Author: bugman
Date: Sun Feb 22 16:23:56 2009
New Revision: 8854
URL: http://svn.gna.org/viewcvs/relax?rev=8854&view=rev
Log:
Redesign for different NMR-STAR dictionary version support.
All class variables have been converted into dictionaries created upon
instantiation.
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=8854&r1=8853&r2=8854&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Sun Feb 22 16:23:56 2009
@@ -110,40 +110,61 @@
class HeteronuclNOEList(TagCategory):
"""Base class for the HeteronuclNOEList tag category."""
- # Tag names for the relaxation data.
- SfCategory = '_Saveframe_category'
- SampleConditionListLabel = '_Sample_conditions_label'
- SpectrometerFrequency1H = '_Spectrometer_frequency_1H'
-
- # Class variables.
- coherence = 'Nz'
-
-
def create(self):
"""Create the HeteronuclNOEList tag category."""
# The save frame category.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SfCategory)],
tagvalues=[[self.sf.label+'_relaxation']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SfCategory'])],
tagvalues=[[self.sf.label+'_relaxation']]))
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleConditionListLabel)],
tagvalues=[['$conditions_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleConditionListLabel'])],
tagvalues=[['$conditions_1']]))
# NMR info.
- 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.tag_names['SpectrometerFrequency1H'])],
tagvalues=[[str(self.sf.frq/1e6)]]))
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @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
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['SfCategory'] = 'Saveframe_category'
+ self.tag_names['SampleConditionListLabel'] =
'Sample_conditions_label'
+ self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
class HeteronuclNOEExperiment(TagCategory):
"""Base class for the HeteronuclNOEExperiment tag category."""
- # Tag names for experiment setup.
- SampleLabel = '_Sample_label'
-
-
- def create(self, frame=None):
+ def create(self):
"""Create the HeteronuclNOEExperiment tag category."""
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleLabel)],
tagvalues=[['$sample_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleLabel'])],
tagvalues=[['$sample_1']]))
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @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
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['SampleLabel'] = 'Sample_label'
class HeteronuclNOESoftware(TagCategory):
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=8854&r1=8853&r2=8854&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Sun Feb 22
16:23:56 2009
@@ -105,44 +105,69 @@
class HeteronuclT1List(TagCategory):
"""Base class for the HeteronuclT1List tag category."""
- # 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."""
# The save frame category.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SfCategory)],
tagvalues=[[self.sf.label+'_relaxation']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SfCategory'])],
tagvalues=[[self.sf.label+'_relaxation']]))
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleConditionListLabel)],
tagvalues=[['$conditions_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleConditionListLabel'])],
tagvalues=[['$conditions_1']]))
# NMR info.
- 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']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SpectrometerFrequency1H'])],
tagvalues=[[str(self.sf.frq/1e6)]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['T1CoherenceType'])],
tagvalues=[[self.variables['coherence']]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['T1ValUnits'])],
tagvalues=[['1/s']]))
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @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
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['SfCategory'] = 'Saveframe_category'
+ self.tag_names['SampleConditionListLabel'] =
'Sample_conditions_label'
+ self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
+ self.tag_names['T1CoherenceType'] = 'T1_coherence_type'
+ self.tag_names['T1ValUnits'] = 'T1_value_units'
+
+ # Class variables.
+ self.variables['coherence'] = 'Nz'
+
class HeteronuclT1Experiment(TagCategory):
"""Base class for the HeteronuclT1Experiment tag category."""
- # Tag names for experiment setup.
- SampleLabel = '_Sample_label'
-
-
def create(self, frame=None):
"""Create the HeteronuclT1Experiment tag category."""
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleLabel)],
tagvalues=[['$sample_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleLabel'])],
tagvalues=[['$sample_1']]))
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @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
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['SampleLabel'] = 'Sample_label'
class HeteronuclT1Software(TagCategory):
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=8854&r1=8853&r2=8854&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Sun Feb 22
16:23:56 2009
@@ -105,44 +105,69 @@
class HeteronuclT2List(TagCategory):
"""Base class for the HeteronuclT2List tag category."""
