Author: bugman
Date: Sun Feb 22 13:15:43 2009
New Revision: 8842
URL: http://svn.gna.org/viewcvs/relax?rev=8842&view=rev
Log:
Split up the T1 saveframe object.
The main object is now called HeteronuclT1Saveframe. The HeteronuclT1List
tag category has been
shifted into its own object, and the other tag categories will be created
next.
Modified:
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
branches/bmrb/bmrblib/nmr_star_dict.py
branches/bmrb/specific_fns/model_free/bmrb.py
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=8842&r1=8841&r2=8842&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Sun Feb 22
13:15:43 2009
@@ -31,25 +31,11 @@
from pystarlib.TagTable import TagTable
-class HeteronuclT1List:
- """Base class for relaxation data support."""
+class HeteronuclT1Saveframe:
+ """The Heteronuclear T1 data saveframe class."""
- # 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'
+ # Saveframe variables.
+ label = 'T1'
def __init__(self, datanodes):
@@ -64,15 +50,14 @@
# The number of relaxation data sets.
self.r1_inc = 0
- self.r2_inc = 0
- self.noe_inc = 0
+
+ # The tag category objects.
+ self.heteronuclT1list = HeteronuclT1List(self)
- def add(self, ri_label=None, 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,
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.
@@ -91,63 +76,18 @@
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 + '.'
+ self.r1_inc = self.r1_inc + 1
+ ri_inc = self.r1_inc
+ coherence = 'Nz'
# Initialise the save frame.
- frame = SaveFrame(title='heteronuclear_'+label+'_list_'+`ri_inc`)
+ frame =
SaveFrame(title='heteronuclear_'+self.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']]))
+ # Create the tag categories.
+ self.heteronuclT1list.create(frame=frame, frq=frq)
# The relaxation tag names.
- tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+label+'_value', '_'+label+'_value_error']
+ tag_names = ['_Residue_seq_code', '_Residue_label', '_Atom_name',
'_'+self.label+'_value', '_'+self.label+'_value_error']
# Add the data.
table = TagTable(tagnames=tag_names, tagvalues=[res_nums, res_names,
atom_names, data, errors])
@@ -157,3 +97,61 @@
# Add the relaxation data save frame.
self.datanodes.append(frame)
+
+
+class HeteronuclT1List:
+ """Base class for the HeteronuclT1List tag category."""
+
+ # Tag category label.
+ HeteronuclT1List = None
+
+ # Tag names for the relaxation data.
+ SfCategory = '_Saveframe_category'
+ SampleConditionListLabel = '_Sample_conditions_label'
+ SpectrometerFrequency1H = '_Spectrometer_frequency_1H'
+ T1CoherenceType = '_T1_coherence_type'
+ T1ValUnits = '_T1_value_units'
+
+ # Tag names for experiment setup.
+ SampleLabel = '_Sample_label'
+
+ # Class variables.
+ coherence = 'Nz'
+
+
+ def __init__(self, sf):
+ """Initialise the tag category object, placing the saveframe into
its namespace.
+
+ @param sf: The heteronuclear T1 saveframe object.
+ @type sf: HeteronuclT1Saveframe instance
+ """
+
+ # Place the saveframe into the namespace.
+ self.sf = sf
+
+
+ def create(self, frame=None, frq=None):
+ """Create the HeteronuclT1List tag category.
+
+ @keyword frame: The Heteronuclear T1 data saveframe object.
+ @type frame: HeteronuclT1Saveframe instance
+ @keyword frq: The spectrometer proton frequency, in Hz.
+ @type frq: float
+ """
+
+ # Tag category label.
+ tag_cat = ''
+ if self.HeteronuclT1List:
+ tag_cat = self.HeteronuclT1List + '.'
+
+ # The save frame category.
+ frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.SfCategory], tagvalues=[[self.sf.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)]]))
+ frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.T1CoherenceType], tagvalues=[[self.coherence]]))
+ frame.tagtables.append(TagTable(free=True, tagnames=[tag_cat +
self.T1ValUnits], tagvalues=[['1/s']]))
Modified: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=8842&r1=8841&r2=8842&view=diff
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (original)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Sun Feb 22 13:15:43 2009
@@ -48,7 +48,7 @@
self.data = File(title=title, filename=file_path)
# Initialise the objects of this class.
- self.heteronucl_T1_relaxation =
heteronucl_T1_relaxation.HeteronuclT1List(self.data.datanodes)
+ self.heteronucl_T1_relaxation =
heteronucl_T1_relaxation.HeteronuclT1Saveframe(self.data.datanodes)
def read(self):
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=8842&r1=8841&r2=8842&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Sun Feb 22 13:15:43 2009
@@ -84,7 +84,8 @@
# Add the relaxation data.
for i in range(cdp.num_ri):
- 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])
+ if cdp.ri_labels[i] == 'R1':
+
star.heteronucl_T1_relaxation.add(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()
r8842 - in /branches/bmrb: bmrblib/ bmrblib/kinetics/ specific_fns/model_free/