) +self.assertEqual(cdp.mol[0].res[3].name, 'MET') +self.assertEqual(len(cdp.mol[0].res[3].spin), 1) +self.assertEqual(cdp.mol[0].res[3].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[3].spin[0].name, None) + +# 5th residue. +self.assertEqual(cdp.mol[0].res[4].num, 36) +self.assertEqual(cdp.mol[0].res[4].name, 'LYS') +self.assertEqual(len(cdp.mol[0].res[4].spin), 1) +self.assertEqual(cdp.mol[0].res[4].spin[0].num, None) +self.assertEqual(cdp.mol[0].res[4].spin[0].name, None) def test_read_spins_peak_list_nmrview(self): ___ 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
r21846 - /trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py
Author: bugman
Date: Fri Dec 6 18:23:38 2013
New Revision: 21846
URL: http://svn.gna.org/viewcvs/relax?rev=21846view=rev
Log:
Fix for a script in the test suite shared data for the recent relaxation
dispersion changes.
Modified:
trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py
Modified: trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py?rev=21846r1=21845r2=21846view=diff
==
--- trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py
(original)
+++ trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py Fri
Dec 6 18:23:38 2013
@@ -131,7 +131,7 @@
file = open('r2eff_data' + sep + file_name, 'w')
# Generate the key.
-key = return_param_key_from_data(frq, point)
+key = return_param_key_from_data(exp_type=exp_type, frq=frq, point=point)
# A header.
file.write(# This data corresponds to:\n)
___
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r21847 - in /trunk/test_suite/shared_data/dispersion/Hansen: ./ r2eff_data/
Author: bugman Date: Fri Dec 6 18:46:11 2013 New Revision: 21847 URL: http://svn.gna.org/viewcvs/relax?rev=21847view=rev Log: Added residue 4 to the R2eff files for the truncated CPMG data from Flemming Hansen. Modified: trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.log trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_1000.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_133.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_200.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_266.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_333.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_400.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_466.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_533.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_600.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_66.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_666.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_733.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_800.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_866.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_933.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_1000.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_133.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_200.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_266.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_333.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_400.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_466.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_533.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_600.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_66.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_666.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_733.33.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_800.00.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_866.67.r2eff trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/800_933.33.r2eff [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.log?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/generate_r2eff_files.py?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_1000.00.r2eff URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_1000.00.r2eff?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_133.33.r2eff URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_133.33.r2eff?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_200.00.r2eff URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_200.00.r2eff?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_266.67.r2eff URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_266.67.r2eff?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_333.33.r2eff URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_333.33.r2eff?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_400.00.r2eff URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_400.00.r2eff?rev=21847r1=21846r2=21847view=diff Modified: trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_466.67.r2eff URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/r2eff_data/500_466.67.r2eff?rev=21847r1=21846r2=21847view=diff Modified:
r21848 - in /trunk/test_suite/shared_data/dispersion/Hansen: ./ cpmg_fit_results/
