Author: bugman
Date: Thu Oct 8 18:50:04 2009
New Revision: 9669
URL: http://svn.gna.org/viewcvs/relax?rev=9669&view=rev
Log:
Clean up of the relaxation data bmrb_write() method.
The abstracted bmrblib API is now being called for all relaxation data.
Modified:
branches/bmrb/bmrblib/kinetics/general_relaxation.py
branches/bmrb/generic_fns/relax_data.py
Modified: branches/bmrb/bmrblib/kinetics/general_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/general_relaxation.py?rev=9669&r1=9668&r2=9669&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/general_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/general_relaxation.py Thu Oct 8 18:50:04
2009
@@ -58,9 +58,11 @@
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None):
+ def add(self, data_type=None, frq=None, res_nums=None, res_names=None,
atom_names=None, isotope=None, data=None, errors=None):
"""Add relaxation data to the data nodes.
+ @keyword data_type: The relaxation data type (one of 'R1' or
'R2').
+ @type data_type: str
@keyword frq: The spectrometer proton frequency, in Hz.
@type frq: float
@keyword res_nums: The residue number list.
@@ -99,6 +101,14 @@
self.rx_inc_list = translate([self.r1_inc] * self.N)
self.generate_data_ids(self.N)
+ # The operators of the relaxation superoperator.
+ operator_pair = []
+ for i in range(cdp.num_ri):
+ if cdp.ri_labels[i] == 'R1':
+ operator_pair.append(['Iz', 'Iz'])
+ elif cdp.ri_labels[i] == 'R2':
+ operator_pair.append(['I+', 'I+'])
+
# Set up the version specific variables.
self.specific_setup()
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=9669&r1=9668&r2=9669&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Thu Oct 8 18:50:04 2009
@@ -228,13 +228,11 @@
-def bmrb_write(star, version='3.1'):
+def bmrb_write(star):
"""Generate the relaxation data saveframes for the NMR-STAR dictionary
object.
- @param star: The NMR-STAR dictionary object.
- @type star: NMR_STAR instance
- @keyword version: The BMRB NMR-STAR dictionary format to output to.
- @type version: str
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
"""
# Get the current data pipe.
@@ -284,33 +282,9 @@
# Other info.
isotope_list.append(int(string.strip(spin.heteronuc_type,
string.ascii_letters)))
- # The operators of the relaxation superoperator.
- operator_pair = []
- for i in range(cdp.num_ri):
- if cdp.ri_labels[i] == 'R1':
- operator_pair.append(['Iz', 'Iz'])
- elif cdp.ri_labels[i] == 'R2':
- operator_pair.append(['I+', 'I+'])
- elif cdp.ri_labels[i] == 'NOE':
- operator_pair.append(['Iz', 'Sz'])
-
# Add the relaxation data.
for i in range(cdp.num_ri):
- # The general relaxation saveframe versions.
- if version in ['3.2']:
- if cdp.ri_labels[i] in ['R1', 'R2']:
- star.relaxation.add(operator_pair=operator_pair[i],
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, isotope=isotope_list,
data=relax_data_list[i], errors=relax_error_list[i])
- elif cdp.ri_labels[i] == 'NOE':
- star.heteronucl_NOEs.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
-
- # Older versions.
- if version in ['3.0', '3.1']:
- if cdp.ri_labels[i] == 'R1':
-
star.heteronucl_T1_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
- elif cdp.ri_labels[i] == 'R2':
-
star.heteronucl_T2_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
- elif cdp.ri_labels[i] == 'NOE':
- star.heteronucl_NOEs.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i])
+ star.relaxation.add(data_type=cdp.ri_labels[i],
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, isotope=isotope_list,
data=relax_data_list[i], errors=relax_error_list[i])
def copy(pipe_from=None, pipe_to=None, ri_label=None, frq_label=None):
r9669 - in /branches/bmrb: bmrblib/kinetics/general_relaxation.py generic_fns/relax_data.py