Author: bugman
Date: Tue Oct 27 16:42:02 2009
New Revision: 9810
URL: http://svn.gna.org/viewcvs/relax?rev=9810&view=rev
Log:
Updated the v3.1 and earlier T1 and T2 saveframes for all the new info.
Modified:
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.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=9810&r1=9809&r2=9810&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Tue Oct 27
16:42:02 2009
@@ -58,41 +58,69 @@
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None):
+ def add(self, sample_cond_list_id=None,
sample_cond_list_label='$conditions_1', frq=None, details=None,
assembly_atom_ids=None, entity_assembly_ids=None, entity_ids=None,
res_nums=None, seq_id=None, res_names=None, atom_names=None, atom_types=None,
isotope=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 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 sample_cond_list_id: The sample conditions list ID
number.
+ @type sample_cond_list_id: str
+ @keyword sample_cond_list_label: The sample conditions list label.
+ @type sample_cond_list_label: str
+ @keyword frq: The spectrometer proton
frequency, in Hz.
+ @type frq: float
+ @keyword details: The details tag.
+ @type details: None or str
+ @keyword assembly_atom_ids: The assembly atom ID numbers.
+ @type assembly_atom_ids: list of int
+ @keyword entity_assembly_ids: The entity assembly ID numbers.
+ @type entity_assembly_ids: list of int
+ @keyword entity_ids: The entity ID numbers.
+ @type entity_ids: int
+ @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 atom_types: The atom types as IUPAC element
abbreviations.
+ @type atom_types: 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
"""
# 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')
+ no_missing(entity_ids, 'entity ID numbers of the ' +
repr(int(frq*1e-6)) + ' MHz R1 data')
+ no_missing(res_nums, 'residue numbers of the ' + repr(int(frq*1e-6))
+ ' MHz R1 data')
+ no_missing(res_names, 'residue names of the ' + repr(int(frq*1e-6))
+ ' MHz R1 data')
+ no_missing(atom_names, 'atom names of the ' + repr(int(frq*1e-6)) +
' MHz R1 data')
# The number of elements.
self.N = len(res_nums)
# Place the args into the namespace.
+ self.sample_cond_list_id = translate(sample_cond_list_id)
+ self.sample_cond_list_label = translate(sample_cond_list_label)
self.frq = frq
- 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)
+ self.details = translate(details)
+
+ # Convert to lists and check the lengths.
+ for name in ['assembly_atom_ids', 'entity_assembly_ids',
'entity_ids', 'res_nums', 'seq_id', 'res_names', 'atom_names', 'atom_types',
'isotope', 'data', 'errors']:
+ # Get the object.
+ obj = locals()[name]
+
+ # None objects.
+ if obj == None:
+ obj = [None] * self.N
+
+ # Check the length.
+ if len(obj) != self.N:
+ raise NameError("The number of elements in the '%s' arg does
not match that of 'res_nums'." % name)
+
+ # Place the args into the namespace, translating for BMRB.
+ setattr(self, name, translate(obj))
# Set up the R1 specific variables.
self.r1_inc = self.r1_inc + 1
@@ -139,12 +167,14 @@
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['HeteronuclT1ListID']],
tagvalues=[[str(self.sf.r1_inc)]]))
# Sample info.
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleConditionListID']],
tagvalues=[[self.sf.sample_cond_list_id]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleConditionListLabel']],
tagvalues=[['$conditions_1']]))
# NMR info.
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SpectrometerFrequency1H']],
tagvalues=[[str(self.sf.frq/1e6)]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['T1CoherenceType']],
tagvalues=[[self.variables['coherence']]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['T1ValUnits']], tagvalues=[['1/s']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Details']], tagvalues=[[self.sf.details]]))
def tag_setup(self, tag_category_label=None, sep=None):
@@ -161,10 +191,12 @@
# Tag names for the relaxation data.
self.tag_names['SfCategory'] = 'Saveframe_category'
+ self.tag_names['SampleConditionListID'] = 'Sample_condition_list_ID'
self.tag_names['SampleConditionListLabel'] =
'Sample_conditions_label'
self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
self.tag_names['T1CoherenceType'] = 'T1_coherence_type'
self.tag_names['T1ValUnits'] = 'T1_value_units'
+ self.tag_names['Details'] = 'Details'
# Class variables.
self.variables['coherence'] = 'Nz'
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=9810&r1=9809&r2=9810&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Tue Oct 27
16:42:02 2009
@@ -58,41 +58,69 @@
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
isotope=None, data=None, errors=None):
+ def add(self, sample_cond_list_id=None,
sample_cond_list_label='$conditions_1', frq=None, details=None,
assembly_atom_ids=None, entity_assembly_ids=None, entity_ids=None,
res_nums=None, seq_id=None, res_names=None, atom_names=None, atom_types=None,
isotope=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 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 sample_cond_list_id: The sample conditions list ID
number.
