Author: bugman
Date: Sun Feb 22 14:43:58 2009
New Revision: 8849
URL: http://svn.gna.org/viewcvs/relax?rev=8849&view=rev
Log:
Shifted the tag name prefix creation code into
bmrblib.tag_category.TagCategory.
Modified:
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py
branches/bmrb/bmrblib/tag_category.py
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=8849&r1=8848&r2=8849&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Sun Feb 22 14:43:58 2009
@@ -84,13 +84,9 @@
self.data = data
self.errors = errors
- # Init.
- tag_cat = ''
-
# Set up the R1 specific variables.
self.r1_inc = self.r1_inc + 1
ri_inc = self.r1_inc
- coherence = 'Nz'
# Initialise the save frame.
self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`ri_inc`)
@@ -105,12 +101,8 @@
self.datanodes.append(self.frame)
-
class HeteronuclNOEList(TagCategory):
"""Base class for the HeteronuclNOEList tag category."""
-
- # Tag category label.
- HeteronuclNOEList = None
# Tag names for the relaxation data.
SfCategory = '_Saveframe_category'
@@ -124,27 +116,18 @@
def create(self):
"""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']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SfCategory)],
tagvalues=[[self.sf.label+'_relaxation']]))
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SampleConditionListLabel], tagvalues=[['$conditions_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleConditionListLabel)],
tagvalues=[['$conditions_1']]))
# 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=[self.create_tag_label(self.SpectrometerFrequency1H)],
tagvalues=[[str(self.sf.frq/1e6)]]))
class HeteronuclNOEExperiment(TagCategory):
"""Base class for the HeteronuclNOEExperiment tag category."""
-
- # Tag category label.
- HeteronuclNOEExperiment = None
# Tag names for experiment setup.
SampleLabel = '_Sample_label'
@@ -153,47 +136,22 @@
def create(self, frame=None):
"""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=[['$sample_1']]))
-
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleLabel)],
tagvalues=[['$sample_1']]))
class HeteronuclNOESoftware(TagCategory):
"""Base class for the HeteronuclNOESoftware tag category."""
- # Tag category label.
- HeteronuclNOESoftware = None
-
-
def create(self):
"""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 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']
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py?rev=8849&r1=8848&r2=8849&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Sun Feb 22
14:43:58 2009
@@ -84,13 +84,9 @@
self.data = data
self.errors = errors
- # Init.
- tag_cat = ''
-
# Set up the R1 specific variables.
self.r1_inc = self.r1_inc + 1
ri_inc = self.r1_inc
- coherence = 'Nz'
# Initialise the save frame.
self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`ri_inc`)
@@ -109,9 +105,6 @@
class HeteronuclT1List(TagCategory):
"""Base class for the HeteronuclT1List tag category."""
- # Tag category label.
- HeteronuclT1List = None
-
# Tag names for the relaxation data.
SfCategory = '_Saveframe_category'
SampleConditionListLabel = '_Sample_conditions_label'
@@ -126,29 +119,20 @@
def create(self):
"""Create the HeteronuclT1List tag category."""
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1List:
- tag_cat = self.HeteronuclT1List + '.'
-
# The save frame category.
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SfCategory], tagvalues=[[self.sf.label+'_relaxation']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SfCategory)],
tagvalues=[[self.sf.label+'_relaxation']]))
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SampleConditionListLabel], tagvalues=[['$conditions_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleConditionListLabel)],
tagvalues=[['$conditions_1']]))
# 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']]))
-
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SpectrometerFrequency1H)],
tagvalues=[[str(self.sf.frq/1e6)]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.T1CoherenceType)],
tagvalues=[[self.coherence]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.T1ValUnits)], tagvalues=[['1/s']]))
class HeteronuclT1Experiment(TagCategory):
"""Base class for the HeteronuclT1Experiment tag category."""
-
- # Tag category label.
