Author: bugman
Date: Tue Oct 13 14:11:27 2009
New Revision: 9748
URL: http://svn.gna.org/viewcvs/relax?rev=9748&view=rev
Log:
Large renamings of the Order_parameters saveframe to Model_free.
The modules still need to be renamed. Everything will be called model_free
unless v3.1 or earlier
saveframes are created, then order_parameters will be used.
Modified:
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
branches/bmrb/bmrblib/nmr_star_dict_v3_2.py
branches/bmrb/bmrblib/thermodynamics/__init__.py
branches/bmrb/bmrblib/thermodynamics/order_parameters.py
branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=9748&r1=9747&r2=9748&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Tue Oct 13 14:11:27 2009
@@ -32,7 +32,7 @@
from bmrblib.experimental_details.software import SoftwareSaveframe
from bmrblib.kinetics.relaxation import Relaxation
from bmrblib.NMR_parameters.chem_shift_anisotropy import
ChemShiftAnisotropySaveframe
-from bmrblib.thermodynamics.order_parameters import OrderParameterSaveframe
+from bmrblib.thermodynamics.model_free import ModelFreeSaveframe
from bmrblib.pystarlib.File import File
@@ -75,7 +75,7 @@
self.relaxation = Relaxation(self.data.datanodes)
# Initialise Supergroup 7 : The thermodynamics saveframe API.
- self.order_parameters = OrderParameterSaveframe(self.data.datanodes)
+ self.model_free = ModelFreeSaveframe(self.data.datanodes)
def read(self):
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=9748&r1=9747&r2=9748&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict_v3_1.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_1.py Tue Oct 13 14:11:27 2009
@@ -32,7 +32,7 @@
from bmrblib.experimental_details.software import SoftwareSaveframe
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.thermodynamics.model_free_v3_1 import ModelFreeSaveframe_v3_1
from bmrblib.nmr_star_dict import NMR_STAR
@@ -59,4 +59,4 @@
self.relaxation = Relaxation_v3_1(self.data.datanodes)
# Initialise Supergroup 7 : The thermodynamics saveframe API.
- self.order_parameters =
OrderParameterSaveframe_v3_1(self.data.datanodes)
+ self.model_free = ModelFreeSaveframe_v3_1(self.data.datanodes)
Modified: branches/bmrb/bmrblib/nmr_star_dict_v3_2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict_v3_2.py?rev=9748&r1=9747&r2=9748&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict_v3_2.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_2.py Tue Oct 13 14:11:27 2009
@@ -32,7 +32,7 @@
from bmrblib.experimental_details.software import SoftwareSaveframe
from bmrblib.kinetics.relaxation import Relaxation_v3_2
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.thermodynamics.model_free_v3_1 import ModelFreeSaveframe_v3_1
from bmrblib.nmr_star_dict import NMR_STAR
@@ -59,4 +59,4 @@
self.relaxation = Relaxation_v3_2(self.data.datanodes)
# Initialise Supergroup 7 : The thermodynamics saveframe API.
- self.order_parameters =
OrderParameterSaveframe_v3_1(self.data.datanodes)
+ self.model_free = ModelFreeSaveframe_v3_1(self.data.datanodes)
Modified: branches/bmrb/bmrblib/thermodynamics/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/__init__.py?rev=9748&r1=9747&r2=9748&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/__init__.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/__init__.py Tue Oct 13 14:11:27 2009
@@ -27,5 +27,5 @@
http://www.bmrb.wisc.edu/dictionary/3.1html/SuperGroupPage.html.
"""
-__all__ = ['order_parameters',
- 'order_parameters_v3_1']
+__all__ = ['model_free',
+ 'model_free_v3_1']
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters.py?rev=9748&r1=9747&r2=9748&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters.py Tue Oct 13
14:11:27 2009
@@ -33,7 +33,7 @@
from bmrblib.pystarlib.TagTable import TagTable
-class OrderParameterSaveframe(BaseSaveframe):
+class ModelFreeSaveframe(BaseSaveframe):
"""The Order parameters saveframe class."""
def __init__(self, datanodes):
@@ -166,10 +166,10 @@
"""Create the v3.1 tag categories."""
