r11527 - in /1.3: prompt/frame_order.py specific_fns/frame_order.py -- August 17, 2010 - 17:45

Author: bugman
Date: Tue Aug 17 17:45:08 2010
New Revision: 11527

URL: http://svn.gna.org/viewcvs/relax?rev=11527&view=rev
Log:
Created the frame_order.domain_to_pdb() user function to associated PDB files 
with domains.

This will be used to rotated the moving domain to the average position within 
pymol.


Modified:
    1.3/prompt/frame_order.py
    1.3/specific_fns/frame_order.py

Modified: 1.3/prompt/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/frame_order.py?rev=11527&r1=11526&r2=11527&view=diff
==============================================================================
--- 1.3/prompt/frame_order.py (original)
+++ 1.3/prompt/frame_order.py Tue Aug 17 17:45:08 2010
@@ -95,6 +95,49 @@
         frame_order_obj._cone_pdb(size=size, inc=inc, file=file, dir=dir, 
force=force)
 
 
+    def domain_to_pdb(self, domain=None, pdb=None):
+        """Match the domains to PDB files.
+
+        Keyword Arguments
+        ~~~~~~~~~~~~~~~~~
+
+        domain:  The domain to associate the PDB file to.
+
+        pdb:  The PDB file to associate the domain to.
+
+
+        Description
+        ~~~~~~~~~~~
+
+        To display the frame order cone models within Pymol, the two domains 
need to be associated
+        with PDB files.  Then the reference domain will be fixed in the PDB 
frame, and the moving
+        domain will be rotated to its average position.
+
+
+        Examples
+        ~~~~~~~~
+
+        To set the 'N' domain to the PDB file 'bax_N_1J7O_1st.pdb', type one 
of:
+
+        relax> frame_order.domain_to_pdb('N', 'bax_N_1J7O_1st.pdb')
+        relax> frame_order.domain_to_pdb(domain='N', 
pdb='bax_N_1J7O_1st.pdb')
+        """
+
+        # Function intro text.
+        if self._exec_info.intro:
+            text = self._exec_info.ps3 + "frame_order.domain_to_pdb("
+            text = text + "domain=" + repr(domain)
+            text = text + ", pdb=" + repr(pdb) + ")"
+            print(text)
+
+        # The argument checks.
+        arg_check.is_str(domain, 'domain')
+        arg_check.is_str(pdb, 'PDB file')
+
+        # Execute the functional code.
+        frame_order_obj._domain_to_pdb(domain=domain, pdb=pdb)
+
+
     def pivot(self, pivot=None):
         """Set the pivot point for the two body motion in the structural 
coordinate system.
 

Modified: 1.3/specific_fns/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=11527&r1=11526&r2=11527&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Tue Aug 17 17:45:08 2010
@@ -332,6 +332,31 @@
         pdb_file = open_write_file(file, dir, force=force)
         structure.write_pdb(pdb_file)
         pdb_file.close()
+
+
+    def _domain_to_pdb(self, domain=None, pdb=None):
+        """Match domains to PDB files.
+
+        @keyword domain:    The domain to associate the PDB file to.
+        @type domain:       str
+        @keyword pdb:       The PDB file to associate the domain to.
+        @type pdb:          str
+        """
+
+        # Check that the domain exists.
+        exists = False
+        for i in range(len(cdp.align_tensors)):
+            if hasattr(cdp.align_tensors[i], 'domain') and domain == 
cdp.align_tensors[i].domain:
+                exists = True
+        if not exists:
+            raise RelaxError("The domain '%s' cannot be found" % domain)
+
+        # Init if needed.
+        if not hasattr(cdp, 'domain_to_pdb'):
+            cdp.domain_to_pdb = []
+
+        # Add the data.
+        cdp.domain_to_pdb.append([domain, pdb])
 
 
     def _grid_row(self, incs, lower, upper, dist_type=None, end_point=True):