Author: bugman
Date: Fri Oct 9 15:49:42 2009
New Revision: 9698
URL: http://svn.gna.org/viewcvs/relax?rev=9698&view=rev
Log:
Reworked the entire GeneralRelaxation saveframe code.
Now a rudimentary NMR-STAR v3.2 formatted file is able to be produced and
read back in.
Modified:
branches/bmrb/bmrblib/kinetics/general_relaxation.py
Modified: branches/bmrb/bmrblib/kinetics/general_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/general_relaxation.py?rev=9698&r1=9697&r2=9698&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/general_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/general_relaxation.py Fri Oct 9 15:49:42
2009
@@ -23,7 +23,7 @@
# Module docstring.
"""The General Relaxation data saveframe category.
-For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_T1_relaxation.
+For example, see
http://www.bmrb.wisc.edu/dictionary/3.2html/SaveFramePage.html#general_relaxation.
"""
# relax module imports.
@@ -38,7 +38,7 @@
"""The General Relaxation data saveframe class."""
# Saveframe variables.
- label = 'T1'
+ label = 'general'
def __init__(self, datanodes):
@@ -52,7 +52,7 @@
self.datanodes = datanodes
# The number of relaxation data sets.
- self.r1_inc = 0
+ self.rx_inc = 0
# Add the specific tag category objects.
self.add_tag_categories()
@@ -80,9 +80,9 @@
"""
# Check the ID info.
- no_missing(res_nums, 'residue numbers of the ' + repr(int(frq*1e-6))
+ ' MHz NOE data')
- no_missing(res_names, 'residue names of the ' + repr(int(frq*1e-6))
+ ' MHz NOE data')
- no_missing(atom_names, 'atom names of the ' + repr(int(frq*1e-6)) +
' MHz NOE data')
+ no_missing(res_nums, 'residue numbers of the %s MHz %s relaxation
data' % (int(frq*1e-6), data_type))
+ no_missing(res_names, 'residue names of the %s MHz %s relaxation
data' % (int(frq*1e-6), data_type))
+ no_missing(atom_names, 'atom names of the %s MHz %s relaxation data'
% (int(frq*1e-6), data_type))
# The number of elements.
self.N = len(res_nums)
@@ -96,30 +96,30 @@
self.data = translate(data)
self.errors = translate(errors)
- # Set up the R1 specific variables.
- self.r1_inc = self.r1_inc + 1
- self.rx_inc_list = translate([self.r1_inc] * self.N)
+ # Set up the Rx specific variables.
+ self.rx_inc = self.rx_inc + 1
+ self.rx_inc_list = translate([self.rx_inc] * self.N)
self.generate_data_ids(self.N)
# The operators of the relaxation superoperator.
- operator_pair = []
- for i in range(cdp.num_ri):
- if cdp.ri_labels[i] == 'R1':
- operator_pair.append(['Iz', 'Iz'])
- elif cdp.ri_labels[i] == 'R2':
- operator_pair.append(['I+', 'I+'])
+ if data_type == 'R1':
+ self.GeneralRelaxationlist.variables['coherence'] = 'Iz'
+ elif data_type == 'R2':
+ self.GeneralRelaxationlist.variables['coherence'] = 'I+'
+ else:
+ raise NameError("The data type '%s' is not one of ['R1', 'R2']."
% data_type)
# Set up the version specific variables.
self.specific_setup()
# Initialise the save frame.
- self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+repr(self.r1_inc))
+ self.frame =
SaveFrame(title=self.label+'_relaxation_list_'+repr(self.rx_inc))
# Create the tag categories.
- self.heteronuclRxlist.create()
- self.heteronuclRxexperiment.create()
- self.heteronuclRxsoftware.create()
- self.Rx.create()
+ self.GeneralRelaxationlist.create()
+ self.GeneralRelaxationexperiment.create()
+ self.GeneralRelaxationsoftware.create()
+ self.GeneralRelaxation.create()
# Add the saveframe to the data nodes.
self.datanodes.append(self.frame)
@@ -129,10 +129,52 @@
"""Create the tag categories."""
# The tag category objects.
- self.heteronuclRxlist = GeneralRelaxationList(self)
- self.heteronuclRxexperiment = GeneralRelaxationExperiment(self)
- self.heteronuclRxsoftware = GeneralRelaxationSoftware(self)
- self.Rx = T1(self)
+ self.GeneralRelaxationlist = GeneralRelaxationList(self)
+ self.GeneralRelaxationexperiment = GeneralRelaxationExperiment(self)
+ self.GeneralRelaxationsoftware = GeneralRelaxationSoftware(self)
+ self.GeneralRelaxation = GeneralRelaxation(self)
+
+
+ def loop(self):
+ """Loop over the GeneralRelaxation saveframes, yielding the
relaxation data.
