Author: bugman
Date: Sun Feb 22 15:31:48 2009
New Revision: 8852
URL: http://svn.gna.org/viewcvs/relax?rev=8852&view=rev
Log:
Started to implement different NMR-STAR version support.
There are obvious design issues here, preventing this from working!
Added:
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py
- copied, changed from r8849,
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
branches/bmrb/bmrblib/nmr_star_dict_v3_1.py
- copied, changed from r8848, branches/bmrb/bmrblib/nmr_star_dict.py
Modified:
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=8852&r1=8851&r2=8852&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Sun Feb 22 15:31:48 2009
@@ -51,6 +51,12 @@
# The number of relaxation data sets.
self.r1_inc = 0
+
+ self.add_tag_categories()
+
+
+ def add_tag_categories(self):
+ """Create the v3.1 tag categories."""
# The tag category objects.
self.heteronuclNOElist = HeteronuclNOEList(self)
Copied: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py (from r8849,
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py?p2=branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py&p1=branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py&r1=8849&r2=8852&rev=8852&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_1.py Sun Feb 22
15:31:48 2009
@@ -27,137 +27,54 @@
"""
# relax module imports.
-from bmrblib.tag_category import TagCategory
-from pystarlib.SaveFrame import SaveFrame
-from pystarlib.TagTable import TagTable
+from bmrblib.kinetics.heteronucl_NOEs import HeteronuclNOESaveframe,
HeteronuclNOEList, HeteronuclNOEExperiment, HeteronuclNOESoftware,
HeteronuclNOE
-class HeteronuclNOESaveframe:
- """The Heteronuclear NOE data saveframe class."""
-
- # Saveframe variables.
- label = 'NOE'
+class HeteronuclNOESaveframe_v3_1(HeteronuclNOESaveframe):
+ """The v3.1 Heteronuclear NOE data saveframe class."""
- def __init__(self, datanodes):
- """Initialise the class, placing the pystarlib data nodes into the
namespace.
+ def add_tag_categories(self):
+ """Create the v3.1 tag categories."""
- @param datanodes: The pystarlib data nodes object.
- @type datanodes: list
+ # The tag category objects.
+ self.heteronuclNOElist = HeteronuclNOEList_v3_1(self)
+ self.heteronuclNOEexperiment = HeteronuclNOEExperiment_v3_1(self)
+ self.heteronuclNOEsoftware = HeteronuclNOESoftware_v3_1(self)
+ self.heteronuclNOE = HeteronuclNOE_v3_1(self)
+
+
+class HeteronuclNOEList_v3_1(HeteronuclNOEList):
+ """v3.1 HeteronuclNOEList tag category."""
+
+ # Tag names for the relaxation data.
+ SfCategory = 'Sf_category'
+ SampleConditionListLabel = 'Sample_condition_list_label'
+ SpectrometerFrequency1H = 'Spectrometer_frequency_1H'
+
+
+ def __init__(self, sf):
+ """Initialise the v3.1 specific tag category.
+
+ @param sf: The saveframe object.
+ @type sf: saveframe instance
"""
- # Place the data nodes into the namespace.
- self.datanodes = datanodes
-
- # The number of relaxation data sets.
- self.r1_inc = 0
-
- # The tag category objects.
- self.heteronuclNOElist = HeteronuclNOEList(self)
- self.heteronuclNOEexperiment = HeteronuclNOEExperiment(self)
- self.heteronuclNOEsoftware = HeteronuclNOESoftware(self)
- self.heteronuclNOE = HeteronuclNOE(self)
+ # Execute the base class __init__() method.
+ TagCategory.__init__(self, sf,
tag_category_label='_Heteronucl_T2_list')
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
data=None, errors=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 data: The relaxation data.
- @type data: list of float
- @keyword errors: The errors associated with the relaxation
data.
- @type errors: list of float
- """
-
- # Place the args into the namespace.
- self.frq = frq
- self.res_nums = res_nums
- self.res_names = res_names
- self.atom_names = atom_names
- self.data = data
- self.errors = errors
-
- # Set up the R1 specific variables.
- self.r1_inc = self.r1_inc + 1
- ri_inc = self.r1_inc
-
- # Initialise the save frame.
- self.frame =
SaveFrame(title='heteronuclear_'+self.label+'_list_'+`ri_inc`)
-
- # Create the tag categories.
- self.heteronuclNOElist.create()
- self.heteronuclNOEexperiment.create()
- self.heteronuclNOEsoftware.create()
- self.heteronuclNOE.create()
-
- # Add the saveframe to the data nodes.
- self.datanodes.append(self.frame)
-
-
-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']]))
-
- # Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleConditionListLabel)],
tagvalues=[['$conditions_1']]))
-
- # NMR info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SpectrometerFrequency1H)],
tagvalues=[[str(self.sf.frq/1e6)]]))
-
-
-class HeteronuclNOEExperiment(TagCategory):
- """Base class for the HeteronuclNOEExperiment tag category."""
+class HeteronuclNOEExperiment_v3_1(HeteronuclNOEExperiment):
+ """v3.1 HeteronuclNOEExperiment tag category."""
