Author: bugman
Date: Mon Oct 26 15:26:13 2009
New Revision: 9783
URL: http://svn.gna.org/viewcvs/relax?rev=9783&view=rev
Log:
The HeteronuclNOE saveframe now only has the temp control and calibration
tags for v3.2.
Added:
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py
- copied, changed from r9782,
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py
Modified:
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
branches/bmrb/bmrblib/kinetics/relaxation.py
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=9783&r1=9782&r2=9783&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Mon Oct 26 15:26:13 2009
@@ -58,7 +58,7 @@
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None, temp_calibration=None,
temp_control=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.
@@ -75,22 +75,12 @@
@type data: list of float
@keyword errors: The errors associated with the
relaxation data.
@type errors: list of float
- @keyword temp_calibration: The temperature calibration method.
- @type temp_calibration: str
- @keyword temp_control: The temperature control method.
- @type temp_control: str
"""
# 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')
-
- # Check the args.
- if not temp_calibration:
- raise NameError("The temperature calibration method has not been
specified.")
- if not temp_control:
- raise NameError("The temperature control method has not been
specified.")
# The number of elements.
self.N = len(res_nums)
@@ -103,8 +93,6 @@
self.isotope = translate(isotope)
self.data = translate(data)
self.errors = translate(errors)
- self.temp_calibration = translate(temp_calibration)
- self.temp_control = translate(temp_control)
# Set up the NOE specific variables.
self.noe_inc = self.noe_inc + 1
Copied: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py (from r9782,
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py?p2=branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py&p1=branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py&r1=9782&r2=9783&rev=9783&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py Mon Oct 26
15:26:13 2009
@@ -21,92 +21,61 @@
###############################################################################
# Module docstring.
-"""The v3.1 Heteronuclear NOE data saveframe category.
+"""The v3.2 Heteronuclear NOE data saveframe category.
-See
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_NOEs.
+See
http://www.bmrb.wisc.edu/dictionary/3.2html/SaveFramePage.html#heteronucl_NOEs.
"""
# relax module imports.
from bmrblib.misc import translate
-from bmrblib.kinetics.heteronucl_NOEs import HeteronuclNOESaveframe,
HeteronuclNOEList, HeteronuclNOEExperiment, HeteronuclNOESoftware,
HeteronuclNOE
+from bmrblib.kinetics.heteronucl_NOEs_v3_1 import
HeteronuclNOESaveframe_v3_1, HeteronuclNOEList_v3_1,
HeteronuclNOEExperiment_v3_1, HeteronuclNOESoftware_v3_1, HeteronuclNOE_v3_1
-class HeteronuclNOESaveframe_v3_1(HeteronuclNOESaveframe):
- """The v3.1 Heteronuclear NOE data saveframe class."""
+class HeteronuclNOESaveframe_v3_2(HeteronuclNOESaveframe_v3_1):
+ """The v3.2 Heteronuclear NOE data saveframe class."""
+
+ def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None, temp_calibration=None,
temp_control=None):
+ """Add relaxation data to the data nodes.
+
+ @keyword frq: The spectrometer proton frequency, in Hz.
+ @type frq: float
+ @keyword res_nums: The residue number list.
+ @type res_nums: list of int
+ @keyword res_names: The residue name list.
+ @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 15 for '15N'.
+ @type isotope: list of int
+ @keyword data: The relaxation data.
+ @type data: list of float
+ @keyword errors: The errors associated with the
relaxation data.
+ @type errors: list of float
+ @keyword temp_calibration: The temperature calibration method.
+ @type temp_calibration: str
+ @keyword temp_control: The temperature control method.
+ @type temp_control: str
+ """
+
+ # Check the args.
+ if not temp_calibration:
+ raise NameError("The temperature calibration method has not been
specified.")
+ if not temp_control:
+ raise NameError("The temperature control method has not been
specified.")
+
+ # Place the args into the namespace.
+ self.temp_calibration = translate(temp_calibration)
+ self.temp_control = translate(temp_control)
+
+ # Execute the v3.1 add method.
+ HeteronuclNOESaveframe_v3_1.add(self, frq=frq, res_nums=res_nums,
res_names=res_names, atom_names=atom_names, isotope=isotope, data=data,
errors=errors)
+
def add_tag_categories(self):
- """Create the v3.1 tag categories."""
+ """Create the v3.2 tag categories."""
