Author: bugman
Date: Sun Feb 22 19:31:56 2009
New Revision: 8857
URL: http://svn.gna.org/viewcvs/relax?rev=8857&view=rev
Log:
Improvements for the relaxation data storage tag categories.
Different NMR-STAR dictionary definitions are supported and the tag names are
now located in the
tag name dictionary.
Modified:
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation_v3_1.py
branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py
branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation_v3_1.py
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=8857&r1=8856&r2=8857&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Sun Feb 22 19:31:56 2009
@@ -182,10 +182,49 @@
"""Create the HeteronuclNOE tag category."""
# The relaxation tag names.
- tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+self.sf.label+'_value', '_'+self.sf.label+'_value_error']
+ tag_names = []
+ missing = []
+ for key in ['SeqID', 'CompID', 'AtomID', 'Val', 'ValErr']:
+ if not self.tag_names.has_key(key):
+ missing.append(key)
+ else:
+ tag_names.append(self.create_tag_label(self.tag_names[key]))
+
+ # The tag values.
+ tag_values = []
+ if 'SeqID' not in missing:
+ tag_values.append(self.sf.res_nums)
+ if 'CompID' not in missing:
+ 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=[self.sf.res_nums,
self.sf.res_names, self.sf.atom_names, self.sf.data, self.sf.errors])
+ table = TagTable(tagnames=tag_names, tagvalues=tag_values)
# 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.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ 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/kinetics/heteronucl_NOEs_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py?rev=8857&r1=8856&r2=8857&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py Sun Feb 22
19:31:56 2009
@@ -77,3 +77,10 @@
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)
+
+ # 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'
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=8857&r1=8856&r2=8857&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Sun Feb 22
19:31:56 2009
@@ -190,10 +190,49 @@
"""Create the T1 tag category."""
# The relaxation tag names.
- tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+self.sf.label+'_value', '_'+self.sf.label+'_value_error']
+ tag_names = []
+ missing = []
+ for key in ['SeqID', 'CompID', 'AtomID', 'Val', 'ValErr']:
+ if not self.tag_names.has_key(key):
+ missing.append(key)
+ else:
+ tag_names.append(self.create_tag_label(self.tag_names[key]))
+
+ # The tag values.
+ tag_values = []
+ if 'SeqID' not in missing:
+ tag_values.append(self.sf.res_nums)
+ if 'CompID' not in missing:
+ 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=[self.sf.res_nums,
self.sf.res_names, self.sf.atom_names, self.sf.data, self.sf.errors])
+ table = TagTable(tagnames=tag_names, tagvalues=tag_values)
# 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.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ 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/kinetics/heteronucl_T1_relaxation_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation_v3_1.py?rev=8857&r1=8856&r2=8857&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation_v3_1.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation_v3_1.py Sun Feb
22 19:31:56 2009
@@ -77,3 +77,10 @@
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
T1.tag_setup(self, tag_category_label='T1', 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'
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=8857&r1=8856&r2=8857&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Sun Feb 22
19:31:56 2009
@@ -190,10 +190,49 @@
"""Create the T2 tag category."""
# The relaxation tag names.
- tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+self.sf.label+'_value', '_'+self.sf.label+'_value_error']
+ tag_names = []
+ missing = []
+ for key in ['SeqID', 'CompID', 'AtomID', 'Val', 'ValErr']:
+ if not self.tag_names.has_key(key):
+ missing.append(key)
+ else:
+ tag_names.append(self.create_tag_label(self.tag_names[key]))
+
+ # The tag values.
+ tag_values = []
+ if 'SeqID' not in missing:
+ tag_values.append(self.sf.res_nums)
+ if 'CompID' not in missing:
+ 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=[self.sf.res_nums,
self.sf.res_names, self.sf.atom_names, self.sf.data, self.sf.errors])
+ table = TagTable(tagnames=tag_names, tagvalues=tag_values)
# 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.
+ TagCategory.tag_setup(self, tag_category_label=tag_category_label,
sep=sep)
+
+ # Tag names for the relaxation data.
+ 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/kinetics/heteronucl_T2_relaxation_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation_v3_1.py?rev=8857&r1=8856&r2=8857&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation_v3_1.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation_v3_1.py Sun Feb
22 19:31:56 2009
@@ -77,3 +77,10 @@
def tag_setup(self, tag_category_label=None, sep=None):
# Execute the base class tag_setup() method.
T2.tag_setup(self, tag_category_label='T2', 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'
r8857 - /branches/bmrb/bmrblib/kinetics/