- HeteronuclT1Experiment = None
# Tag names for experiment setup.
SampleLabel = '_Sample_label'
@@ -157,47 +141,22 @@
def create(self, frame=None):
"""Create the HeteronuclT1Experiment tag category."""
- # Tag category label.
- tag_cat = ''
- if self.HeteronuclT1Experiment:
- tag_cat = self.HeteronuclT1Experiment + '.'
-
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SampleLabel], tagvalues=[['$sample_1']]))
-
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleLabel)],
tagvalues=[['$sample_1']]))
class HeteronuclT1Software(TagCategory):
"""Base class for the HeteronuclT1Software tag category."""
- # Tag category label.
- HeteronuclT1Software = 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
-
-
def create(self):
"""Create the T1 tag category."""
-
- # Tag category label.
- tag_cat = ''
- if self.T1:
- tag_cat = self.T1 + '.'
# 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/kinetics/heteronucl_T2_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py?rev=8849&r1=8848&r2=8849&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Sun Feb 22
14:43:58 2009
@@ -84,13 +84,9 @@
self.data = data
self.errors = errors
- # Init.
- tag_cat = ''
-
# Set up the R1 specific variables.
self.r1_inc = self.r1_inc + 1
ri_inc = self.r1_inc
- coherence = 'Nz'
# Initialise the save frame.
self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`ri_inc`)
@@ -109,9 +105,6 @@
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'
@@ -126,29 +119,20 @@
def create(self):
"""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']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SfCategory)],
tagvalues=[[self.sf.label+'_relaxation']]))
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.SampleConditionListLabel], tagvalues=[['$conditions_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleConditionListLabel)],
tagvalues=[['$conditions_1']]))
# 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.T2CoherenceType], tagvalues=[[self.coherence]]))
- self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat
+ self.T2ValUnits], tagvalues=[['1/s']]))
-
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SpectrometerFrequency1H)],
tagvalues=[[str(self.sf.frq/1e6)]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.T2CoherenceType)],
tagvalues=[[self.coherence]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(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'
@@ -157,47 +141,22 @@
def create(self, frame=None):
"""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=[['$sample_1']]))
-
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleLabel)],
tagvalues=[['$sample_1']]))
class HeteronuclT2Software(TagCategory):
"""Base class for the HeteronuclT2Software tag category."""
- # Tag category label.
- HeteronuclT2Software = None
-
-
def create(self):
"""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 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/tag_category.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/tag_category.py?rev=8849&r1=8848&r2=8849&view=diff
==============================================================================
--- branches/bmrb/bmrblib/tag_category.py (original)
+++ branches/bmrb/bmrblib/tag_category.py Sun Feb 22 14:43:58 2009
@@ -26,12 +26,34 @@
class TagCategory:
"""The base class for tag category classes."""
- def __init__(self, sf):
+ def __init__(self, sf, tag_category_label=None, sep='.'):
"""Initialise the tag category object, placing the saveframe into
its namespace.
- @param sf: The saveframe object.
- @type sf: saveframe instance
+ @param sf: The saveframe object.
+ @type sf: saveframe instance
+ @keyword tag_category_label: The tag name prefix specific for the
tag category.
+ @type tag_category_label: None or str
+ @keyword sep: The string separating the tag name
prefix and suffix.
+ @type sep: str
"""
- # Place the saveframe into the namespace.
+ # Place the saveframe and tag info into the namespace.
self.sf = sf
+ self.tag_category_label = tag_category_label
+ self.sep = sep
+
+
+ def create_tag_label(self, tag_name):
+ """Generate the full NMR-STAR tag name.
+
+ @param tag_name: The name of the tag, without the tag category
label prefix.
+ @type tag_name: str
+ """
+
+ # Create the full tag label.
+ self.tag_category_label_full = ''
+ if self.tag_category_label:
+ self.tag_category_label_full = self.tag_category_label + self.sep
+
+ # The full tag name.
+ return self.tag_category_label_full + tag_name
r8849 - in /branches/bmrb/bmrblib: ./ kinetics/