Author: bugman Date: Fri Dec 6 19:11:30 2013 New Revision: 21848 URL: http://svn.gna.org/viewcvs/relax?rev=21848view=rev Log: Added cpmg_fit results to the software comparison table for Flemming Hansen's CPMG data. The cpmg_fit input and log files have been added as well. Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res4.in trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res4.log trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res70.in trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res70.log trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res71.in trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res71.log trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res4.in trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res4.log trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res70.in trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res70.log trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res71.in trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res71.log Modified: trunk/test_suite/shared_data/dispersion/Hansen/software_comparison [This mail would be too long, it was shortened to contain the URLs only.] Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res4.in URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res4.in?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res4.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res4.log?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res70.in URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res70.in?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res70.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res70.log?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res71.in URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res71.in?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res71.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/cr72_res71.log?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res4.in URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res4.in?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res4.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res4.log?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res70.in URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res70.in?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res70.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res70.log?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res71.in URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res71.in?rev=21848view=auto Added: trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res71.log URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/cpmg_fit_results/ns_2site_res71.log?rev=21848view=auto Modified: trunk/test_suite/shared_data/dispersion/Hansen/software_comparison URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/software_comparison?rev=21848r1=21847r2=21848view=diff ___ 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
r21849 - in /trunk/test_suite/shared_data/dispersion: Hansen/software_comparison software_comparison
Author: bugman Date: Fri Dec 6 19:15:20 2013 New Revision: 21849 URL: http://svn.gna.org/viewcvs/relax?rev=21849view=rev Log: Shifted the software comparison down a directory so it can be used for all the different data. Added: trunk/test_suite/shared_data/dispersion/software_comparison - copied, changed from r21848, trunk/test_suite/shared_data/dispersion/Hansen/software_comparison Removed: trunk/test_suite/shared_data/dispersion/Hansen/software_comparison Removed: trunk/test_suite/shared_data/dispersion/Hansen/software_comparison URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/software_comparison?rev=21848view=auto == --- trunk/test_suite/shared_data/dispersion/Hansen/software_comparison (original) +++ trunk/test_suite/shared_data/dispersion/Hansen/software_comparison (removed) @@ -1,181 +1,0 @@ -Parameter conversions -= - -For the strange CPMGFit parameter conversions to match the other software, see cpmgfit_results/README. - - -The no exchange model -= - -Residue :4 --- - -Param relax NESSY CPMGFit ShereKhan -R2 (500)1.602 1.608 N/A N/A -R2 (800)1.638 1.634 N/A N/A -chi2 29.901 18.311 N/A N/A - -Residue :70 - -Param relax NESSY CPMGFit ShereKhan -R2 (500) 10.534 11.401 N/A N/A -R2 (800) 16.111 16.823 N/A N/A -chi2 8973.848 860.149 N/A N/A - -Residue :71 - -Param relax NESSY CPMGFit ShereKhan -R2 (500)5.831 5.969 N/A N/A -chi2 3908.008 91.093 N/A N/A - - -The LM63 model -== - -Residue :4 --- - -Param relax NESSY CPMGFit ShereKhan -R2 (500)1.583 1.574 1.584 refused -R2 (800)1.589 1.555 1.584 refused -phi 0.001 0.003 0.001 refused -kex 3092.2186109.7323302.510 refused -tex 3.234e-04 1.637e-04 3.028e-04 refused -chi2 24.752 9.923 24.771 refused - -Residue :70 - -Param relax NESSY CPMGFit ShereKhan -R2 (500)6.743 7.639 6.831 6.744 -R2 (800)6.574 7.387 6.831 6.574 -phi 0.313 0.259 0.302 0.313 -kex 4723.0993906.1894616.8054723.051 -tex 2.117e-04 2.560e-04 2.166e-04 2.117e-04 -chi2 363.534 78.223 363.912 363.534 - -Residue :71 - -Param relax NESSY CPMGFit ShereKhan -R2 (500)5.008 5.000 3.945 5.008 -phi 0.055 -0.054 0.182 0.055 -kex 2781.723 -2286.6316365.3722781.723 -tex 3.595e-04 -4.373e-04 1.571e-04 3.594e-04 -chi2 17.078 23.481 196.343 17.078 - - -The CR72 model -== - -Residue :4 --- - -Param relax NESSY CPMGFit ShereKhancpmg_fit -R2 (500)1.569 1.600 1.584 1.583 1.572 -R2 (800)1.587 1.621 1.584 1.589 1.588 -pA 1.000 0.999 0.987 0.995 1.000 -dw 6.100 1.274 0.672 0.536 5.827 -kex 631.962 134.6403299.5003075.776 951.344 -chi2 24.418 19.621 24.771 24.750 24.459 - -Residue :70 - -Param relax NESSY CPMGFit ShereKhancpmg_fit -R2 (500)6.973 7.236 5.957 6.973 6.962 -R2 (800)9.410 10.027 5.957 9.410 9.399 -pA 0.990 0.989 0.989 0.990 0.990 -dw 5.609 5.373 12.239 5.609 5.673 -kex 1752.8881522.0593421.3001752.8841715.859 -chi2 53.838 7.701 190.334 53.838 52.582 - -Residue :71 - -Param relax NESSY CPMGFit ShereKhancpmg_fit -R2 (500)5.003 49.999 3.939 5.003 5.005 -R2 (800)6.902 - 3.939 6.902 6.904 -pA 0.986 0.962 0.886 0.986 0.987 -dw 2.005 6.281 2.531 2.005 2.095 -kex 2481.008 -44.8486356.9002481.0122439.209 -chi2 15.660 8.771 197.324 15.660 15.168 - - -The IT99 model -== - -Residue :4 --- - -Param relax NESSY CPMGFit ShereKhan -R2 (500)1.583 N/A 1.583 N/A -R2 (800)
