Author: bugman
Date: Tue Oct 27 16:14:33 2009
New Revision: 9807
URL: http://svn.gna.org/viewcvs/relax?rev=9807&view=rev
Log:
All the relaxation data saveframes now contain all the equivalent data as in
general relaxation.
Modified:
branches/bmrb/bmrblib/kinetics/general_relaxation.py
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py
branches/bmrb/bmrblib/kinetics/relax_base.py
Modified: branches/bmrb/bmrblib/kinetics/general_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/general_relaxation.py?rev=9807&r1=9806&r2=9807&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/general_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/general_relaxation.py Tue Oct 27 16:14:33
2009
@@ -71,6 +71,8 @@
@type data_type: 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.
@@ -95,11 +97,10 @@
@type temp_calibration: str
@keyword temp_control: The temperature control method.
@type temp_control: str
- @keyword details: The details tag.
- @type details: None or str
"""
# Check the ID info.
+ no_missing(entity_ids, 'entity ID numbers of the ' +
repr(int(frq*1e-6)) + ' MHz NOE data')
no_missing(res_nums, 'residue numbers of the %s MHz %s relaxation
data' % (int(frq*1e-6), data_type))
no_missing(res_names, 'residue names of the %s MHz %s relaxation
data' % (int(frq*1e-6), data_type))
no_missing(atom_names, 'atom names of the %s MHz %s relaxation data'
% (int(frq*1e-6), data_type))
@@ -362,8 +363,8 @@
['AtomID', 'atom_names'],
['AtomType', 'atom_types'],
['AtomIsotopeNumber', 'isotope'],
- ['Val', 'data'],
- ['ValErr', 'errors'],
+ ['Val', 'data'],
+ ['ValErr', 'errors'],
['RexVal', 'rex_val'],
['RexErr', 'rex_err'],
['GeneralRelaxationListID', 'rx_inc_list']
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=9807&r1=9806&r2=9807&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Tue Oct 27 16:14:33 2009
@@ -58,25 +58,37 @@
self.add_tag_categories()
- def add(self, frq=None, entity_ids=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 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 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.
@@ -89,14 +101,26 @@
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.entity_ids = translate(entity_ids)
- 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 NOE specific variables.
self.noe_inc = self.noe_inc + 1
@@ -143,10 +167,12 @@
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['HeteronuclNOEListID']],
tagvalues=[[str(self.sf.noe_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['Details']], tagvalues=[[self.sf.details]]))
def tag_setup(self, tag_category_label=None, sep=None):
@@ -163,8 +189,10 @@
# 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['Details'] = 'Details'
class HeteronuclNOEExperiment(TagCategory):
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py?rev=9807&r1=9806&r2=9807&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs_v3_2.py Tue Oct 27
16:14:33 2009
@@ -35,29 +35,41 @@
class HeteronuclNOESaveframe_v3_2(HeteronuclNOESaveframe_v3_1):
"""The v3.2 Heteronuclear NOE data saveframe class."""
- def add(self, frq=None, entity_ids=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, 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, 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 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 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
+ @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
+ @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.
@@ -99,12 +111,14 @@
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['HeteronuclNOEListID']],
tagvalues=[[str(self.sf.noe_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['TempCalibrationMethod']],
tagvalues=[[self.sf.temp_calibration]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['TempControlMethod']],
tagvalues=[[self.sf.temp_control]]))
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['Details']], tagvalues=[[self.sf.details]]))
def tag_setup(self, tag_category_label=None, sep=None):
Modified: branches/bmrb/bmrblib/kinetics/relax_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/relax_base.py?rev=9807&r1=9806&r2=9807&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/relax_base.py (original)
+++ branches/bmrb/bmrblib/kinetics/relax_base.py Tue Oct 27 16:14:33 2009
@@ -106,10 +106,14 @@
# Keys and objects.
info = [
['RxID', 'data_ids'],
+ ['AssemblyAtomID', 'assembly_atom_ids'],
+ ['EntityAssemblyID', 'entity_assembly_ids'],
['EntityID', 'entity_ids'],
['CompIndexID', 'res_nums'],
+ ['SeqID', 'seq_id'],
['CompID', 'res_names'],
['AtomID', 'atom_names'],
+ ['AtomType', 'atom_types'],
['AtomIsotopeNumber', 'isotope'],
['Val', 'data'],
['ValErr', 'errors'],
@@ -171,10 +175,14 @@
# Tag names for the relaxation data.
self.tag_names['RxID'] = None
+ self.tag_names['AssemblyAtomID'] = 'Assembly_atom_ID'
+ self.tag_names['EntityAssemblyID'] = 'Entity_assembly_ID'
self.tag_names['EntityID'] = 'Entity_ID'
self.tag_names['CompIndexID'] = 'Residue_seq_code'
+ self.tag_names['SeqID'] = 'Seq_ID'
self.tag_names['CompID'] = 'Residue_label'
self.tag_names['AtomID'] = 'Atom_name'
+ self.tag_names['AtomType'] = 'Atom_type'
self.tag_names['AtomIsotopeNumber'] = 'Atom_isotope_number'
self.tag_names['Val'] = self.sf.label+'_value'
self.tag_names['ValErr'] = self.sf.label+'_value_error'
r9807 - in /branches/bmrb/bmrblib/kinetics: general_relaxation.py heteronucl_NOEs.py heteronucl_NOEs_v3_2.py relax_base.py