Author: bugman
Date: Tue Mar 10 15:19:03 2009
New Revision: 8955
URL: http://svn.gna.org/viewcvs/relax?rev=8955&view=rev
Log:
Renamed the bmrblib.tag_category module to bmrblib.base_classes.
Added:
branches/bmrb/bmrblib/base_classes.py
- copied unchanged from r8954, branches/bmrb/bmrblib/tag_category.py
Removed:
branches/bmrb/bmrblib/tag_category.py
Modified:
branches/bmrb/bmrblib/__init__.py
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/thermodynamics/order_parameters.py
Modified: branches/bmrb/bmrblib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/__init__.py?rev=8955&r1=8954&r2=8955&view=diff
==============================================================================
--- branches/bmrb/bmrblib/__init__.py (original)
+++ branches/bmrb/bmrblib/__init__.py Tue Mar 10 15:19:03 2009
@@ -24,7 +24,7 @@
"""Package for interfacing with the BMRB (http://www.bmrb.wisc.edu/) by
handling NMR-STAR formatted files."""
-__all__ = ['misc',
+__all__ = ['base_classes',
+ 'misc',
'nmr_star_dict',
- 'nmr_star_dict_v3_1',
- 'tag_category']
+ 'nmr_star_dict_v3_1']
Modified: branches/bmrb/bmrblib/assembly_supercategory/entity.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/assembly_supercategory/entity.py?rev=8955&r1=8954&r2=8955&view=diff
==============================================================================
--- branches/bmrb/bmrblib/assembly_supercategory/entity.py (original)
+++ branches/bmrb/bmrblib/assembly_supercategory/entity.py Tue Mar 10
15:19:03 2009
@@ -27,8 +27,8 @@
"""
# relax module imports.
+from bmrblib.base_classes import TagCategory
from bmrblib.misc import translate
-from bmrblib.tag_category import TagCategory
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
Modified: branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py?rev=8955&r1=8954&r2=8955&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_NOEs.py Tue Mar 10 15:19:03 2009
@@ -27,9 +27,9 @@
"""
# relax module imports.
+from bmrblib.base_classes import TagCategory
from bmrblib.misc import no_missing, translate
from bmrblib.kinetics.relax_base import HeteronuclRxList, RelaxSaveframe, Rx
-from bmrblib.tag_category import TagCategory
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
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=8955&r1=8954&r2=8955&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T1_relaxation.py Tue Mar 10
15:19:03 2009
@@ -27,9 +27,9 @@
"""
# relax module imports.
+from bmrblib.base_classes import TagCategory
from bmrblib.misc import no_missing, translate
from bmrblib.kinetics.relax_base import HeteronuclRxList, RelaxSaveframe, Rx
-from bmrblib.tag_category import TagCategory
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
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=8955&r1=8954&r2=8955&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py (original)
+++ branches/bmrb/bmrblib/kinetics/heteronucl_T2_relaxation.py Tue Mar 10
15:19:03 2009
@@ -27,9 +27,9 @@
"""
# relax module imports.
+from bmrblib.base_classes import TagCategory
from bmrblib.misc import no_missing, translate
from bmrblib.kinetics.relax_base import HeteronuclRxList, RelaxSaveframe, Rx
-from bmrblib.tag_category import TagCategory
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
Modified: branches/bmrb/bmrblib/kinetics/relax_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/kinetics/relax_base.py?rev=8955&r1=8954&r2=8955&view=diff
==============================================================================
--- branches/bmrb/bmrblib/kinetics/relax_base.py (original)
+++ branches/bmrb/bmrblib/kinetics/relax_base.py Tue Mar 10 15:19:03 2009
@@ -24,7 +24,7 @@
"""Base classes for the relaxation data."""
# relax module imports.
-from bmrblib.tag_category import BaseSaveframe, TagCategory
+from bmrblib.base_classes import BaseSaveframe, TagCategory
class RelaxSaveframe(BaseSaveframe):
Removed: branches/bmrb/bmrblib/tag_category.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/tag_category.py?rev=8954&view=auto
==============================================================================
--- branches/bmrb/bmrblib/tag_category.py (original)
+++ branches/bmrb/bmrblib/tag_category.py (removed)
@@ -1,139 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2009 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""The TagCategory base class."""
-
-# relax module imports.
-from bmrblib.misc import translate
-from pystarlib.TagTable import TagTable
-
-
-class BaseSaveframe:
- """The base class for the saveframe classes."""
-
- def generate_data_ids(self, N):
- """Generate the data ID structure.
-
- @keyword N: The number of data points.
- @type N: int
- """
-
- # The data ID values.
- self.data_ids = translate(range(1,N+1))
-
-
-
-class TagCategory:
- """The base class for tag category classes."""
-
- def __init__(self, sf):
- """Initialise the tag category object, placing the saveframe into
its namespace.
-
- @param sf: The saveframe object.
- @type sf: saveframe instance
- """
-
- # Place the saveframe and tag info into the namespace.
- self.sf = sf
-
- # The tag name dictionary.
- self.tag_names = {}
- self.tag_names_full = {}
-
- # The specific variables dictionary.
- self.variables = {}
-
- # Set up the tag information.
- self.tag_setup()
-
- # Generate the full names.
- for key, name in self.tag_names.iteritems():
- self.tag_names_full[key] = self.create_tag_label(name)
-
-
- def create_tag_label(self, tag_name):
- """Generate the full NMR-STAR tag name.
-
- @param tag_name: The name of the tag, without the tag category
label prefix.
- @type tag_name: str
- """
-
- # The full tag name.
- if tag_name:
- return self.tag_category_label_full + tag_name
-
-
- 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
- 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
- @keyword free: Flag to create a free STAR table.
- @type free: bool
- @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(free=free, tagnames=tag_names, tagvalues=tag_values)
-
-
- def tag_setup(self, tag_category_label=None, sep=None):
- """Setup the tag names.
-
- @keyword tag_category_label: The tag name prefix specific for the
tag category.
- @type tag_category_label: None or str
- @keyword sep: The string separating the tag name
prefix and suffix.
- @type sep: str
- """
-
- # Place the args into the class namespace.
- self.tag_category_label = tag_category_label
- if sep:
- self.sep = sep
- else:
- self.sep = '.'
-
- # Create the full tag label.
- self.tag_category_label_full = '_'
- if self.tag_category_label:
- self.tag_category_label_full = self.tag_category_label_full +
self.tag_category_label + self.sep
Modified: branches/bmrb/bmrblib/thermodynamics/order_parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/thermodynamics/order_parameters.py?rev=8955&r1=8954&r2=8955&view=diff
==============================================================================
--- branches/bmrb/bmrblib/thermodynamics/order_parameters.py (original)
+++ branches/bmrb/bmrblib/thermodynamics/order_parameters.py Tue Mar 10
15:19:03 2009
@@ -27,8 +27,8 @@
"""
# relax module imports.
+from bmrblib.base_classes import TagCategory
from bmrblib.misc import no_missing, translate
-from bmrblib.tag_category import TagCategory
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
r8955 - in /branches/bmrb/bmrblib: ./ assembly_supercategory/ kinetics/ thermodynamics/