+
+ @return: The relaxation data consisting of the proton frequency,
residue numbers, residue
+ names, atom names, values, and errors.
+ @rtype: tuple of float, list of int, list of str, list of str,
list of float, list of
+ float
+ """
+
+ # Set up the version specific variables.
+ self.specific_setup()
+
+ # Get the saveframe name.
+ sf_name = getattr(self, 'cat_name')[0]
+
+ # Loop over all datanodes.
+ for datanode in self.datanodes:
+ # Find the GeneralRelaxation saveframes via the SfCategory tag
index.
+ found = False
+ for index in range(len(datanode.tagtables[0].tagnames)):
+ # First match the tag names.
+ if datanode.tagtables[0].tagnames[index] ==
self.GeneralRelaxationlist.create_tag_label(self.GeneralRelaxationlist.tag_names['SfCategory']):
+ # Then the tag value.
+ if datanode.tagtables[0].tagvalues[index][0] == sf_name:
+ found = True
+ break
+
+ # Skip the datanode.
+ if not found:
+ continue
+
+ # Get general info.
+ data_type, frq =
self.GeneralRelaxationlist.read(datanode.tagtables[0])
+
+ # Get the Rx info.
+ res_nums, res_names, atom_names, values, errors =
self.GeneralRelaxation.read(datanode.tagtables[1])
+
+ # Yield the data.
+ yield data_type, frq, res_nums, res_names, atom_names, values,
errors
+
class GeneralRelaxationList(HeteronuclRxList):
@@ -144,17 +186,42 @@
# The save frame category.
self.sf.frame.tagtables.append(self.create_tag_table([['SfCategory',
'cat_name']], free=True))
- # T1 ID number.
+ # GeneralRelaxation ID number.
if 'GeneralRelaxationListID' in self.tag_names:
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['GeneralRelaxationListID']],
tagvalues=[[str(self.sf.r1_inc)]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['GeneralRelaxationListID']],
tagvalues=[[str(self.sf.rx_inc)]]))
# 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)]]))
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['T1CoherenceType']],
tagvalues=[[self.variables['coherence']]]))
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['T1ValUnits']], tagvalues=[['1/s']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['RxCoherenceType']],
tagvalues=[[self.variables['coherence']]]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['RxValUnits']], tagvalues=[['1/s']]))
+
+
+ def read(self, tagtable):
+ """Extract the GeneralRelaxationList tag category info.
+
+ @param tagtable: The GeneralRelaxationList tagtable.
+ @type tagtable: Tagtable instance
+ @return: The relaxation data type and the proton
frequency in Hz.
+ @rtype: str, float
+ """
+
+ # The general info.
+ coherence =
tagtable.tagvalues[tagtable.tagnames.index(self.tag_names_full['RxCoherenceType'])][0]
+ frq =
float(tagtable.tagvalues[tagtable.tagnames.index(self.tag_names_full['SpectrometerFrequency1H'])][0])
* 1e6
+
+ # Determine the data type.
+ if coherence == 'Iz':
+ data_type = 'R1'
+ elif coherence == 'I+':
+ data_type = 'R2'
+ else:
+ raise NameError("The coherence type '%s' is unknown." %
coherence)
+
+ # Return the data.
+ return data_type, frq
def tag_setup(self, tag_category_label=None, sep=None):
@@ -173,11 +240,8 @@
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'
+ self.tag_names['RxCoherenceType'] = 'Rx_coherence_type'
+ self.tag_names['RxValUnits'] = 'Rx_value_units'
@@ -214,6 +278,43 @@
"""Create the GeneralRelaxationSoftware tag category."""
-class T1(Rx):
- """Base class for the T1 tag category."""
-
+class GeneralRelaxation(Rx):
+ """Base class for the GeneralRelaxation tag category."""
+
+ def create(self):
+ """Create the Rx tag category."""
+
+ # Keys and objects.
+ info = [
+ ['RxID', 'data_ids'],
+ ['CompIndexID', 'res_nums'],
+ ['CompID', 'res_names'],
+ ['AtomID', 'atom_names'],
+ ['AtomIsotopeNumber', 'isotope'],
+ ['Val', 'data'],
+ ['ValErr', 'errors'],
+ ['GeneralRelaxationListID', 'rx_inc_list']
+ ]
+
+ # Get the TabTable.
+ table = self.create_tag_table(info)
+
+ # Add the tagtable to the save frame.
+ self.sf.frame.tagtables.append(table)
+
+
+
+ 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.
+ Rx.tag_setup(self, tag_category_label=tag_category_label, sep=sep)
+
+ # Tag names for the general relaxation data.
+ self.tag_names['GeneralRelaxationListID'] =
'GeneralRelaxation_list_ID'
r9698 - /branches/bmrb/bmrblib/kinetics/general_relaxation.py