Author: bugman
Date: Sun Feb 22 14:00:14 2009
New Revision: 8848
URL: http://svn.gna.org/viewcvs/relax?rev=8848&view=rev
Log:
Created the heteronucl_NOEs and heteronucl_T2_relaxation saveframes.
Added:
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
- copied, changed from r8847,
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py
- copied, changed from r8847,
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
Modified:
branches/bmrb/bmrblib/kinetics/__init__.py
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/kinetics/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/__init__.py?rev=8848&r1=8847&r2=8848&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/__init__.py (original)
+++ branches/bmrb/bmrblib/kinetics/__init__.py Sun Feb 22 14:00:14 2009
@@ -27,4 +27,6 @@
http://www.bmrb.wisc.edu/dictionary/3.1html/SuperGroupPage.html.
"""
-__all__ = []
+__all__ = ['heteronucl_T1_relaxation',
+ 'heteronucl_T2_relaxation',
+ 'heteronucl_NOE_relaxation']
Copied: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (from r8847,
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?p2=branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py&p1=branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py&r1=8847&r2=8848&rev=8848&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Sun Feb 22 14:00:14 2009
@@ -21,9 +21,9 @@
###############################################################################
# Module docstring.
-"""The Heteronuclear T1 data saveframe category.
-
-For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_T1_relaxation.
+"""The Heteronuclear NOE data saveframe category.
+
+For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_NOEs.
"""
# relax module imports.
@@ -32,11 +32,11 @@
from pystarlib.TagTable import TagTable
-class HeteronuclT1Saveframe:
- """The Heteronuclear T1 data saveframe class."""
+class HeteronuclNOESaveframe:
+ """The Heteronuclear NOE data saveframe class."""
# Saveframe variables.
- label = 'T1'
+ label = 'NOE'
def __init__(self, datanodes):
@@ -53,10 +53,10 @@
self.r1_inc = 0
# The tag category objects.
- self.heteronuclT1list = HeteronuclT1List(self)
- self.heteronuclT1experiment = HeteronuclT1Experiment(self)
- self.heteronuclT1software = HeteronuclT1Software(self)
- self.T1 = T1(self)
+ self.heteronuclNOElist = HeteronuclNOEList(self)
+ self.heteronuclNOEexperiment = HeteronuclNOEExperiment(self)
+ self.heteronuclNOEsoftware = HeteronuclNOESoftware(self)
+ self.heteronuclNOE = HeteronuclNOE(self)
def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=None):
@@ -96,40 +96,38 @@
self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`ri_inc`)
# Create the tag categories.
- self.heteronuclT1list.create()
- self.heteronuclT1experiment.create()
- self.heteronuclT1software.create()
- self.T1.create()
+ self.heteronuclNOElist.create()
+ self.heteronuclNOEexperiment.create()
+ self.heteronuclNOEsoftware.create()
+ self.heteronuclNOE.create()
# Add the saveframe to the data nodes.
self.datanodes.append(self.frame)
-class HeteronuclT1List(TagCategory):
- """Base class for the HeteronuclT1List tag category."""
-
- # Tag category label.
- HeteronuclT1List = None
+class HeteronuclNOEList(TagCategory):
+ """Base class for the HeteronuclNOEList tag category."""
+
+ # Tag category label.
+ HeteronuclNOEList = None
# Tag names for the relaxation data.
SfCategory = '_Saveframe_category'
SampleConditionListLabel = '_Sample_conditions_label'
SpectrometerFrequency1H = '_Spectrometer_frequency_1H'
- T1CoherenceType = '_T1_coherence_type'
- T1ValUnits = '_T1_value_units'
# Class variables.
coherence = 'Nz'
def create(self):
- """Create the HeteronuclT1List tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1List:
- tag_cat = self.HeteronuclT1List + '.'
+ """Create the HeteronuclNOEList tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclNOEList:
+ tag_cat = self.HeteronuclNOEList + '.'
# The save frame category.
self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SfCategory], tagvalues=[[self.sf.label+'_relaxation']]))
@@ -139,65 +137,63 @@
# NMR info.
self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SpectrometerFrequency1H], tagvalues=[[str(self.sf.frq/1e6)]]))
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.T1CoherenceType], tagvalues=[[self.coherence]]))
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.T1ValUnits], tagvalues=[['1/s']]))
-
-
-
-class HeteronuclT1Experiment(TagCategory):
- """Base class for the HeteronuclT1Experiment tag category."""
-
- # Tag category label.