# The tag category objects.
self.heteronuclRxlist = HeteronuclNOEList_v3_1(self)
self.heteronuclRxexperiment = HeteronuclNOEExperiment_v3_1(self)
self.heteronuclRxsoftware = HeteronuclNOESoftware_v3_1(self)
self.Rx = HeteronuclNOE_v3_1(self)
-
-
- def specific_setup(self):
- """Method called by self.add() to set up any version specific
data."""
-
- # The category name.
- self.cat_name = ['heteronucl_NOEs']
-
-
-class HeteronuclNOEList_v3_1(HeteronuclNOEList):
- """v3.1 HeteronuclNOEList tag category."""
-
- def tag_setup(self, tag_category_label=None, sep=None):
- """Set 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.
- HeteronuclNOEList.tag_setup(self,
tag_category_label='Heteronucl_NOE_list', sep=sep)
-
- # Tag names for the relaxation data.
- self.tag_names['SfCategory'] = 'Sf_category'
- self.tag_names['HeteronuclNOEListID'] = 'ID'
- self.tag_names['SampleConditionListLabel'] =
'Sample_condition_list_label'
-
-
-class HeteronuclNOEExperiment_v3_1(HeteronuclNOEExperiment):
- """v3.1 HeteronuclNOEExperiment tag category."""
-
- def tag_setup(self, tag_category_label=None, sep=None):
- # Execute the base class tag_setup() method.
- HeteronuclNOEExperiment.tag_setup(self,
tag_category_label='Heteronucl_NOE_experiment', sep=sep)
-
-
-class HeteronuclNOESoftware_v3_1(HeteronuclNOESoftware):
- """v3.1 HeteronuclNOESoftware tag category."""
-
- def tag_setup(self, tag_category_label=None, sep=None):
- # Execute the base class tag_setup() method.
- HeteronuclNOESoftware.tag_setup(self,
tag_category_label='Heteronucl_NOE_software', sep=sep)
-
-
-class HeteronuclNOE_v3_1(HeteronuclNOE):
- """v3.1 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.
- HeteronuclNOE.tag_setup(self, tag_category_label='Heteronucl_NOE',
sep=sep)
-
- # Tag names for the relaxation data.
- self.tag_names['RxID'] = 'ID'
- self.tag_names['CompIndexID'] = 'Comp_index_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/relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/relaxation.py?rev=9783&r1=9782&r2=9783&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/relaxation.py Mon Oct 26 15:26:13 2009
@@ -28,6 +28,7 @@
from bmrblib.kinetics.general_relaxation import GeneralRelaxationSaveframe
from bmrblib.kinetics.heteronucl_NOEs import HeteronuclNOESaveframe
from bmrblib.kinetics.heteronucl_NOEs_v3_1 import HeteronuclNOESaveframe_v3_1
+from bmrblib.kinetics.heteronucl_NOEs_v3_2 import HeteronuclNOESaveframe_v3_2
from bmrblib.kinetics.heteronucl_T1_relaxation import HeteronuclT1Saveframe
from bmrblib.kinetics.heteronucl_T1_relaxation_v3_1 import
HeteronuclT1Saveframe_v3_1
from bmrblib.kinetics.heteronucl_T2_relaxation import HeteronuclT2Saveframe
@@ -50,7 +51,7 @@
self.heteronucl_T2_relaxation = HeteronuclT2Saveframe(datanodes)
- def add(self, data_type=None, frq=None, res_nums=None, res_names=None,
atom_names=None, isotope=None, data=None, errors=None, temp_calibration=None,
temp_control=None):
+ def add(self, data_type=None, 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 data_type: The relaxation data type (one of 'NOE',
'R1', or 'R2').
@@ -69,10 +70,6 @@
@type data: list of float
@keyword errors: The errors associated with the
relaxation data.
@type errors: list of float
- @keyword temp_calibration: The temperature calibration method.
- @type temp_calibration: str
- @keyword temp_control: The temperature control method.
- @type temp_control: str
"""
# Pack specific the data.
@@ -147,6 +144,7 @@
Relaxation_v3_1.__init__(self, datanodes)
# Initialise the kinetic saveframe supergroups.
+ self.heteronucl_NOEs = HeteronuclNOESaveframe_v3_2(datanodes)
self.general_relaxation = GeneralRelaxationSaveframe(datanodes)
r9783 - in /branches/bmrb/bmrblib/kinetics: heteronucl_NOEs.py heteronucl_NOEs_v3_2.py relaxation.py