- # Tag names for the relaxation data.
- SfCategory = '_Saveframe_category'
- SampleConditionListLabel = '_Sample_conditions_label'
- SpectrometerFrequency1H = '_Spectrometer_frequency_1H'
- T2CoherenceType = '_T2_coherence_type'
- T2ValUnits = '_T2_value_units'
-
- # Class variables.
- coherence = 'Ny'
-
def create(self):
"""Create the HeteronuclT2List tag category."""
# The save frame category.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SfCategory)],
tagvalues=[[self.sf.label+'_relaxation']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SfCategory'])],
tagvalues=[[self.sf.label+'_relaxation']]))
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleConditionListLabel)],
tagvalues=[['$conditions_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleConditionListLabel'])],
tagvalues=[['$conditions_1']]))
# NMR info.
- 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']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SpectrometerFrequency1H'])],
tagvalues=[[str(self.sf.frq/1e6)]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['T2CoherenceType'])],
tagvalues=[[self.variables['coherence']]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['T2ValUnits'])],
tagvalues=[['1/s']]))
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @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
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['SfCategory'] = 'Saveframe_category'
+ self.tag_names['SampleConditionListLabel'] =
'Sample_conditions_label'
+ self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
+ self.tag_names['T2CoherenceType'] = 'T2_coherence_type'
+ self.tag_names['T2ValUnits'] = 'T2_value_units'
+
+ # Class variables.
+ self.variables['coherence'] = 'Ny'
class HeteronuclT2Experiment(TagCategory):
"""Base class for the HeteronuclT2Experiment tag category."""
- # Tag names for experiment setup.
- SampleLabel = '_Sample_label'
-
-
def create(self, frame=None):
"""Create the HeteronuclT2Experiment tag category."""
# Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleLabel)],
tagvalues=[['$sample_1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.tag_names['SampleLabel'])],
tagvalues=[['$sample_1']]))
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Replacement method for setting up the tag names.
+
+ @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
+ """
+
+ # Execute the base class tag_setup() method.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ self.tag_names['SampleLabel'] = 'Sample_label'
class HeteronuclT2Software(TagCategory):
Modified: branches/bmrb/bmrblib/tag_category.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/tag_category.py?rev=8854&r1=8853&r2=8854&view=diff
==============================================================================
--- branches/bmrb/bmrblib/tag_category.py (original)
+++ branches/bmrb/bmrblib/tag_category.py Sun Feb 22 16:23:56 2009
@@ -26,21 +26,18 @@
class TagCategory:
"""The base class for tag category classes."""
- def __init__(self, sf, tag_category_label=None, sep='.'):
+ def __init__(self, sf):
"""Initialise the tag category object, placing the saveframe into
its namespace.
@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 and tag info into the namespace.
self.sf = sf
- self.tag_category_label = tag_category_label
- self.sep = sep
+
+ # Set up the tag information.
+ self.tag_setup()
def create_tag_label(self, tag_name):
@@ -50,10 +47,33 @@
@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
+
+
+ def tag_setup(self, tag_category_label=None, sep=None):
+ """Setup the tag names.
+
+ @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 args into the class namespace.
+ self.tag_category_label = tag_category_label
+ if sep:
+ self.sep = sep
+ else:
+ self.sep = '.'
+
+ # Create the full tag label.
+ self.tag_category_label_full = '_'
+ if self.tag_category_label:
+ self.tag_category_label_full = self.tag_category_label_full +
self.tag_category_label + self.sep
+
+ # The tag name dictionary.
+ self.tag_names = {}
+
+ # The specific variables dictionary.
+ self.variables = {}
r8854 - in /branches/bmrb/bmrblib: ./ kinetics/