# The tag category objects.
- self.order_parameter_list = OrderParameterList(self)
- self.order_parameter_experiment = OrderParameterExperiment(self)
- self.order_parameter_software = OrderParameterSoftware(self)
- self.order_parameter = OrderParameter(self)
+ self.order_parameter_list = ModelFreeList(self)
+ self.order_parameter_experiment = ModelFreeExperiment(self)
+ self.order_parameter_software = ModelFreeSoftware(self)
+ self.order_parameter = ModelFree(self)
def specific_setup(self):
@@ -178,18 +178,18 @@
self.cat_name = ['S2_parameters']
-class OrderParameterList(TagCategory):
- """Base class for the OrderParameterList tag category."""
+class ModelFreeList(TagCategory):
+ """Base class for the ModelFreeList tag category."""
def create(self):
- """Create the OrderParameterList tag category."""
+ """Create the ModelFreeList tag category."""
# The save frame category.
self.sf.frame.tagtables.append(self.create_tag_table([['SfCategory',
'cat_name']], free=True))
# Model-free analysis ID number.
- if 'OrderParameterListID' in self.tag_names:
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['OrderParameterListID']], tagvalues=[['1']]))
+ if 'ModelFreeListID' in self.tag_names:
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['ModelFreeListID']], tagvalues=[['1']]))
# Sample info.
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleConditionListLabel']],
tagvalues=[['$conditions_1']]))
@@ -213,11 +213,11 @@
self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
-class OrderParameterExperiment(TagCategory):
- """Base class for the OrderParameterExperiment tag category."""
+class ModelFreeExperiment(TagCategory):
+ """Base class for the ModelFreeExperiment tag category."""
def create(self):
- """Create the OrderParameterExperiment tag category."""
+ """Create the ModelFreeExperiment tag category."""
# Sample info.
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleLabel']], tagvalues=[['$sample_1']]))
@@ -239,22 +239,22 @@
self.tag_names['SampleLabel'] = 'Sample_label'
-class OrderParameterSoftware(TagCategory):
- """Base class for the OrderParameterSoftware tag category."""
+class ModelFreeSoftware(TagCategory):
+ """Base class for the ModelFreeSoftware tag category."""
def create(self):
- """Create the OrderParameterSoftware tag category."""
-
-
-class OrderParameter(TagCategory):
- """Base class for the OrderParameter tag category."""
+ """Create the ModelFreeSoftware tag category."""
+
+
+class ModelFree(TagCategory):
+ """Base class for the ModelFree tag category."""
def create(self):
- """Create the OrderParameter tag category."""
+ """Create the ModelFree tag category."""
# Keys and objects.
info = [
- ['OrderParamID', 'data_ids'],
+ ['ModelFreeID', 'data_ids'],
['CompIndexID', 'res_nums'],
['CompID', 'res_names'],
['AtomID', 'atom_names'],
@@ -296,7 +296,7 @@
TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
# Tag names for the relaxation data.
- self.tag_names['OrderParamID'] = None
+ self.tag_names['ModelFreeID'] = None
self.tag_names['CompIndexID'] = 'Residue_seq_code'
self.tag_names['CompID'] = 'Residue_label'
self.tag_names['AtomID'] = 'Atom_name'
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py?rev=9748&r1=9747&r2=9748&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py Tue Oct 13
14:11:27 2009
@@ -27,20 +27,20 @@
"""
# relax module imports.
-from bmrblib.thermodynamics.order_parameters import OrderParameterSaveframe,
OrderParameterList, OrderParameterExperiment, OrderParameterSoftware,
OrderParameter
+from bmrblib.thermodynamics.order_parameters import ModelFreeSaveframe,
ModelFreeList, ModelFreeExperiment, ModelFreeSoftware, ModelFree
-class OrderParameterSaveframe_v3_1(OrderParameterSaveframe):
+class ModelFreeSaveframe_v3_1(ModelFreeSaveframe):
"""The v3.1 Order parameters data saveframe class."""
def add_tag_categories(self):
"""Create the v3.1 tag categories."""
