Author: bugman
Date: Mon Mar 9 15:10:26 2009
New Revision: 8942
URL: http://svn.gna.org/viewcvs/relax?rev=8942&view=rev
Log:
The order_parameters saveframes are now created (although are missing all the
contents).
Modified:
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
branches/bmrb/bmrblib/thermodynamics/order_parameters.py
branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=8942&r1=8941&r2=8942&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Mon Mar 9 15:10:26 2009
@@ -32,6 +32,7 @@
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.thermodynamics.order_parameters import OrderParameterSaveframe
from pystarlib.File import File
@@ -65,6 +66,9 @@
self.heteronucl_T1_relaxation =
HeteronuclT1Saveframe(self.data.datanodes)
self.heteronucl_T2_relaxation =
HeteronuclT2Saveframe(self.data.datanodes)
+ # Initialise the thermodynamics saveframe supergroup.
+ self.order_parameters = OrderParameterSaveframe(self.data.datanodes)
+
def read(self):
"""Read the data from a BMRB NMR-STAR formatted file."""
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=8942&r1=8941&r2=8942&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict_v3_1.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_1.py Mon Mar 9 15:10:26 2009
@@ -32,6 +32,7 @@
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.thermodynamics.order_parameters_v3_1 import
OrderParameterSaveframe_v3_1
from bmrblib.nmr_star_dict import NMR_STAR
@@ -48,3 +49,6 @@
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 thermodynamics saveframe supergroup.
+ self.order_parameters =
OrderParameterSaveframe_v3_1(self.data.datanodes)
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters.py?rev=8942&r1=8941&r2=8942&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters.py Mon Mar 9
15:10:26 2009
@@ -28,18 +28,13 @@
# relax module imports.
from bmrblib.misc import no_missing, translate
-from bmrblib.kinetics.relax_base import HeteronuclRxList, RelaxSaveframe, Rx
from bmrblib.tag_category import TagCategory
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
-class HeteronuclNOESaveframe(RelaxSaveframe):
- """The Heteronuclear NOE data saveframe class."""
-
- # Saveframe variables.
- label = 'NOE'
-
+class OrderParameterSaveframe:
+ """The Order parameters data saveframe class."""
def __init__(self, datanodes):
"""Initialise the class, placing the pystarlib data nodes into the
namespace.
@@ -51,54 +46,39 @@
# Place the data nodes into the namespace.
self.datanodes = datanodes
- # The number of relaxation data sets.
- self.noe_inc = 0
-
# Add the specific tag category objects.
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=None):
+ def add(self, res_nums=None, res_names=None, atom_names=None):
"""Add relaxation data to the data nodes.
- @keyword frq: The spectrometer proton frequency, in Hz.
- @type frq: float
@keyword res_nums: The residue number list.
@type res_nums: list of int
@keyword res_names: The residue name list.
@type res_names: list of str
@keyword atom_names: The atom name list.
@type atom_names: list of str
- @keyword data: The relaxation data.
- @type data: list of float
- @keyword errors: The errors associated with the relaxation
data.
- @type errors: list of float
"""
# Check the ID info.
- no_missing(res_nums, 'residue numbers of the ' + `int(frq*1e-6)` + '
MHz NOE data')
- no_missing(res_names, 'residue names of the ' + `int(frq*1e-6)` + '
MHz NOE data')
- no_missing(atom_names, 'atom names of the ' + `int(frq*1e-6)` + '
MHz NOE data')
+ no_missing(res_nums, 'residue numbers of the model-free data')
+ no_missing(res_names, 'residue names of the model-free data')
+ no_missing(atom_names, 'atom names of the model-free data')
# Place the args into the namespace.
- self.frq = frq
self.res_nums = translate(res_nums)
self.res_names = translate(res_names)
self.atom_names = translate(atom_names)
- self.data = translate(data)
- self.errors = translate(errors)
-
- # Set up the NOE specific variables.
