r9142 - /branches/frame_order/prompt/frame_order.py -- June 25, 2009 - 12:00

Author: bugman
Date: Thu Jun 25 12:00:41 2009
New Revision: 9142

URL: http://svn.gna.org/viewcvs/relax?rev=9142&view=rev
Log:
Created the interface to the frame_order.cone_pdb() user function.


Modified:
    branches/frame_order/prompt/frame_order.py

Modified: branches/frame_order/prompt/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order/prompt/frame_order.py?rev=9142&r1=9141&r2=9142&view=diff
==============================================================================
--- branches/frame_order/prompt/frame_order.py (original)
+++ branches/frame_order/prompt/frame_order.py Thu Jun 25 12:00:41 2009
@@ -30,7 +30,7 @@
 # relax module imports.
 import help
 from specific_fns.setup import frame_order_obj
-from relax_errors import RelaxStrError
+from relax_errors import RelaxBoolError, RelaxLenError, RelaxListError, 
RelaxListNumError, RelaxNoneStrError, RelaxNumError, RelaxStrError
 
 
 class Frame_order:
@@ -44,6 +44,87 @@
 
         # Place relax in the class namespace.
         self.__relax__ = relax
+
+
+    def cone_pdb(self, pivot=None, scale=1.0, file='cone.pdb', dir=None, 
force=False):
+        """Create a PDB file representing the Frame Order cone models.
+
+        Keyword Arguments
+        ~~~~~~~~~~~~~~~~~
+
+        pivot:  The pivot point for the motion (e.g. the position between 
the 2 domains in PDB
+            coordinates).
+
+        scale:  Value for scaling the cone, which defaults to 10 Angstrom.
+
+        file:  The name of the PDB file to create.
+
+        dir:  The directory where the file is to be located.
+
+        force:  A flag which, if set to True, will overwrite the any 
pre-existing file.
+
+
+        Description
+        ~~~~~~~~~~~
+
+        This function creates a PDB file containing an artificial geometric 
structure representing
+        the Frame Order cone models.
+
+        There are four different types of residue within the PDB.  The pivot 
point is represented as
+        as a single carbon atom of the residue 'PIV'.  The cone consists of 
numerous H atoms of the
+        residue 'CON'.  The cone axis vector is presented as the residue 
'AXE' with one carbon atom
+        positioned at the pivot and the other 10 Angstrom away on the cone 
axis (modified by the
+        scale argument).  Finally, if Monte Carlo have been performed, there 
will be multiple 'MCC'
+        residues representing the cone for each simulation, and multiple 
'MCA' residues representing
+        the multiple cone axes.
+
+        To create the diffusion in a cone PDB representation, a uniform 
distribution of vectors on a
+        sphere is generated using spherical coordinates with the polar angle 
defined by the cone
+        axis.  By incrementing the polar angle using an arccos distribution, 
a radial array of
+        vectors representing latitude are created while incrementing the 
azimuthal angle evenly
+        creates the longitudinal vectors.  These are all placed into the PDB 
file as H atoms and are
+        all connected using PDB CONECT records.  Each H atom is connected to 
its two neighbours on
+        the both the longitude and latitude.  This creates a geometric PDB 
object with longitudinal
+        and latitudinal lines representing the filled cone.
+        """
+
+        # Function intro text.
+        if self.__relax__.interpreter.intro:
+            text = sys.ps3 + "frame_order.cone_pdb("
+            text = text + "pivot=" + `pivot`
+            text = text + ", scale=" + `scale`
+            text = text + ", file=" + `file`
+            text = text + ", dir=" + `dir`
+            text = text + ", force=" + `force` + ")"
+            print text
+
+        # Pivot point argument.
+        if type(pivot) != list:
+            raise RelaxListError, ('pivot point', pivot)
+        if len(pivot) != 3:
+            raise RelaxLenError, ('pivot point', 3)
+        for i in xrange(len(pivot)):
+            if type(pivot[i]) != int and type(pivot[i]) != float:
+                raise RelaxListNumError, ('pivot point', pivot)
+
+        # Scaling.
+        if type(scale) != float and type(scale) != int:
+            raise RelaxNumError, ('scaling factor', scale)
+
+        # File name.
+        if type(file) != str:
+            raise RelaxStrError, ('file name', file)
+
+        # Directory.
+        if dir != None and type(dir) != str:
+            raise RelaxNoneStrError, ('directory name', dir)
+
+        # The force flag.
+        if type(force) != bool:
+            raise RelaxBoolError, ('force flag', force)
+
+        # Execute the functional code.
+        frame_order_obj.cone_pdb(pivot=pivot, scale=scale, file=file, 
dir=dir, force=force)
 
 
     def select_model(self, model=None):