Author: bugman
Date: Tue Oct 27 16:34:45 2009
New Revision: 9809
URL: http://svn.gna.org/viewcvs/relax?rev=9809&view=rev
Log:
Expansion of the chemical shift anisotropy saveframe.
Modified:
branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py
Modified: branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py?rev=9809&r1=9808&r2=9809&view=diff
==============================================================================
--- branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py (original)
+++ branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py Tue Oct 27
16:34:45 2009
@@ -46,30 +46,46 @@
# Place the data nodes into the namespace.
self.datanodes = datanodes
+ # The number of CSA data sets.
+ self.csa_inc = 0
+
# Add the specific tag category objects.
self.add_tag_categories()
- def add(self, frq=None, res_nums=None, res_names=None, atom_names=None,
atom_types=None, isotope=None, csa=None, units='ppm'):
+ 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, csa=None, csa_error=None, units='ppm'):
"""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 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 csa: The CSA values in ppm.
- @type csa: 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 csa: The CSA values in ppm.
+ @type csa: list of float
"""
# Check the ID info.
+ no_missing(entity_ids, 'entity ID numbers')
no_missing(res_nums, 'residue numbers')
no_missing(res_names, 'residue names')
no_missing(atom_names, 'atom names')
@@ -87,7 +103,25 @@
self.isotope = translate(isotope)
self.csa = translate(csa)
+ # 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', 'csa', 'csa_error']:
+ # 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 CSA specific variables.
+ self.csa_inc = self.csa_inc + 1
+ self.csa_inc_list = translate([self.csa_inc] * N)
self.generate_data_ids(N)
# Set up the version specific variables.
@@ -243,13 +277,19 @@
# Keys and objects.
info = [
- ['CSAnisotropyID', 'data_ids'],
- ['CompIndexID', 'res_nums'],
- ['CompID', 'res_names'],
- ['AtomID', 'atom_names'],
- ['AtomType', 'atom_types'],
- ['AtomIsotopeNumber', 'isotope'],
- ['Val', 'csa']
+ ['CSAnisotropyID', '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', 'csa'],
+ ['ValErr', 'csa_error'],
+ ['ChemShiftAnisotropyID', 'csa_inc_list']
]
# Get the TabTable.
@@ -300,10 +340,15 @@
# Tag names for the relaxation data.
self.tag_names['CSAnisotropyID'] = 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'] = 'value'
self.tag_names['ValErr'] = 'value_error'
+ self.tag_names['ChemShiftAnisotropyID'] = 'Chem_shift_anisotropy_ID'
r9809 - /branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py