Author: bugman
Date: Wed Jan 14 14:07:39 2009
New Revision: 8438
URL: http://svn.gna.org/viewcvs/relax?rev=8438&view=rev
Log:
Created a new structural API method, pack_structs().
This has the fun job of mapping the original models and molecules of the PDB
(or which ever other
file format is read in the future) into the models and molecules stored
within relax. I.e.
molecules can be converted to models and vice versa.
Modified:
branches/multi_structure/generic_fns/structure/api_base.py
Modified: branches/multi_structure/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/api_base.py?rev=8438&r1=8437&r2=8438&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/api_base.py (original)
+++ branches/multi_structure/generic_fns/structure/api_base.py Wed Jan 14
14:07:39 2009
@@ -275,6 +275,70 @@
return len(self.structural_data)
+ def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None):
+ """From the given structural data, expand the structural data data
structure.
+
+ @param data_matrix: A matrix of structural objects.
+ @type data_matrix: list of lists of structural objects
+ @keyword orig_model_num: The original model numbers (for storage).
+ @type orig_model_num: list of int
+ @keyword set_model_num: The new model numbers (for model
renumbering).
+ @type set_model_num: list of int
+ @keyword orig_mol_num: The original molecule numbers (for
storage).
+ @type orig_mol_num: list of int
+ @keyword set_mol_name: The molecule names (for naming the
molecules).
+ @type set_mol_name: list of str
+ """
+
+ # Test the number of models.
+ if len(orig_model_num) != len(data_matrix):
+ raise RelaxError, "Structural data mismatch, %s original models
verses %s in the structural data." % (len(orig_model_num), len(data_matrix))
+
+ # Test the number of molecules.
+ if len(orig_mol_num) != len(data_matrix[0]):
+ raise RelaxError, "Structural data mismatch, %s original
molecules verses %s in the structural data." % (len(orig_mol_num),
len(data_matrix[0]))
+
+ # Test the model mapping.
+ if len(set_model_num) != len(data_matrix):
+ raise RelaxError, "Failure of the mapping of new model numbers,
%s new model numbers verses %s models in the structural data." %
(len(set_model_num), len(data_matrix))
+
+ # Test the structure mapping.
+ if len(set_mol_num) != len(data_matrix[0]):
+ raise RelaxError, "Failure of the mapping of new molecule names,
%s new molecule names verses %s molecules in the structural data." %
(len(set_mol_num), len(data_matrix[0]))
+
+ # Test that the target models and structures are absent, and get the
already existing model numbers.
+ current_models = []
+ for i in range(len(self.structural_data)):
+ # Create a list of current models.
+ current_models.append(self.structural_data[i].num)
+
+ # Loop over the structures.
+ for j in range(len(self.structural_data[i])):
+ if self.structural_data[i].num in set_model_num and
self.structural_data[i].mol[j].name in set_mol_name:
+ raise RelaxError, "The molecule %s of model %s already
exists." % (self.structural_data[i].mol[j].name, self.structural_data[i].num)
+
+ # Loop over the models.
+ for i in range(len(set_model_num)):
+ # The model doesn't currently exist.
+ if set_model_num[i] not in current_models:
+ # Create the model.
+ self.structural_data.add_item(set_model_num[i])
+
+ # Add the model number to the current_models list.
+ current_models.append(set_model_num[i])
+
+ # Get the model.
+ model = self.structural_data[-1]
+
+ # Otherwise get the pre-existing model.
+ else:
+ model =
self.structural_data[current_models.index(set_model_num[i])]
+
+ # Pack the structures.
+ for j in range(len(set_mol_name)):
+ model.add_item(mol_name=set_mol_name[j],
mol_cont=data_matrix[i][j])
+
+
def to_xml(self, doc, element):
"""Prototype method for converting the structural object to an XML
representation.
r8438 - /branches/multi_structure/generic_fns/structure/api_base.py