- self.noe_inc = self.noe_inc + 1
# Initialise the save frame.
- self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`self.noe_inc`)
+ self.frame = SaveFrame(title='order_parameters')
# Create the tag categories.
- self.heteronuclRxlist.create()
- self.heteronuclRxexperiment.create()
- self.heteronuclRxsoftware.create()
- self.Rx.create()
+ self.order_parameter_list.create()
+ self.order_parameter_experiment.create()
+ self.order_parameter_software.create()
+ self.order_parameter.create()
# Add the saveframe to the data nodes.
self.datanodes.append(self.frame)
@@ -108,30 +88,27 @@
"""Create the v3.1 tag categories."""
# The tag category objects.
- self.heteronuclRxlist = HeteronuclNOEList(self)
- self.heteronuclRxexperiment = HeteronuclNOEExperiment(self)
- self.heteronuclRxsoftware = HeteronuclNOESoftware(self)
- self.Rx = HeteronuclNOE(self)
-
-
-class HeteronuclNOEList(HeteronuclRxList):
- """Base class for the HeteronuclNOEList tag category."""
-
- def create(self):
- """Create the HeteronuclNOEList tag category."""
+ self.order_parameter_list = OrderParameterList(self)
+ self.order_parameter_experiment = OrderParameterExperiment(self)
+ self.order_parameter_software = OrderParameterSoftware(self)
+ self.order_parameter = OrderParameter(self)
+
+
+class OrderParameterList(TagCategory):
+ """Base class for the OrderParameterList tag category."""
+
+ def create(self):
+ """Create the OrderParameterList tag category."""
# The save frame category.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SfCategory']],
tagvalues=[[self.sf.label+'_relaxation']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SfCategory']], tagvalues=[['S2_parameters']]))
# NOE ID number.
- if self.tag_names.has_key('HeteronuclNOEListID'):
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['HeteronuclNOEListID']],
tagvalues=[[str(self.sf.noe_inc)]]))
+ if self.tag_names.has_key('OrderParameterListID'):
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['OrderParameterListID']], tagvalues=[['1']]))
# Sample info.
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleConditionListLabel']],
tagvalues=[['$conditions_1']]))
-
- # NMR info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SpectrometerFrequency1H']],
tagvalues=[[str(self.sf.frq/1e6)]]))
def tag_setup(self, tag_category_label=None, sep=None):
@@ -152,11 +129,11 @@
self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
-class HeteronuclNOEExperiment(TagCategory):
- """Base class for the HeteronuclNOEExperiment tag category."""
-
- def create(self):
- """Create the HeteronuclNOEExperiment tag category."""
+class OrderParameterExperiment(TagCategory):
+ """Base class for the OrderParameterExperiment tag category."""
+
+ def create(self):
+ """Create the OrderParameterExperiment tag category."""
# Sample info.
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleLabel']], tagvalues=[['$sample_1']]))
@@ -178,23 +155,23 @@
self.tag_names['SampleLabel'] = 'Sample_label'
-class HeteronuclNOESoftware(TagCategory):
- """Base class for the HeteronuclNOESoftware tag category."""
-
- def create(self):
- """Create the HeteronuclNOESoftware tag category."""
-
-
-class HeteronuclNOE(Rx):
- """Base class for the HeteronuclNOE tag category."""
-
- def create(self):
- """Create the HeteronuclNOE tag category."""
+class OrderParameterSoftware(TagCategory):
+ """Base class for the OrderParameterSoftware tag category."""
+
+ def create(self):
+ """Create the OrderParameterSoftware tag category."""
+
+
+class OrderParameter(TagCategory):
+ """Base class for the OrderParameter tag category."""
+
+ def create(self):
+ """Create the OrderParameter tag category."""
# The relaxation tag names.
tag_names = []
missing = []
- for key in ['SeqID', 'CompID', 'AtomID', 'Val', 'ValErr']:
+ for key in ['SeqID', 'CompID', 'AtomID']:
if not self.tag_names.has_key(key):
missing.append(key)
else:
@@ -208,10 +185,6 @@
tag_values.append(self.sf.res_names)
if 'AtomID' not in missing:
tag_values.append(self.sf.atom_names)
- if 'Val' not in missing:
- tag_values.append(self.sf.data)
- if 'ValErr' not in missing:
- tag_values.append(self.sf.errors)
# Add the data.
table = TagTable(tagnames=tag_names, tagvalues=tag_values)
@@ -236,5 +209,3 @@
self.tag_names['SeqID'] = 'Residue_seq_code'
self.tag_names['CompID'] = 'Residue_label'
self.tag_names['AtomID'] = 'Atom_name'
- self.tag_names['Val'] = self.sf.label+'_value'
- self.tag_names['ValErr'] = self.sf.label+'_value_error'
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=8942&r1=8941&r2=8942&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py Mon Mar 9
15:10:26 2009
@@ -27,61 +27,59 @@
"""
