r14922 - /1.3/prompt/structure.py -- October 26, 2011 - 11:25

Author: bugman
Date: Wed Oct 26 11:25:27 2011
New Revision: 14922

URL: http://svn.gna.org/viewcvs/relax?rev=14922&view=rev
Log:
Implemented the front end of the structure.superimpose user function.


Modified:
    1.3/prompt/structure.py

Modified: 1.3/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14922&r1=14921&r2=14922&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Wed Oct 26 11:25:27 2011
@@ -531,6 +531,68 @@
     _build_doc(rotate)
 
 
+    def superimpose(self, models=None, method='fit to mean', atom_id=None):
+        # Function intro text.
+        if self._exec_info.intro:
+            text = self._exec_info.ps3 + "structure.superimpose("
+            text = text + "models=" + repr(models)
+            text = text + ", method=" + repr(method)
+            text = text + ", atom_id=" + repr(atom_id) + ")"
+            print(text)
+
+        # The argument checks.
+        arg_check.is_int_list(models, 'model list', can_be_none=True)
+        arg_check.is_str(method, 'superimposition method')
+        arg_check.is_str(atom_id, 'atom identification string', 
can_be_none=True)
+
+        # Execute the functional code.
+        generic_fns.structure.main.superimpose(models=models, method=method, 
atom_id=atom_id)
+
+    # The function doc info.
+    superimpose._doc_title = "Superimpose a set of models of the same 
structure."
+    superimpose._doc_title_short = "Structural superimposition."
+    superimpose._doc_args = [
+        ["models", "The list of models to superimpose."],
+        ["method", "The superimposition method."],
+        ["atom_id", "The atom identification string."],
+    ]
+    superimpose._doc_desc = """
+        This allows a set of models of the same structure to be superimposed 
to each other.  Two superimposition methods are currently supported:
+
+            'fit to mean':  All models are fit to the mean structure.  This 
is the default and most accurate method for an ensemble description.  It is 
an iterative method which first calculates a mean structure and then fits 
each model to the mean structure using the Kabsch algorithm.  This is 
repeated until convergence.
+            'fit to first':  This is quicker but is not as accurate for an 
ensemble description.  The Kabsch algorithm is used to rotate and translate 
each model to be superimposed onto the first model.
+
+        If the list of models is not supplied, then all models will be 
superimposed.
+
+        The atom ID, which uses the same notation as the spin ID strings, 
can be used to restrict the superimpose calculation to certain molecules, 
residues, or atoms.  For example to only superimpose backbone heavy atoms in 
a protein, use the atom ID of '@N,C,CA,O', assuming those are the names of 
the atoms from the structural file.
+        """
+    superimpose._doc_examples = """
+        To superimpose all sets of models, type one of:
+
+        relax> structure.superimpose()
+        relax> structure.superimpose(method='fit to mean')
+
+
+        To superimpose the models 1, 2, 3, 5 onto model 4, type:
+
+        relax> structure.superimpose(models=[4, 1, 2, 3, 5], method='fit to 
first')
+
+
+        To superimpose an ensemble of protein structures using only the 
backbone heavy atoms, type
+        one of:
+
+        relax> structure.superimpose(atom_id='@N,C,CA,O')
+        relax> structure.superimpose(method='fit to mean', 
atom_id='@N,C,CA,O')
+
+
+        To superimpose model 2 onto model 3 using backbone heavy atoms, type 
one of:
+
+        relax> structure.superimpose([3, 2], 'fit to first', '@N,C,CA,O')
+        relax> structure.superimpose(models=[3, 2], method='fit to first', 
atom_id='@N,C,CA,O')
+         """
+    _build_doc(superimpose)
+
+
     def vectors(self, attached='H', spin_id=None, model=None, verbosity=1, 
ave=True, unit=True):
         # Function intro text.
         if self._exec_info.intro: