Author: bugman
Date: Fri Oct 25 13:17:57 2013
New Revision: 21227
URL: http://svn.gna.org/viewcvs/relax?rev=21227&view=rev
Log:
Created a relax state for the R2eff SQ data of Korzhnev et al., 2005.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.log
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.py
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/sq_state.bz2
(with props)
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.log
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.log?rev=21227&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.log
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.log
Fri Oct 25 13:17:57 2013
@@ -1,0 +1,122 @@
+
+
+
+ relax repository checkout r21218
+
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp
+
+ Molecular dynamics by NMR data analysis
+
+ Copyright (C) 2001-2006 Edward d'Auvergne
+ Copyright (C) 2006-2013 the relax development team
+
+This is free software which you are welcome to modify and redistribute under
the conditions of the
+GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
+and comes with absolutely no warranty. For details type 'GPL' within the
relax prompt.
+
+Assistance in using the relax prompt and scripting interface can be accessed
by typing 'help' within
+the prompt.
+
+Processor fabric: Uni-processor.
+
+script = 'relax_state_sq.py'
+----------------------------------------------------------------------------------------------------
+# Create a relax state file for the 1H and 15N SQ data.
+
+# relax module imports.
+from specific_analyses.relax_disp.disp_data import return_param_key_from_data
+
+
+# Create a data pipe.
+pipe.create('R2eff', 'relax_disp')
+
+# Create the spin system.
+spin.create(res_name='Asp', res_num=9, spin_name='H')
+spin.create(res_name='Asp', res_num=9, spin_name='N')
+spin.isotope('1H', spin_id='@H')
+spin.isotope('15N', spin_id='@N')
+
+# Initialise the global data structures.
+cdp.cpmg_frqs = {}
+cdp.cpmg_frqs_list = []
+cdp.exp_type = {}
+cdp.relax_times = {}
+cdp.spectrometer_frq = {}
+cdp.spectrometer_frq_list = []
+cdp.spectrometer_frq_count = 0
+cdp.spectrum_ids = []
+
+# Loop over the spin data.
+for spin_label in ['hs', 'ns']:
+ # Alias the spin container.
+ spin_cont = cdp.mol[0].res[0].spin[0]
+ if spin_label == 'ns':
+ spin_cont = cdp.mol[0].res[0].spin[1]
+
+ # Initialise the data structures.
+ spin_cont.model = 'R2eff'
+ spin_cont.r2eff = {}
+ spin_cont.r2eff_err = {}
+
+ # Loop over the spectrometer frequencies.
+ for frq in [500, 600, 800]:
+ # The file data.
+ file_name = "%s_%s.res" % (spin_label, frq)
+ print("Reading the data from the file '%s'." % file_name)
+ file = open(file_name)
+ lines = file.readlines()
+ file.close()
+
+ # Loop over the dispersion points.
+ for i in range(len(lines)):
+ # Split up the line.
+ row = lines[i].split()
+
+ # Convert the data.
+ cpmg_frq = float(row[0])
+ r2eff = float(row[1])
+ r2eff_err = float(row[2])
+
+ # A key for the global data.
+ key = "%s_%s" % (frq, row[0])
+
+ # Update the global data.
+ if key not in cdp.spectrum_ids:
+ cdp.spectrum_ids.append(key)
+ cdp.cpmg_frqs[key] = cpmg_frq
+ cdp.cpmg_frqs_list.append(cpmg_frq)
+ cdp.exp_type[key] = 'CPMG'
+ cdp.relax_times[key] = 500000
+ cdp.spectrometer_frq[key] = frq * 1e6
+ cdp.spectrometer_frq_list.append(frq * 1e6)
+ cdp.spectrometer_frq_count += 1
+
+ # The dispersion point key.
+ key = return_param_key_from_data(frq=frq*1e6, point=cpmg_frq)
+
+ # Store the spin data.
+ spin_cont.r2eff[key] = r2eff
+ spin_cont.r2eff_err[key] = r2eff_err
+
+# Save the state.