# relax module imports.
-from bmrblib.kinetics.heteronucl_NOEs import HeteronuclNOESaveframe,
HeteronuclNOEList, HeteronuclNOEExperiment, HeteronuclNOESoftware,
HeteronuclNOE
+from bmrblib.thermodynamics.order_parameters import OrderParameterSaveframe,
OrderParameterList, OrderParameterExperiment, OrderParameterSoftware,
OrderParameter
-class HeteronuclNOESaveframe_v3_1(HeteronuclNOESaveframe):
- """The v3.1 Heteronuclear NOE data saveframe class."""
+class OrderParameterSaveframe_v3_1(OrderParameterSaveframe):
+ """The v3.1 Order parameters data saveframe class."""
def add_tag_categories(self):
"""Create the v3.1 tag categories."""
# The tag category objects.
- self.heteronuclRxlist = HeteronuclNOEList_v3_1(self)
- self.heteronuclRxexperiment = HeteronuclNOEExperiment_v3_1(self)
- self.heteronuclRxsoftware = HeteronuclNOESoftware_v3_1(self)
- self.Rx = HeteronuclNOE_v3_1(self)
+ 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)
-class HeteronuclNOEList_v3_1(HeteronuclNOEList):
- """v3.1 HeteronuclNOEList tag category."""
+class OrderParameterList_v3_1(OrderParameterList):
+ """v3.1 OrderParameterList tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- HeteronuclNOEList.tag_setup(self,
tag_category_label='Heteronucl_NOE_list', sep=sep)
+ OrderParameterList.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['HeteronuclNOEListID'] = 'ID'
+ self.tag_names['OrderParameterListID'] = 'ID'
self.tag_names['SampleConditionListLabel'] =
'Sample_condition_list_label'
-class HeteronuclNOEExperiment_v3_1(HeteronuclNOEExperiment):
- """v3.1 HeteronuclNOEExperiment tag category."""
+class OrderParameterExperiment_v3_1(OrderParameterExperiment):
+ """v3.1 OrderParameterExperiment tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- HeteronuclNOEExperiment.tag_setup(self,
tag_category_label='Heteronucl_NOE_experiment', sep=sep)
+ OrderParameterExperiment.tag_setup(self,
tag_category_label='Order_parameter_experiment', sep=sep)
-class HeteronuclNOESoftware_v3_1(HeteronuclNOESoftware):
- """v3.1 HeteronuclNOESoftware tag category."""
+class OrderParameterSoftware_v3_1(OrderParameterSoftware):
+ """v3.1 OrderParameterSoftware tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- HeteronuclNOESoftware.tag_setup(self,
tag_category_label='Heteronucl_NOE_software', sep=sep)
+ OrderParameterSoftware.tag_setup(self,
tag_category_label='Order_parameter_software', sep=sep)
-class HeteronuclNOE_v3_1(HeteronuclNOE):
- """v3.1 HeteronuclNOE tag category."""
+class OrderParameter_v3_1(OrderParameter):
+ """v3.1 OrderParameter tag category."""
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
- HeteronuclNOE.tag_setup(self, tag_category_label='Heteronucl_NOE',
sep=sep)
+ OrderParameter.tag_setup(self, tag_category_label='Order_param',
sep=sep)
# Tag names for the relaxation data.
self.tag_names['SeqID'] = 'Seq_ID'
self.tag_names['CompID'] = 'Comp_ID'
self.tag_names['AtomID'] = 'Atom_ID'
- self.tag_names['Val'] = 'Val'
- self.tag_names['ValErr'] = 'Val_err'
r8942 - in /branches/bmrb/bmrblib: ./ thermodynamics/