Author: bugman
Date: Wed Oct 14 19:09:27 2009
New Revision: 9779
URL: http://svn.gna.org/viewcvs/relax?rev=9779&view=rev
Log:
Expanded the General_relaxation saveframe to accept almost all info into
bmrblib.
Modified:
branches/bmrb/bmrblib/kinetics/general_relaxation.py
Modified: branches/bmrb/bmrblib/kinetics/general_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/general_relaxation.py?rev=9779&r1=9778&r2=9779&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/general_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/general_relaxation.py Wed Oct 14 19:09:27
2009
@@ -57,7 +57,7 @@
self.add_tag_categories()
- def add(self, data_type=None, frq=None, res_nums=None, res_names=None,
atom_names=None, isotope=None, data=None, errors=None,
sample_cond_list_id=None, sample_cond_list_label='$conditions_1',
temp_calibration=None, temp_control=None):
+ def add(self, data_type=None, sample_cond_list_id=None,
sample_cond_list_label='$conditions_1', temp_calibration=None,
temp_control=None, frq=None, details=None, assembly_atom_ids=None,
entity_assembly_ids=None, res_nums=None, seq_id=None, res_names=None,
atom_names=None, atom_types=None, isotope=None, data=None, errors=None,
rex_val=None, rex_err=None):
"""Add relaxation data to the data nodes.
@keyword data_type: The relaxation data type (one of 'R1' or
'R2').
@@ -70,6 +70,8 @@
@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.
@@ -80,6 +82,8 @@
@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.
@@ -94,25 +98,36 @@
raise NameError("The temperature control method has not been
specified.")
# The number of elements.
- self.N = len(res_nums)
+ N = len(res_nums)
# Place the args into the namespace.
- 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.sample_cond_list_id = translate(sample_cond_list_id)
self.sample_cond_list_label = translate(sample_cond_list_label)
self.temp_calibration = translate(temp_calibration)
self.temp_control = translate(temp_control)
+ self.frq = frq
+ self.details = translate(details)
+
+ # Convert to lists and check the lengths.
+ for name in ['assembly_atom_ids', 'entity_assembly_ids', 'res_nums',
'seq_id', 'res_names', 'atom_names', 'atom_types', 'isotope', 'data',
'errors', 'rex_val', 'rex_err']:
+ # Get the object.
+ obj = locals()[name]
+
+ # None objects.
+ if obj == None:
+ obj = [None] * N
+
+ # Check the length.
+ if len(obj) != 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 Rx specific variables.
self.rx_inc = self.rx_inc + 1
- self.rx_inc_list = translate([self.rx_inc] * self.N)
- self.generate_data_ids(self.N)
+ self.rx_inc_list = translate([self.rx_inc] * N)
+ self.generate_data_ids(N)
# The operators of the relaxation superoperator.
if data_type == 'R1':
@@ -216,6 +231,7 @@
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['RelaxationCoherenceType']],
tagvalues=[[self.variables['coherence']]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['RelaxationTypeCommonName']],
tagvalues=[[self.variables['coherence_common_name']]]))
self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['RelaxationValUnits']], tagvalues=[['s-1']]))
+ self.sf.frame.tagtables.append(TagTable(free=True,
tagnames=[self.tag_names_full['Details']], tagvalues=[[self.sf.details]]))
def read(self, tagtable):
@@ -266,6 +282,7 @@
self.tag_names['RelaxationCoherenceType'] =
'Relaxation_coherence_type'
self.tag_names['RelaxationTypeCommonName'] =
'Relaxation_type_common_name'
self.tag_names['RelaxationValUnits'] = 'Relaxation_val_units'
+ self.tag_names['Details'] = 'Details'
@@ -323,12 +340,18 @@
# Keys and objects.
info = [
['RxID', 'data_ids'],
+ ['AssemblyAtomID', 'assembly_atom_ids'],
+ ['EntityAssemblyID', 'entity_assembly_ids'],
['CompIndexID', 'res_nums'],
+ ['SeqID', 'seq_id'],
['CompID', 'res_names'],
['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']
]
@@ -354,9 +377,17 @@
# Tag names for the general relaxation data.
self.tag_names['RxID'] = 'ID'
+ self.tag_names['AssemblyAtomID'] = 'Assembly_atom_ID'
+ self.tag_names['EntityAssemblyID'] = 'Entity_assembly_ID'
+ self.tag_names['EntityID'] = 'Entity_ID'
self.tag_names['CompIndexID'] = 'Comp_index_ID'
+ self.tag_names['SeqID'] = 'Seq_ID'
self.tag_names['CompID'] = 'Comp_ID'
self.tag_names['AtomID'] = 'Atom_ID'
- self.tag_names['Val'] = 'Val'
- self.tag_names['ValErr'] = 'Val_err'
- self.tag_names['GeneralRelaxationListID'] =
'General_Relaxation_list_ID'
+ self.tag_names['AtomType'] = 'Atom_type'
+ self.tag_names['AtomIsotopeNumber'] = 'Atom_isotope_number'
+ self.tag_names['Val'] = 'General_relaxation_val'
+ self.tag_names['ValErr'] = 'General_relaxation_val_err'
+ self.tag_names['RexVal'] = 'Rex_val'
+ self.tag_names['RexErr'] = 'Rex_err'
+ self.tag_names['GeneralRelaxationListID'] =
'General_relaxation_list_ID'
r9779 - /branches/bmrb/bmrblib/kinetics/general_relaxation.py