- HeteronuclT1Experiment = None
+
+
+
+class HeteronuclNOEExperiment(TagCategory):
+ """Base class for the HeteronuclNOEExperiment tag category."""
+
+ # Tag category label.
+ HeteronuclNOEExperiment = None
# Tag names for experiment setup.
SampleLabel = '_Sample_label'
def create(self, frame=None):
- """Create the HeteronuclT1Experiment tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1Experiment:
- tag_cat = self.HeteronuclT1Experiment + '.'
+ """Create the HeteronuclNOEExperiment tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclNOEExperiment:
+ tag_cat = self.HeteronuclNOEExperiment + '.'
# Sample info.
self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SampleLabel], tagvalues=[['$sample_1']]))
-class HeteronuclT1Software(TagCategory):
- """Base class for the HeteronuclT1Software tag category."""
-
- # Tag category label.
- HeteronuclT1Software = None
+class HeteronuclNOESoftware(TagCategory):
+ """Base class for the HeteronuclNOESoftware tag category."""
+
+ # Tag category label.
+ HeteronuclNOESoftware = None
def create(self):
- """Create the HeteronuclT1Software tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1Software:
- tag_cat = self.HeteronuclT1Software + '.'
-
-
-
-class T1(TagCategory):
- """Base class for the T1 tag category."""
-
- # Tag category label.
- T1 = None
+ """Create the HeteronuclNOESoftware tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclNOESoftware:
+ tag_cat = self.HeteronuclNOESoftware + '.'
+
+
+
+class HeteronuclNOE(TagCategory):
+ """Base class for the HeteronuclNOE tag category."""
+
+ # Tag category label.
+ HeteronuclNOE = None
def create(self):
- """Create the T1 tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.T1:
- tag_cat = self.T1 + '.'
+ """Create the HeteronuclNOE tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclNOE:
+ tag_cat = self.HeteronuclNOE + '.'
# The relaxation tag names.
tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+self.sf.label+'_value', '_'+self.sf.label+'_value_error']
Copied: branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (from
r8847, branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py?p2=branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py&p1=branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py&r1=8847&r2=8848&rev=8848&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Sun Feb 22
14:00:14 2009
@@ -21,9 +21,9 @@
###############################################################################
# Module docstring.
-"""The Heteronuclear T1 data saveframe category.
-
-For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_T1_relaxation.
+"""The Heteronuclear T2 data saveframe category.
+
+For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_T2_relaxation.
"""
# relax module imports.
@@ -32,11 +32,11 @@
from pystarlib.TagTable import TagTable
-class HeteronuclT1Saveframe:
- """The Heteronuclear T1 data saveframe class."""
+class HeteronuclT2Saveframe:
+ """The Heteronuclear T2 data saveframe class."""
# Saveframe variables.
- label = 'T1'
+ label = 'T2'
def __init__(self, datanodes):
@@ -53,10 +53,10 @@
self.r1_inc = 0
# The tag category objects.
- self.heteronuclT1list = HeteronuclT1List(self)
- self.heteronuclT1experiment = HeteronuclT1Experiment(self)
- self.heteronuclT1software = HeteronuclT1Software(self)
- self.T1 = T1(self)
+ self.heteronuclT2list = HeteronuclT2List(self)
+ self.heteronuclT2experiment = HeteronuclT2Experiment(self)
+ self.heteronuclT2software = HeteronuclT2Software(self)
+ self.T2 = T2(self)
def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=None):
@@ -96,40 +96,40 @@
self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`ri_inc`)
# Create the tag categories.
- self.heteronuclT1list.create()
- self.heteronuclT1experiment.create()
- self.heteronuclT1software.create()
- self.T1.create()
+ self.heteronuclT2list.create()
+ self.heteronuclT2experiment.create()
+ self.heteronuclT2software.create()
+ self.T2.create()
# Add the saveframe to the data nodes.
self.datanodes.append(self.frame)
-class HeteronuclT1List(TagCategory):
- """Base class for the HeteronuclT1List tag category."""
-
- # Tag category label.
- HeteronuclT1List = None
+class HeteronuclT2List(TagCategory):
+ """Base class for the HeteronuclT2List tag category."""
+
+ # Tag category label.
