Author: bugman
Date: Thu Mar 12 18:55:46 2009
New Revision: 8975
URL: http://svn.gna.org/viewcvs/relax?rev=8975&view=rev
Log:
Started to implement support for the General_relaxation saveframe category.
Modified:
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
branches/bmrb/generic_fns/relax_data.py
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=8975&r1=8974&r2=8975&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Thu Mar 12 18:55:46 2009
@@ -29,9 +29,6 @@
# relax module imports.
from bmrblib.assembly_supercategory.entity import EntitySaveframe
-from bmrblib.kinetics.heteronucl_NOEs import HeteronuclNOESaveframe
-from bmrblib.kinetics.heteronucl_T1_relaxation import HeteronuclT1Saveframe
-from bmrblib.kinetics.heteronucl_T2_relaxation import HeteronuclT2Saveframe
from bmrblib.NMR_parameters.chem_shift_anisotropy import ChemShiftAnisotropy
from bmrblib.thermodynamics.order_parameters import OrderParameterSaveframe
from pystarlib.File import File
@@ -69,10 +66,8 @@
# Initialise the NMR parameters saveframe supergroup.
self.chem_shift_anisotropy = ChemShiftAnisotropy(self.data.datanodes)
- # Initialise the kinetic saveframe supergroup.
- self.heteronucl_NOEs = HeteronuclNOESaveframe(self.data.datanodes)
- self.heteronucl_T1_relaxation =
HeteronuclT1Saveframe(self.data.datanodes)
- self.heteronucl_T2_relaxation =
HeteronuclT2Saveframe(self.data.datanodes)
+ # Initialise the kinetic saveframe supergroup API.
+ self.relaxation = Relaxation(self.data.datanodes)
# Initialise the thermodynamics saveframe supergroup.
self.order_parameters = OrderParameterSaveframe(self.data.datanodes)
Modified: branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict_v3_1.py?rev=8975&r1=8974&r2=8975&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict_v3_1.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_1.py Thu Mar 12 18:55:46 2009
@@ -29,9 +29,7 @@
# relax module imports.
from bmrblib.assembly_supercategory.entity_v3_1 import EntitySaveframe_v3_1
-from bmrblib.kinetics.heteronucl_NOEs_v3_1 import HeteronuclNOESaveframe_v3_1
-from bmrblib.kinetics.heteronucl_T1_relaxation_v3_1 import
HeteronuclT1Saveframe_v3_1
-from bmrblib.kinetics.heteronucl_T2_relaxation_v3_1 import
HeteronuclT2Saveframe_v3_1
+from bmrblib.kinetics.relaxation import Relaxation_v3_1
from bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1 import
ChemShiftAnisotropySaveframe_v3_1
from bmrblib.thermodynamics.order_parameters_v3_1 import
OrderParameterSaveframe_v3_1
from bmrblib.nmr_star_dict import NMR_STAR
@@ -53,10 +51,8 @@
# Initialise the NMR parameters saveframe supergroup.
self.chem_shift_anisotropy =
ChemShiftAnisotropySaveframe_v3_1(self.data.datanodes)
- # Initialise the kinetic saveframe supergroup.
- self.heteronucl_NOEs =
HeteronuclNOESaveframe_v3_1(self.data.datanodes)
- self.heteronucl_T1_relaxation =
HeteronuclT1Saveframe_v3_1(self.data.datanodes)
- self.heteronucl_T2_relaxation =
HeteronuclT2Saveframe_v3_1(self.data.datanodes)
+ # Initialise the kinetic saveframe supergroup API.
+ self.relaxation = Relaxation_v3_1(self.data.datanodes)
# Initialise the thermodynamics saveframe supergroup.
self.order_parameters =
OrderParameterSaveframe_v3_1(self.data.datanodes)
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=8975&r1=8974&r2=8975&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Thu Mar 12 18:55:46 2009
@@ -288,14 +288,25 @@
# 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):
- 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(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])
+ #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])
def copy(pipe_from=None, pipe_to=None, ri_label=None, frq_label=None):
r8975 - in /branches/bmrb: bmrblib/nmr_star_dict.py bmrblib/nmr_star_dict_v3_1.py generic_fns/relax_data.py