Author: bugman
Date: Sun Feb 22 11:14:22 2009
New Revision: 8841
URL: http://svn.gna.org/viewcvs/relax?rev=8841&view=rev
Log:
Shifted the code for the relaxation data into
bmrblib.kinetics.heteronucl_T1_relaxation.
Added:
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
- copied, changed from r8839, branches/bmrb/bmrblib/nmr_star_dict.py
Modified:
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/specific_fns/model_free/bmrb.py
Copied: branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (from
r8839, branches/bmrb/bmrblib/nmr_star_dict.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py?p2=branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py&p1=branches/bmrb/bmrblib/nmr_star_dict.py&r1=8839&r2=8841&rev=8841&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Sun Feb 22
11:14:22 2009
@@ -21,52 +21,17 @@
###############################################################################
# Module docstring.
-"""The base classes for the NMR-STAR dictionary support within relax.
+"""The Heteronuclear T1 data saveframe category.
-The most up to date NMR-STAR dictionary relax uses is the v3.1 version
documented at
-http://www.bmrb.wisc.edu/dictionary/3.1html/SuperGroupPage.html.
+For example, see
http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_T1_relaxation.
"""
# relax module imports.
-from pystarlib.File import File
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
-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.relax_data = Relaxation_data(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 Relaxation_data:
+class HeteronuclT1List:
"""Base class for relaxation data support."""
# Tag categories.
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=8841&r1=8840&r2=8841&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Sun Feb 22 11:14:22 2009
@@ -28,9 +28,8 @@
"""
# relax module imports.
+from bmrblib.kinetics import heteronucl_T1_relaxation
from pystarlib.File import File
-from pystarlib.SaveFrame import SaveFrame
-from pystarlib.TagTable import TagTable
class NMR_STAR:
@@ -49,7 +48,7 @@
self.data = File(title=title, filename=file_path)
# Initialise the objects of this class.
- self.relax_data = Relaxation_data(self.data.datanodes)
+ self.heteronucl_T1_relaxation =
heteronucl_T1_relaxation.HeteronuclT1List(self.data.datanodes)
def read(self):
@@ -64,131 +63,3 @@
# Write the contents to the STAR formatted file.
self.data.write()
-
-
-class Relaxation_data:
- """Base class for relaxation data support."""
-
- # Tag categories.
- HeteronuclNOEList = None
- HeteronuclT1List = None
- HeteronuclT2List = None
-
- # Tag names for the relaxation data.
- SfCategory = '_Saveframe_category'
- SampleConditionListLabel = '_Sample_conditions_label'
- SpectrometerFrequency1H = '_Spectrometer_frequency_1H'
- T1CoherenceType = '_T1_coherence_type'
- T2CoherenceType = '_T2_coherence_type'
- T1ValUnits = '_T1_value_units'
- T2ValUnits = '_T2_value_units'
-
- # Tag names for experiment setup.
- SampleLabel = '_Sample_label'
-
-
- def __init__(self, datanodes):
- """Initialise the class, placing the pystarlib data nodes into the
namespace.
-
- @param datanodes: The pystarlib data nodes object.
- @type datanodes: list
- """
-
- # Place the data nodes into the namespace.
- self.datanodes = datanodes
-
- # The number of relaxation data sets.
- self.r1_inc = 0
- self.r2_inc = 0
- self.noe_inc = 0
-
-
- def add(self, ri_label=None, frq=None, res_nums=None, res_names=None,
atom_names=None, data=None, errors=None):
- """Add relaxation data to the data nodes.
-
- @keyword ri_label: The relaxation data label, one of 'R1',
'R2', or 'NOE'.
- @type ri_label: str
- @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
- """
-
- # Init.
- tag_cat = ''
-
- # Set up the R1 specific variables.
- if ri_label == 'R1':
- # Misc.
- self.r1_inc = self.r1_inc + 1
- ri_inc = self.r1_inc
- label = 'T1'
- coherence = 'Nz'
-
- # Tag categories.
- if self.HeteronuclT1List:
- tag_cat = self.HeteronuclT1List + '.'
- else:
- tag_cat = ''
-
- # Set up the R2 specific variables.
- elif ri_label == 'R2':
- # Misc.
- self.r2_inc = self.r2_inc + 1
- ri_inc = self.r2_inc
- label = 'T2'
- coherence = 'Ny'
-
- # Tag categories.
- if self.HeteronuclT2List:
- tag_cat = self.HeteronuclT2List + '.'
-
- # Set up the NOE specific variables.
- elif ri_label == 'NOE':
- # Misc.
- self.noe_inc = self.noe_inc + 1
- ri_inc = self.noe_inc
- label = 'NOE'
-
- # Tag categories.
- if self.HeteronuclNOEList:
- tag_cat = self.HeteronuclNOEList + '.'
-
- # Initialise the save frame.
- frame = SaveFrame(title='heteronuclear_'+label+'_list_'+`ri_inc`)
-
- # The save frame category.
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.SfCategory], tagvalues=[[label+'_relaxation']]))
-
- # Sample info.
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.SampleLabel], tagvalues=[['$sample_1']]))
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.SampleConditionListLabel], tagvalues=[['$conditions_1']]))
-
- # NMR info.
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.SpectrometerFrequency1H], tagvalues=[[str(frq/1e6)]]))
- if label == 'T1':
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.T1CoherenceType], tagvalues=[[coherence]]))
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.T1ValUnits], tagvalues=[['1/s']]))
- elif label == 'T2':
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.T2CoherenceType], tagvalues=[[coherence]]))
- frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.T2ValUnits], tagvalues=[['1/s']]))
-
- # The relaxation tag names.
- tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+label+'_value', '_'+label+'_value_error']
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=[res_nums, res_names,
atom_names, data, errors])
-
- # Add the tag table to the save frame.
- frame.tagtables.append(table)
-
- # Add the relaxation data save frame.
- self.datanodes.append(frame)
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=8841&r1=8840&r2=8841&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Sun Feb 22 11:14:22 2009
@@ -84,7 +84,7 @@
# Add the relaxation data.
for i in range(cdp.num_ri):
- star.relax_data.add(ri_label=cdp.ri_labels[i],
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, data=relax_data_list[i],
errors=relax_error_list[i])
+ star.heteronucl_T1_relaxation.add(ri_label=cdp.ri_labels[i],
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list,
res_names=res_name_list, atom_names=atom_name_list, data=relax_data_list[i],
errors=relax_error_list[i])
# Write the contents to the STAR formatted file.
star.write()
r8841 - in /branches/bmrb: bmrblib/ bmrblib/kinetics/ specific_fns/model_free/