+ HeteronuclT2List = None
# Tag names for the relaxation data.
SfCategory = '_Saveframe_category'
SampleConditionListLabel = '_Sample_conditions_label'
SpectrometerFrequency1H = '_Spectrometer_frequency_1H'
- T1CoherenceType = '_T1_coherence_type'
- T1ValUnits = '_T1_value_units'
+ T2CoherenceType = '_T2_coherence_type'
+ T2ValUnits = '_T2_value_units'
# Class variables.
- coherence = 'Nz'
+ coherence = 'Ny'
def create(self):
- """Create the HeteronuclT1List tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1List:
- tag_cat = self.HeteronuclT1List + '.'
+ """Create the HeteronuclT2List tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclT2List:
+ tag_cat = self.HeteronuclT2List + '.'
# The save frame category.
self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SfCategory], tagvalues=[[self.sf.label+'_relaxation']]))
@@ -139,65 +139,65 @@
# NMR info.
self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SpectrometerFrequency1H], tagvalues=[[str(self.sf.frq/1e6)]]))
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.T1CoherenceType], tagvalues=[[self.coherence]]))
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.T1ValUnits], tagvalues=[['1/s']]))
-
-
-
-class HeteronuclT1Experiment(TagCategory):
- """Base class for the HeteronuclT1Experiment tag category."""
-
- # Tag category label.
- HeteronuclT1Experiment = None
+ self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.T2CoherenceType], tagvalues=[[self.coherence]]))
+ self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.T2ValUnits], tagvalues=[['1/s']]))
+
+
+
+class HeteronuclT2Experiment(TagCategory):
+ """Base class for the HeteronuclT2Experiment tag category."""
+
+ # Tag category label.
+ HeteronuclT2Experiment = None
# Tag names for experiment setup.
SampleLabel = '_Sample_label'
def create(self, frame=None):
- """Create the HeteronuclT1Experiment tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1Experiment:
- tag_cat = self.HeteronuclT1Experiment + '.'
+ """Create the HeteronuclT2Experiment tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclT2Experiment:
+ tag_cat = self.HeteronuclT2Experiment + '.'
# Sample info.
self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SampleLabel], tagvalues=[['$sample_1']]))
-class HeteronuclT1Software(TagCategory):
- """Base class for the HeteronuclT1Software tag category."""
-
- # Tag category label.
- HeteronuclT1Software = None
+class HeteronuclT2Software(TagCategory):
+ """Base class for the HeteronuclT2Software tag category."""
+
+ # Tag category label.
+ HeteronuclT2Software = None
def create(self):
- """Create the HeteronuclT1Software tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1Software:
- tag_cat = self.HeteronuclT1Software + '.'
-
-
-
-class T1(TagCategory):
- """Base class for the T1 tag category."""
-
- # Tag category label.
- T1 = None
+ """Create the HeteronuclT2Software tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclT2Software:
+ tag_cat = self.HeteronuclT2Software + '.'
+
+
+
+class T2(TagCategory):
+ """Base class for the T2 tag category."""
+
+ # Tag category label.
+ T2 = None
def create(self):
- """Create the T1 tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.T1:
- tag_cat = self.T1 + '.'
+ """Create the T2 tag category."""
+
+ # Tag category label.
+ tag_cat = ''
+ if self.T2:
+ tag_cat = self.T2 + '.'
# The relaxation tag names.
tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+self.sf.label+'_value', '_'+self.sf.label+'_value_error']
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=8848&r1=8847&r2=8848&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Sun Feb 22 14:00:14 2009
@@ -28,7 +28,7 @@
"""
# relax module imports.
-from bmrblib.kinetics import heteronucl_T1_relaxation
+from bmrblib.kinetics import heteronucl_NOEs, heteronucl_T1_relaxation,
heteronucl_T2_relaxation
from pystarlib.File import File
@@ -49,6 +49,8 @@
# Initialise the objects of this class.
self.heteronucl_T1_relaxation =
heteronucl_T1_relaxation.HeteronuclT1Saveframe(self.data.datanodes)
+ self.heteronucl_T2_relaxation =
heteronucl_T2_relaxation.HeteronuclT2Saveframe(self.data.datanodes)
+ self.heteronucl_NOEs =
heteronucl_NOEs.HeteronuclNOESaveframe(self.data.datanodes)
def read(self):
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=8848&r1=8847&r2=8848&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Sun Feb 22 14:00:14 2009
@@ -86,6 +86,10 @@
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,
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,
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,
data=relax_data_list[i], errors=relax_error_list[i])
# Write the contents to the STAR formatted file.
star.write()
r8848 - in /branches/bmrb: bmrblib/ bmrblib/kinetics/ specific_fns/model_free/