Author: bugman
Date: Tue Mar 10 11:26:10 2009
New Revision: 8947
URL: http://svn.gna.org/viewcvs/relax?rev=8947&view=rev
Log:
Added the isotope arg to the relaxation data API parts.
The tag_setup() method has been abstracted back into the
kinetics.relax_base.Rx base class.
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/kinetics/relax_base.py
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=8947&r1=8946&r2=8947&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Tue Mar 10 11:26:10 2009
@@ -58,7 +58,7 @@
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=None):
+ def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None):
"""Add relaxation data to the data nodes.
@keyword frq: The spectrometer proton frequency, in Hz.
@@ -69,6 +69,8 @@
@type res_names: list of str
@keyword atom_names: The atom name list.
@type atom_names: list of str
+ @keyword isotope: The isotope type list, ie '15N', '1H',
'13C', '2H', etc.
+ @type isotope: list of str
@keyword data: The relaxation data.
@type data: list of float
@keyword errors: The errors associated with the relaxation
data.
@@ -85,6 +87,7 @@
self.res_nums = translate(res_nums)
self.res_names = translate(res_names)
self.atom_names = translate(atom_names)
+ self.isotope = translate(isotope)
self.data = translate(data)
self.errors = translate(errors)
@@ -187,22 +190,3 @@
class HeteronuclNOE(Rx):
"""Base class for the HeteronuclNOE tag category."""
-
- 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['CompIndexID'] = '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.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py?rev=8947&r1=8946&r2=8947&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Tue Mar 10
11:26:10 2009
@@ -58,7 +58,7 @@
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=None):
+ def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None):
"""Add relaxation data to the data nodes.
@keyword frq: The spectrometer proton frequency, in Hz.
@@ -69,6 +69,8 @@
@type res_names: list of str
@keyword atom_names: The atom name list.
@type atom_names: list of str
+ @keyword isotope: The isotope type list, ie '15N', '1H',
'13C', '2H', etc.
+ @type isotope: list of str
@keyword data: The relaxation data.
@type data: list of float
@keyword errors: The errors associated with the relaxation
data.
@@ -85,6 +87,7 @@
self.res_nums = translate(res_nums)
self.res_names = translate(res_names)
self.atom_names = translate(atom_names)
+ self.isotope = translate(isotope)
self.data = translate(data)
self.errors = translate(errors)
@@ -197,21 +200,3 @@
class T1(Rx):
"""Base class for the T1 tag category."""
- 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['CompIndexID'] = '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.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py?rev=8947&r1=8946&r2=8947&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Tue Mar 10
11:26:10 2009
@@ -58,7 +58,7 @@
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=None):
+ def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None):
"""Add relaxation data to the data nodes.
@keyword frq: The spectrometer proton frequency, in Hz.
@@ -69,6 +69,8 @@
@type res_names: list of str
@keyword atom_names: The atom name list.
@type atom_names: list of str
+ @keyword isotope: The isotope type list, ie '15N', '1H',
'13C', '2H', etc.
+ @type isotope: list of str
@keyword data: The relaxation data.
@type data: list of float
@keyword errors: The errors associated with the relaxation
data.
@@ -85,6 +87,7 @@
self.res_nums = translate(res_nums)
self.res_names = translate(res_names)
self.atom_names = translate(atom_names)
+ self.isotope = translate(isotope)
self.data = translate(data)
self.errors = translate(errors)
@@ -196,22 +199,3 @@
class T2(Rx):
"""Base class for the T2 tag category."""
-
- 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['CompIndexID'] = '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/relax_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/relax_base.py?rev=8947&r1=8946&r2=8947&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/relax_base.py (original)
+++ branches/bmrb/bmrblib/kinetics/relax_base.py Tue Mar 10 11:26:10 2009
@@ -93,11 +93,12 @@
# Keys and objects.
info = [
- ['CompIndexID', 'res_nums'],
- ['CompID', 'res_names'],
- ['AtomID', 'atom_names'],
- ['Val', 'data'],
- ['ValErr', 'errors']
+ ['CompIndexID', 'res_nums'],
+ ['CompID', 'res_names'],
+ ['AtomID', 'atom_names'],
+ ['AtomIsotopeNumber', 'isotope'],
+ ['Val', 'data'],
+ ['ValErr', 'errors']
]
# Get the TabTable.
@@ -132,3 +133,24 @@
# Return the data.
return res_nums, res_names, atom_names, values, errors
+
+
+ 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['CompIndexID'] = 'Residue_seq_code'
+ self.tag_names['CompID'] = 'Residue_label'
+ self.tag_names['AtomID'] = 'Atom_name'
+ self.tag_names['AtomIsotopeNumber'] = 'Atom_isotope_number'
+ self.tag_names['Val'] = self.sf.label+'_value'
+ self.tag_names['ValErr'] = self.sf.label+'_value_error'
r8947 - /branches/bmrb/bmrblib/kinetics/