+ @type sample_cond_list_id: str
+ @keyword sample_cond_list_label: The sample conditions list label.
+ @type sample_cond_list_label: str
+ @keyword frq: The spectrometer proton
frequency, in Hz.
+ @type frq: float
+ @keyword details: The details tag.
+ @type details: None or str
+ @keyword assembly_atom_ids: The assembly atom ID numbers.
+ @type assembly_atom_ids: list of int
+ @keyword entity_assembly_ids: The entity assembly ID numbers.
+ @type entity_assembly_ids: list of int
+ @keyword entity_ids: The entity ID numbers.
+ @type entity_ids: int
+ @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 atom_types: The atom types as IUPAC element
abbreviations.
+ @type atom_types: 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
"""
# 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')
+ no_missing(entity_ids, 'entity ID numbers of the ' +
repr(int(frq*1e-6)) + ' MHz R2 data')
+ no_missing(res_nums, 'residue numbers of the ' + repr(int(frq*1e-6))
+ ' MHz R2 data')
+ no_missing(res_names, 'residue names of the ' + repr(int(frq*1e-6))
+ ' MHz R2 data')
+ no_missing(atom_names, 'atom names of the ' + repr(int(frq*1e-6)) +
' MHz R2 data')
# The number of elements.
self.N = len(res_nums)
# Place the args into the namespace.
+ self.sample_cond_list_id = translate(sample_cond_list_id)
+ self.sample_cond_list_label = translate(sample_cond_list_label)
self.frq = frq
- 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)
+ self.details = translate(details)
+
+ # Convert to lists and check the lengths.
+ for name in ['assembly_atom_ids', 'entity_assembly_ids',
'entity_ids', 'res_nums', 'seq_id', 'res_names', 'atom_names', 'atom_types',
'isotope', 'data', 'errors']:
+ # Get the object.
+ obj = locals()[name]
+
+ # None objects.
+ if obj == None:
+ obj = [None] * self.N
+
+ # Check the length.
+ if len(obj) != self.N:
+ raise NameError("The number of elements in the '%s' arg does
not match that of 'res_nums'." % name)
+
+ # Place the args into the namespace, translating for BMRB.
+ setattr(self, name, translate(obj))
# Set up the R2 specific variables.
self.r2_inc = self.r2_inc + 1
@@ -141,12 +169,14 @@
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['HeteronuclT2ListID']],
tagvalues=[[str(self.sf.r2_inc)]]))
# Sample info.
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleConditionListID']],
tagvalues=[[self.sf.sample_cond_list_id]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SampleConditionListLabel']],
tagvalues=[['$conditions_1']]))
# NMR info.
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['SpectrometerFrequency1H']],
tagvalues=[[str(self.sf.frq/1e6)]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['T2CoherenceType']],
tagvalues=[[self.variables['coherence']]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['T2ValUnits']], tagvalues=[['1/s']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Details']], tagvalues=[[self.sf.details]]))
def tag_setup(self, tag_category_label=None, sep=None):
@@ -163,10 +193,12 @@
# Tag names for the relaxation data.
self.tag_names['SfCategory'] = 'Saveframe_category'
+ self.tag_names['SampleConditionListID'] = 'Sample_condition_list_ID'
self.tag_names['SampleConditionListLabel'] =
'Sample_conditions_label'
self.tag_names['SpectrometerFrequency1H'] =
'Spectrometer_frequency_1H'
self.tag_names['T2CoherenceType'] = 'T2_coherence_type'
self.tag_names['T2ValUnits'] = 'T2_value_units'
+ self.tag_names['Details'] = 'Details'
# Class variables.
self.variables['coherence'] = 'Ny'
r9810 - in /branches/bmrb/bmrblib/kinetics: heteronucl_T1_relaxation.py heteronucl_T2_relaxation.py