r21852 - /trunk/test_suite/system_tests/chemical_shift.py
Author: tlinnet Date: Fri Dec 6 19:24:03 2013 New Revision: 21852 URL: http://svn.gna.org/viewcvs/relax?rev=21852view=rev Log: Additional chemical shift reading test for SeriesTab formatted file. Work in progress for Support Request #3044, (https://gna.org/support/index.php?3044) - Load spins from SPARKY list. Modified: trunk/test_suite/system_tests/chemical_shift.py Modified: trunk/test_suite/system_tests/chemical_shift.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/chemical_shift.py?rev=21852r1=21851r2=21852view=diff == --- trunk/test_suite/system_tests/chemical_shift.py (original) +++ trunk/test_suite/system_tests/chemical_shift.py Fri Dec 6 19:24:03 2013 @@ -47,13 +47,33 @@ Test the reading of chemical shifts from an NMRPipe seriesTab peak list. # Read the spins from peak list. -self.interpreter.spectrum.read_spins(file=seriesTab.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', dim=1) +self.interpreter.spectrum.read_spins(file=seriesTab.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') # Read the chemical shift from the list. self.interpreter.chemical_shift.read(file=seriesTab.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') # Test the data. cs = [128.374, 127.066, 124.523] +i = 0 +for spin in spin_loop(): +# Check the shift. +self.assertEqual(spin.chemical_shift, cs[i]) + +# Increment the index. +i += 1 + + +def test_read_nmrpipe_seriestab_multi(self): +Test the reading of chemical shifts from an NMRPipe seriesTab peak list with multi columns. + +# Read the spins from peak list. +self.interpreter.spectrum.read_spins(file=seriesTab_multi.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') + +# Read the chemical shift from the list. +self.interpreter.chemical_shift.read(file=seriesTab_multi.ser, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists') + +# Test the data. +cs = [115.994, 125.899, 123.001, 120.839, 128.998] i = 0 for spin in spin_loop(): # Check the shift. ___ 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
r21850 - /trunk/test_suite/system_tests/chemical_shift.py
Author: tlinnet
Date: Fri Dec 6 19:23:58 2013
New Revision: 21850
URL: http://svn.gna.org/viewcvs/relax?rev=21850view=rev
Log:
Added system test for reading chemical shift from NMRPipe SeriesTab file.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/test_suite/system_tests/chemical_shift.py
Modified: trunk/test_suite/system_tests/chemical_shift.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/chemical_shift.py?rev=21850r1=21849r2=21850view=diff
==
--- trunk/test_suite/system_tests/chemical_shift.py (original)
+++ trunk/test_suite/system_tests/chemical_shift.py Fri Dec 6 19:23:58 2013
@@ -41,6 +41,26 @@
# Create the data pipe.
self.interpreter.pipe.create('cs', 'mf')
+
+
+def test_read_nmrpipe_seriestab(self):
+Test the reading of chemical shifts from an NMRPipe seriesTab peak
list.
+
+# Read the spins from peak list.
+self.interpreter.spectrum.read_spins(file=seriesTab.ser,
dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists',
dim=1)
+
+# Read the chemical shift from the list.
+self.interpreter.chemical_shift.read(file=seriesTab.ser,
dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists')
+
+# Test the data.
+cs = [128.374, 127.066, 124.523]
+i = 0
+for spin in spin_loop():
+# Check the shift.
+self.assertEqual(spin.chemical_shift, cs[i])
+
+# Increment the index.
+i += 1
def test_read_nmrview(self):
___
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r21851 - /trunk/lib/spectrum/nmrpipe.py
Author: tlinnet
Date: Fri Dec 6 19:24:02 2013
New Revision: 21851
URL: http://svn.gna.org/viewcvs/relax?rev=21851view=rev
Log:
Implemented reading of chemical shifts from NMRPipe SeriesTab formatted files.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/lib/spectrum/nmrpipe.py
Modified: trunk/lib/spectrum/nmrpipe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=21851r1=21850r2=21851view=diff
==
--- trunk/lib/spectrum/nmrpipe.py (original)
+++ trunk/lib/spectrum/nmrpipe.py Fri Dec 6 19:24:02 2013
@@ -80,6 +80,16 @@
# Find index of assignment ASS.
ass_i = varsline.index('ASS')
+# Chemical shifts preparation.
+w1_col = None
+w2_col = None
+
+# Find index of chemical shift Y_PPM which in sparky is w1.
+w1_col = varsline.index('Y_PPM')
+
+# Find index of chemical shift X_PPM which in sparky is w2.
+w2_col = varsline.index('X_PPM')
+
# Make a regular search for Z_A entries.
Z_A = re.compile(Z_A*)
spectra = list(filter(Z_A.search, varsline))
@@ -160,5 +170,19 @@
except ValueError:
raise RelaxError(The peak intensity value %s from the line %s is
invalid. % (intensity, line))
+# Chemical shifts.
+w1 = None
+w2 = None
+if w1_col != None:
+try:
+w1 = float(line[w1_col])
+except ValueError:
+raise RelaxError(The chemical shift from the line %s is
invalid. % line)
+if w2_col != None:
+try:
+w2 = float(line[w2_col])
+except ValueError:
+raise RelaxError(The chemical shift from the line %s is
invalid. % line)
+
# Add the assignment to the peak list object.
-peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1,
res_name2], spin_names=[name1, name2], intensity=intensities,
intensity_name=spectra)
+peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1,
res_name2], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensities,
intensity_name=spectra)
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