Author: bugman
Date: Mon Jan 19 11:00:55 2009
New Revision: 8503
URL: http://svn.gna.org/viewcvs/relax?rev=8503&view=rev
Log:
Redesigned add_molecule(). The method now is one line long!!!
Modified:
branches/multi_structure/generic_fns/structure/api_base.py
branches/multi_structure/generic_fns/structure/internal.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=8503&r1=8502&r2=8503&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/api_base.py (original)
+++ branches/multi_structure/generic_fns/structure/api_base.py Mon Jan 19
11:00:55 2009
@@ -62,19 +62,13 @@
self.structural_data = ModelList()
- def add_molecule(self, name=None, model=None, file=None, path=None,
str=None):
+ def add_molecule(self, name=None, model=None):
"""Prototype method stub for adding the given molecule to the store.
@keyword name: The molecule identification string.
@type name: str
@keyword model: The number of the model to add the molecule to.
@type model: int or None
- @keyword file: The name of the file containing the molecule.
- @type file: str
- @keyword path: The optional path where the file is located.
- @type path: str
- @keyword str: The molecule object, containing the structural
data.
- @type str: class instance
"""
# Raise the error.
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8503&r1=8502&r2=8503&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 19
11:00:55 2009
@@ -53,64 +53,17 @@
id = 'internal'
- def add_molecule(self, name=None, model=None, file=None, path=None,
str=None):
- """Add the given structure to the store.
-
- @keyword name: The structural identifier.
+ def add_molecule(self, name=None, model=None):
+ """Add a new molecule to the store.
+
+ @keyword name: The molecule identifier string.
@type name: str
@keyword model: The number of the model to add the molecule to.
@type model: int or None
- @keyword file: The name of the file containing the structure.
- @type file: str
- @keyword path: The optional path where the file is located.
- @type path: str
- @keyword str: The object containing the structural data.
- @type str: Structure_container instance
- """
-
- # Get the model.
- model_cont = self.get_model(model)
-
- # Check that the name does not already exist.
-
- # Some checks.
- if model != None:
- # Index check.
- if struct_index >= self.num:
- raise RelaxError, "The structure index of " + `struct_index` +
" cannot be more than the total number of structures of " + `self.num` + "."
-
- # ID check.
- if name != self.name[struct_index]:
- raise RelaxError, "The ID names " + `name` + " and " +
`self.name[struct_index]` + " do not match."
-
- # Model.
- if model != self.model[struct_index]:
- raise RelaxError, "The models " + `model` + " and " +
`self.model[struct_index]` + " do not match."
-
- # File name.
- if file != self.file[struct_index]:
- raise RelaxError, "The file names of " + `file` + " and " +
`self.file[struct_index]` + " do not match."
-
- # Initialise.
- else:
- self.num = self.num + 1
- self.name.append(name)
- self.model.append(model)
- self.file.append(file)
- self.path.append(path)
-
- # Initialise the structural object if not provided.
- if str == None:
- str = Structure_container()
-
- # Add the structural data.
- if struct_index != None:
- if struct_index >= len(self.structural_data):
- self.structural_data.append(str)
- else:
- self.structural_data[struct_index] = str
- else:
- self.structural_data.append(str)
+ """
+
+ # Create the structural data data structures.
+ self.pack_structs([[MolContainer()]], orig_model_num=[model],
set_mol_name=[name])
def __bonded_atom(self, attached_atom, index, struct_index):
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