# Tag names for experiment setup.
SampleLabel = '_Sample_label'
- def create(self, frame=None):
- """Create the HeteronuclNOEExperiment tag category."""
-
- # Sample info.
- self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.create_tag_label(self.SampleLabel)],
tagvalues=[['$sample_1']]))
+class HeteronuclNOESoftware_v3_1(HeteronuclNOESoftware):
+ """v3.1 HeteronuclNOESoftware tag category."""
-class HeteronuclNOESoftware(TagCategory):
- """Base class for the HeteronuclNOESoftware tag category."""
+class HeteronuclNOE_v3_1(HeteronuclNOE):
+ """v3.1 HeteronuclNOE tag category."""
- def create(self):
- """Create the HeteronuclNOESoftware tag category."""
-
-
-class HeteronuclNOE(TagCategory):
- """Base class for the HeteronuclNOE tag category."""
-
- def create(self):
- """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']
-
- # 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])
-
- # Add the tagtable to the save frame.
- self.sf.frame.tagtables.append(table)
Copied: branches/bmrb/bmrblib/nmr_star_dict_v3_1.py (from r8848,
branches/bmrb/bmrblib/nmr_star_dict.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict_v3_1.py?p2=branches/bmrb/bmrblib/nmr_star_dict_v3_1.py&p1=branches/bmrb/bmrblib/nmr_star_dict.py&r1=8848&r2=8852&rev=8852&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict_v3_1.py Sun Feb 22 15:31:48 2009
@@ -21,47 +21,18 @@
###############################################################################
# Module docstring.
-"""The base classes for the NMR-STAR dictionary support within relax.
+"""The NMR-STAR dictionary API for version 3.1.
-The most up to date NMR-STAR dictionary relax uses is the v3.1 version
documented at
+The v3.1 NMR-STAR dictionary is documented at
http://www.bmrb.wisc.edu/dictionary/3.1html/SuperGroupPage.html.
"""
# relax module imports.
-from bmrblib.kinetics import heteronucl_NOEs, heteronucl_T1_relaxation,
heteronucl_T2_relaxation
-from pystarlib.File import File
+from bmrblib.kinetics.heteronucl_NOEs_v3_1 import
HeteronuclNOESaveframe_v3_1 as HeteronuclNOESaveframe
+#from bmrblib.kinetics.heteronucl_T1_relaxation_v3_1 import
HeteronuclT1Saveframe_v3_1 as HeteronuclT1Saveframe
+#from bmrblib.kinetics.heteronucl_T2_relaxation_v3_1 import
HeteronuclT2Saveframe_v3_1 as HeteronuclT2Saveframe
+from bmrblib.nmr_star_dict import NMR_STAR
-class NMR_STAR:
- """The base object for the NMR-STAR dictionary."""
-
- def __init__(self, title, file_path):
- """Initialise the NMR-STAR dictionary object.
-
- @param title: The title of the NMR-STAR data.
- @type title: str
- @param file_path: The full file path.
- @type file_path: str
- """
-
- # Initialise the pystarlib File object.
- self.data = File(title=title, filename=file_path)
-
- # Initialise the objects of this class.
- self.heteronucl_T1_relaxation =
heteronucl_T1_relaxation.HeteronuclT1Saveframe(self.data.datanodes)
- self.heteronucl_T2_relaxation =
heteronucl_T2_relaxation.HeteronuclT2Saveframe(self.data.datanodes)
- self.heteronucl_NOEs =
heteronucl_NOEs.HeteronuclNOESaveframe(self.data.datanodes)
-
-
- def read(self):
- """Read the data from a BMRB NMR-STAR formatted file."""
-
- # Read the contents of the STAR formatted file.
- self.data.read()
-
-
- def write(self):
- """Write the data to a BMRB NMR-STAR formatted file."""
-
- # Write the contents to the STAR formatted file.
- self.data.write()
+class NMR_STAR_v3_1(NMR_STAR):
+ """The v3.1 NMR-STAR dictionary."""
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=8852&r1=8851&r2=8852&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Sun Feb 22 15:31:48 2009
@@ -21,7 +21,7 @@
###############################################################################
# relax module imports.
-from bmrblib.nmr_star_dict import NMR_STAR
+from bmrblib.nmr_star_dict_v3_1 import NMR_STAR_v3_1
from generic_fns.mol_res_spin import spin_loop
from generic_fns.pipes import get_pipe
@@ -37,7 +37,7 @@
"""
# Initialise the NMR-STAR data object.
- star = NMR_STAR('relax_model_free_results', file_path)
+ star = NMR_STAR_v3_1('relax_model_free_results', file_path)
# Read the contents of the STAR formatted file.
star.read()
@@ -51,7 +51,7 @@
"""
# Initialise the NMR-STAR data object.
- star = NMR_STAR('relax_model_free_results', file_path)
+ star = NMR_STAR_v3_1('relax_model_free_results', file_path)
# Get the current data pipe.
cdp = get_pipe()
r8852 - in /branches/bmrb: bmrblib/ bmrblib/kinetics/ specific_fns/model_free/