+state.save('sq_state', force=True)
+----------------------------------------------------------------------------------------------------
+
+relax> pipe.create(pipe_name='R2eff', pipe_type='relax_disp', bundle=None)
+
+relax> spin.create(spin_name='H', spin_num=None, res_name='Asp', res_num=9,
mol_name=None)
+
+relax> spin.create(spin_name='N', spin_num=None, res_name='Asp', res_num=9,
mol_name=None)
+
+relax> spin.isotope(isotope='1H', spin_id='@H', force=False)
+
+relax> spin.isotope(isotope='15N', spin_id='@N', force=False)
+Reading the data from the file 'hs_500.res'.
+Reading the data from the file 'hs_600.res'.
+Reading the data from the file 'hs_800.res'.
+Reading the data from the file 'ns_500.res'.
+Reading the data from the file 'ns_600.res'.
+Reading the data from the file 'ns_800.res'.
+
+relax> state.save(state='sq_state', dir=None, compress_type=1, force=True)
+Opening the file 'sq_state.bz2' for writing.
+
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.py?rev=21227&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.py
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/relax_state_sq.py
Fri Oct 25 13:17:57 2013
@@ -1,0 +1,79 @@
+# Create a relax state file for the 1H and 15N SQ data.
+
+# relax module imports.
+from specific_analyses.relax_disp.disp_data import return_param_key_from_data
+
+
+# Create a data pipe.
+pipe.create('R2eff', 'relax_disp')
+
+# Create the spin system.
+spin.create(res_name='Asp', res_num=9, spin_name='H')
+spin.create(res_name='Asp', res_num=9, spin_name='N')
+spin.isotope('1H', spin_id='@H')
+spin.isotope('15N', spin_id='@N')
+
+# Initialise the global data structures.
+cdp.cpmg_frqs = {}
+cdp.cpmg_frqs_list = []
+cdp.exp_type = {}
+cdp.relax_times = {}
+cdp.spectrometer_frq = {}
+cdp.spectrometer_frq_list = []
+cdp.spectrometer_frq_count = 0
+cdp.spectrum_ids = []
+
+# Loop over the spin data.
+for spin_label in ['hs', 'ns']:
+ # Alias the spin container.
+ spin_cont = cdp.mol[0].res[0].spin[0]
+ if spin_label == 'ns':
+ spin_cont = cdp.mol[0].res[0].spin[1]
+
+ # Initialise the data structures.
+ spin_cont.model = 'R2eff'
+ spin_cont.r2eff = {}
+ spin_cont.r2eff_err = {}
+
+ # Loop over the spectrometer frequencies.
+ for frq in [500, 600, 800]:
+ # The file data.
+ file_name = "%s_%s.res" % (spin_label, frq)
+ print("Reading the data from the file '%s'." % file_name)
+ file = open(file_name)
+ lines = file.readlines()
+ file.close()
+
+ # Loop over the dispersion points.
+ for i in range(len(lines)):
+ # Split up the line.
+ row = lines[i].split()
+
+ # Convert the data.
+ cpmg_frq = float(row[0])
+ r2eff = float(row[1])
+ r2eff_err = float(row[2])
+
+ # A key for the global data.
+ key = "%s_%s" % (frq, row[0])
+
+ # Update the global data.
+ if key not in cdp.spectrum_ids:
+ cdp.spectrum_ids.append(key)
+ cdp.cpmg_frqs[key] = cpmg_frq
+ cdp.cpmg_frqs_list.append(cpmg_frq)
+ cdp.exp_type[key] = 'CPMG'
+ cdp.relax_times[key] = 500000
+ cdp.spectrometer_frq[key] = frq * 1e6
+ cdp.spectrometer_frq_list.append(frq * 1e6)
+ cdp.spectrometer_frq_count += 1
+
+ # The dispersion point key.
+ key = return_param_key_from_data(frq=frq*1e6, point=cpmg_frq)
+
+ # Store the spin data.
+ spin_cont.r2eff[key] = r2eff
+ spin_cont.r2eff_err[key] = r2eff_err
+
+# Save the state.
+state.save('sq_state', force=True)
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/sq_state.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/sq_state.bz2?rev=21227&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/sq_state.bz2
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svn:mime-type = application/octet-stream
r21227 - /branches/relax_disp/test_suite/shared_data/dispersion/Korzhnev_et_al_2005/