Author: bugman
Date: Mon Oct 26 18:18:08 2009
New Revision: 9787
URL: http://svn.gna.org/viewcvs/relax?rev=9787&view=rev
Log:
Atom info changes in the model-free saveframe.
The 'Atom_ID' tag is now changed to 'Obs_atom_ID' for v3.2. The
Obs_atom_type and
Obs_atom_isotope_number tags have been added to the saveframe.
Modified:
branches/bmrb/bmrblib/thermodynamics/model_free.py
branches/bmrb/bmrblib/thermodynamics/model_free_v3_2.py
Modified: branches/bmrb/bmrblib/thermodynamics/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/model_free.py?rev=9787&r1=9786&r2=9787&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/model_free.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/model_free.py Mon Oct 26 18:18:08
2009
@@ -53,7 +53,7 @@
self.add_tag_categories()
- def add(self, sample_cond_list_id=None,
sample_cond_list_label='$conditions_1', te_units='s', tf_units='s',
ts_units='s', global_chi2=None, details=None, software_ids=None,
software_labels=None, assembly_atom_ids=None, entity_assembly_ids=None,
entity_id=None, res_nums=None, res_names=None, atom_names=None,
atom_types=None, local_tc=None, local_tc_err=None, s2=None, s2_err=None,
s2f=None, s2f_err=None, s2s=None, s2s_err=None, te=None, te_err=None,
tf=None, tf_err=None, ts=None, ts_err=None, rex=None, rex_err=None,
rex_frq=None, chi2=None, model_fit=None):
+ def add(self, sample_cond_list_id=None,
sample_cond_list_label='$conditions_1', te_units='s', tf_units='s',
ts_units='s', global_chi2=None, details=None, software_ids=None,
software_labels=None, assembly_atom_ids=None, entity_assembly_ids=None,
entity_id=None, res_nums=None, res_names=None, atom_names=None,
atom_types=None, isotope=None, local_tc=None, local_tc_err=None, s2=None,
s2_err=None, s2f=None, s2f_err=None, s2s=None, s2s_err=None, te=None,
te_err=None, tf=None, tf_err=None, ts=None, ts_err=None, rex=None,
rex_err=None, rex_frq=None, chi2=None, model_fit=None):
"""Add model-free data to the data nodes.
Note the te, tf, and ts units include the hidden radian unit as
these are angular correlation times, e.g. the default of 's' is really
's/rad', the average time it take to rotate 1 radian.
@@ -114,6 +114,8 @@
@type atom_names: list of str
@keyword atom_types: The atom types as IUPAC element
abbreviations for each spin.
@type atom_types: list of str
+ @keyword isotope: The isotope type list, ie 15 for
'15N'.
+ @type isotope: list of int
@keyword local_tc: The spin specific diffusional
correlation time.
@type local_tc: lost of float
@keyword local_tc_err: The spin specific diffusional
correlation time errors.
@@ -227,7 +229,7 @@
N = len(res_nums)
# Convert and translate all the spin specific args.
- names = ['assembly_atom_ids', 'entity_assembly_ids', 'entity_id',
'res_nums', 'res_names', 'atom_names', 'atom_types', 'local_tc',
'local_tc_err', 's2', 's2_err', 's2f', 's2f_err', 's2s', 's2s_err', 'te',
'te_err', 'tf', 'tf_err', 'ts', 'ts_err', 'rex', 'rex_err', 'chi2',
'model_fit']
+ names = ['assembly_atom_ids', 'entity_assembly_ids', 'entity_id',
'res_nums', 'res_names', 'atom_names', 'atom_types', 'isotope', 'local_tc',
'local_tc_err', 's2', 's2_err', 's2f', 's2f_err', 's2s', 's2s_err', 'te',
'te_err', 'tf', 'tf_err', 'ts', 'ts_err', 'rex', 'rex_err', 'chi2',
'model_fit']
for name in names:
# Get the object.
obj = locals()[name]
@@ -414,6 +416,7 @@
['CompID', 'res_names'],
['AtomID', 'atom_names'],
['AtomType', 'atom_types'],
+ ['AtomIsotopeNumber', 'isotope'],
['S2Val', 's2'],
['S2ValErr', 's2_err'],
['S2fVal', 's2f'],
@@ -459,6 +462,7 @@
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['S2Val'] = 'S2_value'
self.tag_names['S2ValErr'] = 'S2_value_fit_error'
self.tag_names['TauEVal'] = 'Tau_e_value'
Modified: branches/bmrb/bmrblib/thermodynamics/model_free_v3_2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/model_free_v3_2.py?rev=9787&r1=9786&r2=9787&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/model_free_v3_2.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/model_free_v3_2.py Mon Oct 26
18:18:08 2009
@@ -132,6 +132,7 @@
['CompID', 'res_names'],
['AtomID', 'atom_names'],
['AtomType', 'atom_types'],
+ ['AtomIsotopeNumber', 'isotope'],
['S2Val', 's2'],
['S2ValErr', 's2_err'],
['S2fVal', 's2f'],
@@ -182,7 +183,9 @@
self.tag_names['EntityID'] = 'Entity_ID'
self.tag_names['CompIndexID'] = 'Comp_index_ID'
self.tag_names['CompID'] = 'Comp_ID'
- self.tag_names['AtomID'] = 'Atom_ID'
+ self.tag_names['AtomID'] = 'Obs_atom_ID'
+ self.tag_names['AtomType'] = 'Obs_atom_type'
+ self.tag_names['AtomIsotopeNumber'] = 'Obs_atom_isotope_number'
self.tag_names['S2Val'] = 'S2_val'
self.tag_names['S2ValErr'] = 'S2_val_err'
self.tag_names['S2fVal'] = 'S2f_val'
r9787 - in /branches/bmrb/bmrblib/thermodynamics: model_free.py model_free_v3_2.py