r2698 - in /branches/tensor_pdb: generic_fns/molmol.py prompt/molmol.py -- October 29, 2006 - 07:38

Author: bugman
Date: Sun Oct 29 07:37:48 2006
New Revision: 2698

URL: http://svn.gna.org/viewcvs/relax?rev=2698&view=rev
Log:
Created the user function 'molmol.ribbon()'.

This function applies the Molmol ribbon style and is equivalent to clicking 
on 'ribbon' in the
Molmol side menu.


Modified:
    branches/tensor_pdb/generic_fns/molmol.py
    branches/tensor_pdb/prompt/molmol.py

Modified: branches/tensor_pdb/generic_fns/molmol.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/molmol.py?rev=2698&r1=2697&r2=2698&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/molmol.py (original)
+++ branches/tensor_pdb/generic_fns/molmol.py Sun Oct 29 07:37:48 2006
@@ -169,6 +169,27 @@
             self.command_history = self.command_history + command + "\n"
 
 
+    def ribbon(self, run=None):
+        """Apply the Molmol ribbon style."""
+
+        # Arguments.
+        self.run = run
+
+        # Test if the run exists.
+        if not self.run in self.relax.data.run_names:
+            raise RelaxNoRunError, self.run
+
+        # Calculate the protons.
+        self.pipe_write("CalcAtom 'H'")
+        self.pipe_write("CalcAtom 'HN'")
+
+        # Calculate the secondary structure.
+        self.pipe_write("CalcSecondary")
+
+        # Execute the ribbon macro.
+        self.pipe_write("XMacStand ribbon.mac")
+
+
     def view(self, run=None):
         """Function for running Molmol."""
 

Modified: branches/tensor_pdb/prompt/molmol.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/molmol.py?rev=2698&r1=2697&r2=2698&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/molmol.py (original)
+++ branches/tensor_pdb/prompt/molmol.py Sun Oct 29 07:37:48 2006
@@ -77,7 +77,9 @@
         Example
         ~~~~~~~
 
-        relax> molmol.command("InitAll yes")
+        To reinitialise the Molmol instance for the run 'aic', type:
+
+        relax> molmol.command("aic", "InitAll yes")
         """
 
         # Function intro text.
@@ -197,6 +199,48 @@
         # Execute the functional code.
         self.__relax__.generic.molmol.macro_exec(run=run, 
data_type=data_type, style=style, colour_start=colour_start, 
colour_end=colour_end, colour_list=colour_list)
 
+
+    def ribbon(self, run=None):
+        """Apply the Molmol ribbon style.
+
+        Keyword Arguments
+        ~~~~~~~~~~~~~~~~~
+
+        run:  The name of the run.
+
+
+        Description
+        ~~~~~~~~~~~
+
+        This function applies the Molmol ribbon style.  To do this, the 
following commands are
+        executed:
+
+            CalcAtom 'H'
+            CalcAtom 'HN'
+            CalcSecondary
+            XMacStand ribbon.mac
+
+
+        Example
+        ~~~~~~~
+
+        To apply the ribbon style to the PDB file loaded for the run 
'final', type:
+
+        relax> molmol.ribbon("final")
+        """
+
+        # Function intro text.
+        if self.__relax__.interpreter.intro:
+            text = sys.ps3 + "molmol.ribbon("
+            text = text + "run=" + `run` + ")"
+            print text
+
+        # The run name.
+        if type(run) != str:
+            raise RelaxStrError, ('run', run)
+
+        # Execute the functional code.
+        self.__relax__.generic.molmol.ribbon(run=run)
 
 
     def view(self, run=None):