Author: bugman
Date: Mon Mar 9 19:44:09 2009
New Revision: 8943
URL: http://svn.gna.org/viewcvs/relax?rev=8943&view=rev
Log:
Support for all model-free parameters has been added to the BMRB library.
Modified:
branches/bmrb/bmrblib/tag_category.py
branches/bmrb/bmrblib/thermodynamics/order_parameters.py
branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
Modified: branches/bmrb/bmrblib/tag_category.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/tag_category.py?rev=8943&r1=8942&r2=8943&view=diff
==============================================================================
--- branches/bmrb/bmrblib/tag_category.py (original)
+++ branches/bmrb/bmrblib/tag_category.py Mon Mar 9 19:44:09 2009
@@ -22,6 +22,10 @@
# Module docstring.
"""The TagCategory base class."""
+
+# relax module imports.
+from pystarlib.TagTable import TagTable
+
class TagCategory:
"""The base class for tag category classes."""
@@ -62,6 +66,38 @@
return self.tag_category_label_full + tag_name
+ def create_tag_table(self, info):
+ """Create and return a tag table based on the info structure.
+
+ @param info: The key and object pair list. This consists of the
keys of
+ self.tag_names being the first element and the names
of the objects being
+ the second element, both of the second dimension.
The fist dimension are
+ the different pairs.
+ @type info: list of list of str
+ @return: The tag table.
+ @rtype: TagTable instance
+ """
+
+ # Init.
+ keys = self.tag_names.keys()
+ tag_names = []
+ tag_values = []
+
+ # Loop over the keys and object names of the info structure.
+ for key, name in info:
+ # Key check.
+ if key not in keys:
+ raise NameError, "The key '%s' is not located in the
self.tag_names structure." % key
+
+ # The tag names and values (skipping empty entries in
self.tag_names).
+ if self.tag_names[key] != None:
+ tag_names.append(self.tag_names_full[key])
+ tag_values.append(getattr(self.sf, name))
+
+ # Add the data and return the table.
+ return TagTable(tagnames=tag_names, tagvalues=tag_values)
+
+
def tag_setup(self, tag_category_label=None, sep=None):
"""Setup the tag names.
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters.py?rev=8943&r1=8942&r2=8943&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters.py Mon Mar 9
19:44:09 2009
@@ -50,7 +50,7 @@
self.add_tag_categories()
- def add(self, res_nums=None, res_names=None, atom_names=None):
+ 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):
"""Add relaxation data to the data nodes.
@keyword res_nums: The residue number list.
@@ -59,6 +59,30 @@
@type res_names: list of str
@keyword atom_names: The atom name list.
@type atom_names: list of str
+ @keyword s2: The S2 values.
+ @type s2: list of float
+ @keyword s2_err: The S2 errors.
+ @type s2_err: list of float
+ @keyword s2f: The S2f values.
+ @type s2f: list of float
+ @keyword s2f_err: The S2f errors.
+ @type s2f_err: list of float
+ @keyword s2s: The S2s values.
+ @type s2s: list of float
+ @keyword s2s_err: The S2s errors.
+ @type s2s_err: list of float
+ @keyword te: The te values.
+ @type te: list of float
+ @keyword te_err: The te errors.
+ @type te_err: list of float
+ @keyword tf: The tf values.
+ @type tf: list of float
+ @keyword tf_err: The tf errors.
+ @type tf_err: list of float
+ @keyword ts: The ts values.
+ @type ts: list of float
+ @keyword ts_err: The ts errors.
+ @type ts_err: list of float
"""
# Check the ID info.
@@ -66,10 +90,27 @@
no_missing(res_names, 'residue names of the model-free data')
no_missing(atom_names, 'atom names of the model-free data')
- # Place the args into the namespace.
- self.res_nums = translate(res_nums)
- self.res_names = translate(res_names)
- self.atom_names = translate(atom_names)
+ # 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']
+
+ # Number of elements.
+ N = len(res_nums)
+
+ # Loop over the objects.
+ for name in names:
+ # 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))
# Initialise the save frame.
self.frame = SaveFrame(title='order_parameters')
@@ -168,26 +209,29 @@
def create(self):
"""Create the OrderParameter tag category."""
- # The relaxation tag names.