# The tag category objects.
- self.order_parameter_list = OrderParameterList_v3_1(self)
- self.order_parameter_experiment = OrderParameterExperiment_v3_1(self)
- self.order_parameter_software = OrderParameterSoftware_v3_1(self)
- self.order_parameter = OrderParameter_v3_1(self)
+ self.order_parameter_list = ModelFreeList_v3_1(self)
+ self.order_parameter_experiment = ModelFreeExperiment_v3_1(self)
+ self.order_parameter_software = ModelFreeSoftware_v3_1(self)
+ self.order_parameter = ModelFree_v3_1(self)
def specific_setup(self):
"""Method called by self.add() to set up any version specific
data."""
@@ -48,44 +48,44 @@
self.cat_name = ['order_parameters']
-class OrderParameterList_v3_1(OrderParameterList):
- """v3.1 OrderParameterList tag category."""
+class ModelFreeList_v3_1(ModelFreeList):
+ """v3.1 ModelFreeList tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- OrderParameterList.tag_setup(self,
tag_category_label='Order_parameter_list', sep=sep)
+ ModelFreeList.tag_setup(self,
tag_category_label='Order_parameter_list', sep=sep)
# Tag names for the relaxation data.
self.tag_names['SfCategory'] = 'Sf_category'
- self.tag_names['OrderParameterListID'] = 'ID'
+ self.tag_names['ModelFreeListID'] = 'ID'
self.tag_names['SampleConditionListLabel'] =
'Sample_condition_list_label'
-class OrderParameterExperiment_v3_1(OrderParameterExperiment):
- """v3.1 OrderParameterExperiment tag category."""
+class ModelFreeExperiment_v3_1(ModelFreeExperiment):
+ """v3.1 ModelFreeExperiment tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- OrderParameterExperiment.tag_setup(self,
tag_category_label='Order_parameter_experiment', sep=sep)
+ ModelFreeExperiment.tag_setup(self,
tag_category_label='Order_parameter_experiment', sep=sep)
-class OrderParameterSoftware_v3_1(OrderParameterSoftware):
- """v3.1 OrderParameterSoftware tag category."""
+class ModelFreeSoftware_v3_1(ModelFreeSoftware):
+ """v3.1 ModelFreeSoftware tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- OrderParameterSoftware.tag_setup(self,
tag_category_label='Order_parameter_software', sep=sep)
+ ModelFreeSoftware.tag_setup(self,
tag_category_label='Order_parameter_software', sep=sep)
-class OrderParameter_v3_1(OrderParameter):
- """v3.1 OrderParameter tag category."""
+class ModelFree_v3_1(ModelFree):
+ """v3.1 ModelFree tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- OrderParameter.tag_setup(self, tag_category_label='Order_param',
sep=sep)
+ ModelFree.tag_setup(self, tag_category_label='Order_param', sep=sep)
# Tag names for the relaxation data.
- self.tag_names['OrderParamID'] = 'ID'
+ self.tag_names['ModelFreeID'] = 'ID'
self.tag_names['CompIndexID'] = 'Comp_index_ID'
self.tag_names['CompID'] = 'Comp_ID'
self.tag_names['AtomID'] = 'Atom_ID'
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=9748&r1=9747&r2=9748&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Tue Oct 13 14:11:27 2009
@@ -200,7 +200,7 @@
######################################################
# Generate the model-free data saveframe.
- star.order_parameters.add(res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, atom_types=element_list,
s2=s2_list, s2f=s2f_list, s2s=s2s_list, te=te_list, tf=tf_list, ts=ts_list,
rex=rex_list, s2_err=s2_err_list, s2f_err=s2f_err_list, s2s_err=s2s_err_list,
te_err=te_err_list, tf_err=tf_err_list, ts_err=ts_err_list,
rex_err=rex_err_list, rex_frq=rex_frq, chi2=chi2_list)
+ star.model_free.add(res_nums=res_num_list, res_names=res_name_list,
atom_names=atom_name_list, atom_types=element_list, s2=s2_list, s2f=s2f_list,
s2s=s2s_list, te=te_list, tf=tf_list, ts=ts_list, rex=rex_list,
s2_err=s2_err_list, s2f_err=s2f_err_list, s2s_err=s2s_err_list,
te_err=te_err_list, tf_err=tf_err_list, ts_err=ts_err_list,
rex_err=rex_err_list, rex_frq=rex_frq, chi2=chi2_list)
# Write the contents to the STAR formatted file.
r9748 - in /branches/bmrb: bmrblib/ bmrblib/thermodynamics/ specific_fns/model_free/