Author: bugman
Date: Tue Mar 10 11:09:26 2009
New Revision: 8946
URL: http://svn.gna.org/viewcvs/relax?rev=8946&view=rev
Log:
Large code simplification via abstraction.
Most of the code from the create() method of the non-free TagTables has been
abstracted away into
the TagCategory.create_tag_table() method.
Modified:
branches/bmrb/bmrblib/assembly_supercategory/entity.py
branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py
branches/bmrb/bmrblib/kinetics/relax_base.py
branches/bmrb/bmrblib/tag_category.py
Modified: branches/bmrb/bmrblib/assembly_supercategory/entity.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/assembly_supercategory/entity.py?rev=8946&r1=8945&r2=8946&view=diff
==============================================================================
--- branches/bmrb/bmrblib/assembly_supercategory/entity.py (original)
+++ branches/bmrb/bmrblib/assembly_supercategory/entity.py Tue Mar 10
11:09:26 2009
@@ -81,6 +81,9 @@
# Increment the number of entities.
self.entity_num = self.entity_num + 1
+
+ # The entity ID list.
+ self.entity_ids = [str(self.entity_num)]*len(self.res_nums)
# Initialise the save frame.
self.frame = SaveFrame(title=mol_name)
@@ -196,26 +199,15 @@
def create(self):
"""Create the Entity tag category."""
- # The tag names.
- tag_names = []
- missing = []
- for key in ['EntityCompIndexID', 'AuthSeqID', 'CompID', 'CompLabel',
'SfID', 'EntryID', 'EntityID']:
- 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 'EntityCompIndexID' not in missing:
- tag_values.append(self.sf.res_nums)
- if 'CompID' not in missing:
- tag_values.append(self.sf.res_names)
- if 'EntityID' not in missing:
-
tag_values.append([str(self.sf.entity_num)]*len(self.sf.res_nums))
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=tag_values)
+ # Keys and objects.
+ info = [
+ ['EntityCompIndexID', 'res_nums'],
+ ['CompID', 'res_names'],
+ ['EntityID', 'entity_ids']
+ ]
+
+ # Get the TabTable.
+ table = self.create_tag_table(info)
# Add the tagtable to the save frame.
self.sf.frame.tagtables.append(table)
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=8946&r1=8945&r2=8946&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Tue Mar 10 11:09:26 2009
@@ -188,38 +188,6 @@
class HeteronuclNOE(Rx):
"""Base class for the HeteronuclNOE tag category."""
- def create(self):
- """Create the HeteronuclNOE tag category."""
-
- # The relaxation tag names.
- tag_names = []
- missing = []
- for key in ['CompIndexID', 'CompID', 'AtomID', 'Val', 'ValErr']:
- 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 'CompIndexID' 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)
- if 'Val' not in missing:
- tag_values.append(self.sf.data)
- if 'ValErr' not in missing:
- tag_values.append(self.sf.errors)
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=tag_values)
-
- # Add the tagtable to the save frame.
- self.sf.frame.tagtables.append(table)
-
-
def tag_setup(self, tag_category_label=None, sep=None):
"""Replacement method for setting up the tag names.
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py?rev=8946&r1=8945&r2=8946&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Tue Mar 10
11:09:26 2009
@@ -197,38 +197,6 @@
class T1(Rx):
"""Base class for the T1 tag category."""
- def create(self):
- """Create the T1 tag category."""
-
- # The relaxation tag names.
- tag_names = []
- missing = []
- for key in ['CompIndexID', 'CompID', 'AtomID', 'Val', 'ValErr']:
- 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 'CompIndexID' 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)
- if 'Val' not in missing:
- tag_values.append(self.sf.data)
- if 'ValErr' not in missing:
- tag_values.append(self.sf.errors)
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=tag_values)
-
- # Add the tagtable to the save frame.
- self.sf.frame.tagtables.append(table)
-
-
def tag_setup(self, tag_category_label=None, sep=None):
"""Replacement method for setting up the tag names.
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py?rev=8946&r1=8945&r2=8946&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Tue Mar 10
11:09:26 2009
@@ -197,38 +197,6 @@
class T2(Rx):
"""Base class for the T2 tag category."""
- def create(self):
- """Create the T2 tag category."""
-
- # The relaxation tag names.
- tag_names = []
- missing = []
- for key in ['CompIndexID', 'CompID', 'AtomID', 'Val', 'ValErr']:
- 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 'CompIndexID' 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)
- if 'Val' not in missing:
- tag_values.append(self.sf.data)
- if 'ValErr' not in missing:
- tag_values.append(self.sf.errors)
-
- # Add the data.
- table = TagTable(tagnames=tag_names, tagvalues=tag_values)
-
- # Add the tagtable to the save frame.
- self.sf.frame.tagtables.append(table)
-
-
def tag_setup(self, tag_category_label=None, sep=None):
"""Replacement method for setting up the tag names.
Modified: branches/bmrb/bmrblib/kinetics/relax_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/relax_base.py?rev=8946&r1=8945&r2=8946&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/relax_base.py (original)
+++ branches/bmrb/bmrblib/kinetics/relax_base.py Tue Mar 10 11:09:26 2009
@@ -88,6 +88,25 @@
class Rx(TagCategory):
"""Base class for the Rx tag categories."""
+ def create(self):
+ """Create the Rx tag category."""
+
+ # Keys and objects.
+ info = [
+ ['CompIndexID', 'res_nums'],
+ ['CompID', 'res_names'],
+ ['AtomID', 'atom_names'],
+ ['Val', 'data'],
+ ['ValErr', 'errors']
+ ]
+
+ # Get the TabTable.
+ table = self.create_tag_table(info)
+
+ # Add the tagtable to the save frame.
+ self.sf.frame.tagtables.append(table)
+
+
def read(self, tagtable):
"""Extract the Rx tag category info.
Modified: branches/bmrb/bmrblib/tag_category.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/tag_category.py?rev=8946&r1=8945&r2=8946&view=diff
==============================================================================
--- branches/bmrb/bmrblib/tag_category.py (original)
+++ branches/bmrb/bmrblib/tag_category.py Tue Mar 10 11:09:26 2009
@@ -66,7 +66,7 @@
return self.tag_category_label_full + tag_name
- def create_tag_table(self, info):
+ def create_tag_table(self, info, free=False):
"""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
@@ -74,6 +74,8 @@
the second element, both of the second dimension.
The fist dimension are
the different pairs.
@type info: list of list of str
+ @keyword free: Flag to create a free STAR table.
+ @type free: bool
@return: The tag table.
@rtype: TagTable instance
"""
@@ -95,7 +97,7 @@
tag_values.append(getattr(self.sf, name))
# Add the data and return the table.
- return TagTable(tagnames=tag_names, tagvalues=tag_values)
+ return TagTable(free=free, tagnames=tag_names, tagvalues=tag_values)
def tag_setup(self, tag_category_label=None, sep=None):
r8946 - in /branches/bmrb/bmrblib: ./ assembly_supercategory/ kinetics/