r9738 - in /branches/bmrb/bmrblib: NMR_parameters/chem_shift_anisotropy.py thermodynamics/order_parameters.py -- October 11, 2009 - 19:40

Author: bugman
Date: Sun Oct 11 19:40:06 2009
New Revision: 9738

URL: http://svn.gna.org/viewcvs/relax?rev=9738&view=rev
Log:
The element type is now being recorded in the CSA and model-free saveframes.


Modified:
    branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py
    branches/bmrb/bmrblib/thermodynamics/order_parameters.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=9738&r1=9737&r2=9738&view=diff
==============================================================================
--- branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py (original)
+++ branches/bmrb/bmrblib/NMR_parameters/chem_shift_anisotropy.py Sun Oct 11 
19:40:06 2009
@@ -50,7 +50,7 @@
         self.add_tag_categories()
 
 
-    def add(self, frq=None, res_nums=None, res_names=None, atom_names=None, 
isotope=None, csa=None, units='ppm'):
+    def add(self, frq=None, res_nums=None, res_names=None, atom_names=None, 
atom_types=None, isotope=None, csa=None, units='ppm'):
         """Add relaxation data to the data nodes.
 
         @keyword frq:           The spectrometer proton frequency, in Hz.
@@ -61,6 +61,8 @@
         @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 csa:           The CSA values in ppm.
@@ -81,6 +83,7 @@
         self.res_nums = translate(res_nums)
         self.res_names = translate(res_names)
         self.atom_names = translate(atom_names)
+        self.atom_types = translate(atom_types)
         self.isotope = translate(isotope)
         self.csa = translate(csa)
 
@@ -244,6 +247,7 @@
             ['CompIndexID',         'res_nums'],
             ['CompID',              'res_names'],
             ['AtomID',              'atom_names'],
+            ['AtomType',            'atom_types'],
             ['AtomIsotopeNumber',   'isotope'],
             ['Val',                 'csa']
         ]
@@ -299,6 +303,7 @@
         self.tag_names['CompIndexID'] = 'Residue_seq_code'
         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'

Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters.py?rev=9738&r1=9737&r2=9738&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters.py Sun Oct 11 
19:40:06 2009
@@ -50,7 +50,7 @@
         self.add_tag_categories()
 
 
-    def add(self, res_nums=None, res_names=None, atom_names=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):
+    def add(self, res_nums=None, res_names=None, atom_names=None, 
atom_types=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):
         """Add relaxation data to the data nodes.
 
         Note that units of 1/s are actually rad/s in NMR.  This is the 
hidden radian unit, which if
@@ -64,6 +64,8 @@
         @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 s2:            The S2 values.
         @type s2:               list of float
         @keyword s2_err:        The S2 errors.
@@ -126,7 +128,7 @@
         N = len(res_nums)
 
         # Object names.
-        names = ['res_nums', 'res_names', 'atom_names', 's2', 's2_err', 
's2f', 's2f_err', 's2s', 's2s_err', 'te', 'te_err', 'tf', 'tf_err', 'ts', 
'ts_err', 'rex', 'rex_err', 'chi2']
+        names = ['res_nums', 'res_names', 'atom_names', 'atom_types', 's2', 
's2_err', 's2f', 's2f_err', 's2s', 's2s_err', 'te', 'te_err', 'tf', 'tf_err', 
'ts', 'ts_err', 'rex', 'rex_err', 'chi2']
 
         # Loop over the objects.
         for name in names:
@@ -256,6 +258,7 @@
             ['CompIndexID',     'res_nums'],
             ['CompID',          'res_names'],
             ['AtomID',          'atom_names'],
+            ['AtomType',        'atom_types'],
             ['S2Val',           's2'],
             ['S2ValErr',        's2_err'],
             ['S2fVal',          's2f'],
@@ -297,6 +300,7 @@
         self.tag_names['CompIndexID'] = 'Residue_seq_code'
         self.tag_names['CompID'] = 'Residue_label'
         self.tag_names['AtomID'] = 'Atom_name'
+        self.tag_names['AtomType'] = 'Atom_type'
         self.tag_names['S2Val'] = 'S2_value'
         self.tag_names['S2ValErr'] = 'S2_value_fit_error'
         self.tag_names['TauEVal'] = 'Tau_e_value'