r2923 - in /1.3: generic_fns/pymol.py prompt/pymol.py -- December 07, 2006 - 06:43

Author: bugman
Date: Thu Dec  7 06:43:09 2006
New Revision: 2923

URL: http://svn.gna.org/viewcvs/relax?rev=2923&view=rev
Log:
Addition of the user function 'structure.vector_dist()'.

This function will display the PDB representation of the XH vector 
distribution overlain over the
macromolecular structure within PyMOL.


Modified:
    1.3/generic_fns/pymol.py
    1.3/prompt/pymol.py

Modified: 1.3/generic_fns/pymol.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol.py?rev=2923&r1=2922&r2=2923&view=diff
==============================================================================
--- 1.3/generic_fns/pymol.py (original)
+++ 1.3/generic_fns/pymol.py Thu Dec  7 06:43:09 2006
@@ -260,6 +260,36 @@
         self.pipe_write("cmd.delete('sele')")
 
 
+    def vector_dist(self, run=None, file=None):
+        """Display the XH bond vector distribution.
+
+        @param run:     The run
+        @type run:      str
+        @param file:    The vector distribution PDB file.
+        @type file:     str
+        """
+
+        # Arguments.
+        self.run = run
+
+        # Test if the run exists.
+        if not self.run in self.relax.data.run_names:
+            raise RelaxNoRunError, self.run
+
+        # The file root.
+        file_root = self.relax.IO.file_root(file)
+
+        # Read in the vector distribution PDB file.
+        self.pipe_write("load " + file)
+
+
+        # Create a surface.
+        ###################
+
+        # Select the vector distribution.
+        self.pipe_write("cmd.show('surface', " + `file_root` + ")")
+
+
     def view(self, run=None):
         """Function for running PyMOL."""
 

Modified: 1.3/prompt/pymol.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/pymol.py?rev=2923&r1=2922&r2=2923&view=diff
==============================================================================
--- 1.3/prompt/pymol.py (original)
+++ 1.3/prompt/pymol.py Thu Dec  7 06:43:09 2006
@@ -303,6 +303,50 @@
         self.__relax__.generic.pymol.tensor_pdb(run=run, file=file)
 
 
+    def vector_dist(self, run=None, file='XH_dist.pdb'):
+        """Function displaying the PDB file representation of the XH vector 
distribution.
+
+        Keyword Arguments
+        ~~~~~~~~~~~~~~~~~
+
+        run:  The name of the run.
+
+        file:  The name of the PDB file containing the vector distribution.
+
+
+        Description
+        ~~~~~~~~~~~
+
+        A PDB file of the macromolecule must have previously been loaded as 
the vector distribution
+        will be overlain with the macromolecule within PyMOL.  The PDB file 
containing the vector
+        distribution must be created using the complementary 
'pdb.create_vector_dist()' user
+        function.
+
+        The vector distribution PDB file is read in using the command:
+
+            load file
+
+        """
+
+        # Function intro text.
+        if self.__relax__.interpreter.intro:
+            text = sys.ps3 + "pymol.vector_dist("
+            text = text + "run=" + `run`
+            text = text + ", file=" + `file` + ")"
+            print text
+
+        # The run name.
+        if type(run) != str:
+            raise RelaxStrError, ('run', run)
+
+        # The file name.
+        if type(file) != str:
+            raise RelaxStrError, ('file name', file)
+
+        # Execute the functional code.
+        self.__relax__.generic.pymol.vector_dist(run=run, file=file)
+
+
     def view(self, run=None):
         """Function for viewing the collection of molecules extracted from 
the PDB file.