Author: bugman
Date: Fri Oct 9 20:24:11 2009
New Revision: 9711
URL: http://svn.gna.org/viewcvs/relax?rev=9711&view=rev
Log:
Created a data container for storing experimental details.
This will be used extensively for the BMRB file generation.
Added:
branches/bmrb/data/exp_info.py
Modified:
branches/bmrb/data/data_classes.py
branches/bmrb/data/pipe_container.py
Modified: branches/bmrb/data/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/data_classes.py?rev=9711&r1=9710&r2=9711&view=diff
==============================================================================
--- branches/bmrb/data/data_classes.py (original)
+++ branches/bmrb/data/data_classes.py Fri Oct 9 20:24:11 2009
@@ -22,6 +22,9 @@
# Python module imports.
from re import search
+
+# relax module imports.
+from relax_xml import fill_object_contents, xml_to_object
# Empty data container.
@@ -51,6 +54,17 @@
return text
+ def from_xml(self, exp_info_node):
+ """Recreate the container data structure from the XML container node.
+
+ @param exp_info_node: The container XML node.
+ @type exp_info_node: xml.dom.minicompat.Element instance
+ """
+
+ # Recreate all the data structures.
+ xml_to_object(exp_info_node, self)
+
+
def is_empty(self):
"""Method for testing if the Element container is empty.
@@ -73,3 +87,26 @@
# The Element container is empty.
return True
+
+
+ def to_xml(self, doc, element):
+ """Create an XML element for the container.
+
+ The variables self.name and self.desc must exist.
+
+
+ @param doc: The XML document object.
+ @type doc: xml.dom.minidom.Document instance
+ @param element: The element to add the container element to.
+ @type element: XML element object
+ """
+
+ # Create the container element and add it to the higher level
element.
+ tensor_element = doc.createElement(self.name)
+ element.appendChild(tensor_element)
+
+ # Set the container attributes.
+ tensor_element.setAttribute('desc', self.desc)
+
+ # Add all simple python objects within the PipeContainer to the pipe
element.
+ fill_object_contents(doc, tensor_element, object=self,
blacklist=['type'] + list(self.__class__.__dict__.keys()))
Added: branches/bmrb/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/exp_info.py?rev=9711&view=auto
==============================================================================
--- branches/bmrb/data/exp_info.py (added)
+++ branches/bmrb/data/exp_info.py Fri Oct 9 20:24:11 2009
@@ -1,0 +1,40 @@
+###############################################################################
+#
#
+# 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.
+"""Module holding the experimental information data container."""
+
+# relax module imports.
+from data_classes import Element
+
+
+class ExpInfo(Element):
+ """The experimental information data container."""
+
+ def __init__(self):
+ """Initialise the data container."""
+
+ # The name of the container.
+ self.name = 'exp_info'
+
+ # The description of the container.
+ self.desc = 'Experimental information'
Modified: branches/bmrb/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/pipe_container.py?rev=9711&r1=9710&r2=9711&view=diff
==============================================================================
--- branches/bmrb/data/pipe_container.py (original)
+++ branches/bmrb/data/pipe_container.py Fri Oct 9 20:24:11 2009
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2008 Edward d'Auvergne
#
+# Copyright (C) 2007-2009 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -27,6 +27,7 @@
# relax module imports.
from align_tensor import AlignTensorList
from diff_tensor import DiffTensorData
+from exp_info import ExpInfo
import generic_fns
from mol_res_spin import MoleculeList
from prototype import Prototype
@@ -62,7 +63,7 @@
text = "The data pipe storage object.\n"
# Special objects/methods (to avoid the getattr() function call on).
- spec_obj = ['mol', 'diff_tensor', 'structure']
+ spec_obj = ['exp_info', 'mol', 'diff_tensor', 'structure']
# Objects.
text = text + "\n"
@@ -80,6 +81,10 @@
if name == 'structure':
text = text + " structure: The 3D molecular data object\n"
+ # The experimental info data container.
+ if name == 'exp_info':
+ text = text + " exp_info: The data container for
experimental information\n"
+
# Skip the PipeContainer methods.
if name in list(self.__class__.__dict__.keys()):
continue
@@ -117,6 +122,15 @@
hybrid_node = relax_node.getElementsByTagName('hybrid')[0]
pipes_node = hybrid_node.getElementsByTagName('pipes')[0]
setattr(self, 'hybrid_pipes',
node_value_to_python(pipes_node.childNodes[0]))
+
+ # Get the experimental information data nodes and, if they exist,
fill the contents.
+ exp_info_nodes = relax_node.getElementsByTagName('exp_info')
+ if exp_info_nodes:
+ # Create the data container.
+ self.exp_info = ExpInfo()
+
+ # Fill its contents.
+ self.exp_info.from_xml(exp_info_nodes[0])
# Get the diffusion tensor data nodes and, if they exist, fill the
contents.
diff_tensor_nodes = relax_node.getElementsByTagName('diff_tensor')
@@ -214,10 +228,14 @@
global_element = doc.createElement('global')
element.appendChild(global_element)
global_element.setAttribute('desc', 'Global data located in the top
level of the data pipe')
- fill_object_contents(doc, global_element, object=self,
blacklist=['align_tensors', 'diff_tensor', 'hybrid_pipes', 'mol',
'pipe_type', 'structure'] + list(self.__class__.__dict__.keys()))
+ fill_object_contents(doc, global_element, object=self,
blacklist=['align_tensors', 'diff_tensor', 'exp_info', 'hybrid_pipes', 'mol',
'pipe_type', 'structure'] + list(self.__class__.__dict__.keys()))
# Hybrid info.
self.xml_create_hybrid_element(doc, element)
+
+ # Add the experimental information.
+ if hasattr(self, 'exp_info'):
+ self.exp_info.to_xml(doc, element)
# Add the diffusion tensor data.
if hasattr(self, 'diff_tensor'):
r9711 - in /branches/bmrb/data: data_classes.py exp_info.py pipe_container.py