- tag_names = []
- missing = []
- for key in ['SeqID', 'CompID', 'AtomID']:
- if not self.tag_names.has_key(key):
- missing.append(key)
- else:
- tag_names.append(self.tag_names_full[key])
-
- # The tag values.
- tag_values = []
- if 'SeqID' not in missing:
- tag_values.append(self.sf.res_nums)
- if 'CompID' not in missing:
- tag_values.append(self.sf.res_names)
- if 'AtomID' not in missing:
- tag_values.append(self.sf.atom_names)
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=tag_values)
+ # Keys and objects.
+ info = [
+ ['SeqID', 'res_nums'],
+ ['CompID', 'res_names'],
+ ['AtomID', 'atom_names'],
+ ['OrderParamVal', 's2'],
+ ['OrderParamValErr', 's2_err'],
+ ['TauEVal', 'te'],
+ ['TauEValErr', 'te_err'],
+ ['TauFVal', 'tf'],
+ ['TauFValErr', 'tf_err'],
+ ['TauSVal', 'ts'],
+ ['TauSValErr', 'ts_err'],
+ ['RexVal', 'rex'],
+ ['RexValErr', 'rex_err'],
+ ['Sf2Val', 's2f'],
+ ['Sf2ValErr', 's2f_err'],
+ ['Ss2Val', 's2s'],
+ ['Ss2ValErr', 's2s_err']
+ ]
+
+ # Get the TabTable.
+ table = self.create_tag_table(info)
# Add the tagtable to the save frame.
self.sf.frame.tagtables.append(table)
@@ -209,3 +253,17 @@
self.tag_names['SeqID'] = 'Residue_seq_code'
self.tag_names['CompID'] = 'Residue_label'
self.tag_names['AtomID'] = 'Atom_name'
+ self.tag_names['OrderParamVal'] = 'S2_value'
+ self.tag_names['OrderParamValErr'] = 'S2_value_fit_error'
+ self.tag_names['TauEVal'] = 'Tau_e_value'
+ self.tag_names['TauEValErr'] = 'Tau_e_value_fit_error'
+ self.tag_names['TauFVal'] = 'Tau_f_value'
+ self.tag_names['TauFValErr'] = 'Tau_f_value_fit_error'
+ self.tag_names['TauSVal'] = 'Tau_s_value'
+ self.tag_names['TauSValErr'] = 'Tau_s_value_fit_error'
+ self.tag_names['RexVal'] = None
+ self.tag_names['RexValErr'] = None
+ self.tag_names['Sf2Val'] = 'S2f_value'
+ self.tag_names['Sf2ValErr'] = 'S2f_value_fit_error'
+ self.tag_names['Ss2Val'] = 'S2s_value'
+ self.tag_names['Ss2ValErr'] = 'S2s_value_fit_error'
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py?rev=8943&r1=8942&r2=8943&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters_v3_1.py Mon Mar 9
19:44:09 2009
@@ -83,3 +83,17 @@
self.tag_names['SeqID'] = 'Seq_ID'
self.tag_names['CompID'] = 'Comp_ID'
self.tag_names['AtomID'] = 'Atom_ID'
+ self.tag_names['OrderParamVal'] = 'Order_param_val'
+ self.tag_names['OrderParamValErr'] = 'Order_param_val_fit_err'
+ self.tag_names['TauEVal'] = 'Tau_e_val'
+ self.tag_names['TauEValErr'] = 'Tau_e_val_fit_err'
+ self.tag_names['TauFVal'] = 'Tau_f_val'
+ self.tag_names['TauFValErr'] = 'Tau_f_val_fit_err'
+ self.tag_names['TauSVal'] = 'Tau_s_val'
+ self.tag_names['TauSValErr'] = 'Tau_s_val_fit_err'
+ self.tag_names['RexVal'] = 'Rex_val'
+ self.tag_names['RexValErr'] = 'Rex_val_fit_err'
+ self.tag_names['Sf2Val'] = 'S2f_val'
+ self.tag_names['Sf2ValErr'] = 'S2f_val_fit_err'
+ self.tag_names['Ss2Val'] = 'S2s_val'
+ self.tag_names['Ss2ValErr'] = 'S2s_val_fit_err'
r8943 - in /branches/bmrb/bmrblib: tag_category.py thermodynamics/order_parameters.py thermodynamics/order_parameters_v3_1.py