r2667 - /branches/tensor_pdb/generic_fns/pdb.py -- October 26, 2006 - 08:20

Author: bugman
Date: Thu Oct 26 08:08:47 2006
New Revision: 2667

URL: http://svn.gna.org/viewcvs/relax?rev=2667&view=rev
Log:
Creation of a rudimentary PDB file for representing the diffusion tensor.

The new function 'self.write_pdb_file()' has been added which creates a 
properly formatted PDB file.
It creates HET, HETNAM, and FORMUL records for the pseudo-residue 'TNS'.  It 
also adds HETATM
records for each atom, adds the TER record, and then connects the appropriate 
atoms using CONECT
records.  The file is terminated with the MASTER and END records.  For a 
description of this, see
the post at https://mail.gna.org/public/relax-devel/2006-10/msg00136.html 
(Message-id:
<7f080ed10610252045r3dcbba38q58aa53142af96e5a@xxxxxxxxxxxxxx>).

The function 'self.create_tensor_pdb()' has been modified to create the data 
for the new
'self.write_pdb_file()' function.


Modified:
    branches/tensor_pdb/generic_fns/pdb.py

Modified: branches/tensor_pdb/generic_fns/pdb.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2667&r1=2666&r2=2667&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Thu Oct 26 08:08:47 2006
@@ -121,6 +121,7 @@
         # Final print out.
         print "    Total mass:      M = " + `M`
         print "    Center of mass:  R = " + `R`
+        print
 
         # Return the center of mass.
         return R
@@ -135,6 +136,9 @@
         self.dir = dir
         self.force = force
 
+        # Tests.
+        ########
+
         # Test if the run exists.
         if not run in self.relax.data.run_names:
             raise RelaxNoRunError, run
@@ -147,13 +151,50 @@
         if not self.load_seq and not len(self.relax.data.res[self.run]):
             raise RelaxNoSequenceError, self.run
 
-        # Open the PDB file for writing.
-        tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir, 
self.force)
+
+        # Initialise the PDB data.
+        ##########################
+
+        # PDB HETATM and CONECT data.
+        hetatm = []
+        conect = []
+
+        # Chain ID, residue number, residue name.
+        chain_id = 'A'
+        res_num = 1
+        res_name = 'TNS'
+        chemical_name = 'Tensor'
+        occupancy = 1.0
+        element = 'C'
+
+
+        # Center of mass.
+        #################
 
         # Calculate the center of mass.
         R = self.center_of_mass()
 
-        # Close the PDB file.
+        # Add the central atom.
+        hetatm.append(R)
+
+
+        # Connectivities.
+        #################
+
+        #conect.append(['1', '2'])
+        #conect.append(['2', '1'])
+
+
+        # Create the PDB file.
+        ######################
+
+        # Open the PDB file for writing.
+        tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir, 
force=self.force)
+
+        # Write the data.
+        self.write_pdb_file(tensor_pdb_file, hetatm, conect, chain_id, 
res_num, res_name, chemical_name, occupancy, element)
+
+        # Close the file.
         tensor_pdb_file.close()
 
 
@@ -485,3 +526,63 @@
 
             # Replace the temporary vector list with the normalised average 
vector.
             data.xh_vect = ave_vector / sqrt(dot(ave_vector, ave_vector))
+
+
+    def write_pdb_file(self, file, hetatm, conect, chain_id, res_num, 
res_name, chemical_name, occupancy, element):
+        """Function for creating a PDB file from the given data."""
+
+        # The HET record.
+        file.write("%-6s %3s  %1s%4s%1s  %5s     %-40s\n" % ('HET', 
res_name, chain_id, res_num, '', len(hetatm), ''))
+
+        # The HETNAM record.
+        file.write("%-6s  %2s %3s %-55s\n" % ('HETNAM', '', res_name, 
chemical_name))
+
+        # The FORMUL record (chemical formula).
+        file.write("%-6s  %2s  %3s %2s%1s%-51s\n" % ('FORMUL', 1, res_name, 
'', '', element+`len(hetatm)`))
+
+        # Loop over the HETATMs.
+        serial_num = 1
+        for vector in hetatm:
+            # Write the HETATM record.
+            file.write("%-6s%5s %4s%1s%3s %1s%4s%1s   
%8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n" % ('HETATM', serial_num, 
element+`serial_num`, '', res_name, chain_id, res_num, '', vector[0], 
vector[1], vector[2], occupancy, 0, '', element, ''))
+
+            # Increment the atom number.
+            serial_num = serial_num + 1
+
+        # Terminate (TER record).
+        file.write("%-6s%5s      %3s %1s%4s%1s\n" % ('TER', serial_num, 
res_name, chain_id, '', ''))
+
+        # Loop over the connections.
+        for array in conect:
+            # The atom.
+            atom_serial_num = array[0]
+
+            # First bonded atom.
+            bonded1 = array[1]
+
+            # Second bonded atom.
+            if len(array) > 2:
+                bonded2 = array[2]
+            else:
+                bonded2 = ''
+
+            # Third bonded atom.
+            if len(array) > 3:
+                bonded3 = array[3]
+            else:
+                bonded3 = ''
+
+            # Forth bonded atom.
+            if len(array) > 4:
+                bonded4 = array[4]
+            else:
+                bonded4 = ''
+
+            # Write the CONECT record.
+            file.write("%-6s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" % 
('CONECT', atom_serial_num, bonded1, bonded2, bonded3, bonded4, '', '', '', 
'', '', ''))
+
+        # MASTER record.
+        file.write("%-6s    %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" % 
('MASTER', 0, 0, 1, 0, 0, 0, 0, 0, len(hetatm), 1, len(conect), 0))
+
+        # END.
+        file.write("END\n")