r2695 - /branches/tensor_pdb/generic_fns/pdb.py -- October 29, 2006 - 06:52

Author: bugman
Date: Sun Oct 29 06:51:32 2006
New Revision: 2695

URL: http://svn.gna.org/viewcvs/relax?rev=2695&view=rev
Log:
Changed the CONECT record algorithm (for the tensor PDB) to allow more than 
four bonded atoms.

Multiple CONECT records are now generated for an atom if it is bonded to more 
than 4 other atoms.


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=2695&r1=2694&r2=2695&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Oct 29 06:51:32 2006
@@ -851,40 +851,48 @@
         # Create the CONECT records.
         connect_count = 0
         for array in atomic_arrays:
+            # No bonded atoms, hence no CONECT record is required.
+            if len(array) == 4:
+                continue
+
             # The atom number.
             atom_num = array[0]
 
-            # First bonded atom.
-            if len(array) > 5:
-                bonded1 = array[5]
-
-            # No CONECT record required!
-            else:
-                continue
-
-            # Second bonded atom.
-            if len(array) > 6:
-                bonded2 = array[6]
-            else:
-                bonded2 = ''
-
-            # Third bonded atom.
-            if len(array) > 7:
-                bonded3 = array[7]
-            else:
-                bonded3 = ''
-
-            # Forth bonded atom.
-            if len(array) > 8:
-                bonded4 = array[8]
-            else:
-                bonded4 = ''
-
-            # Write the CONECT record.
-            file.write("%-6s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" % 
('CONECT', atom_num, bonded1, bonded2, bonded3, bonded4, '', '', '', '', '', 
''))
-
-            # Increment the CONECT record count.
-            connect_count = connect_count + 1
+
+            # Initialise some data structures.
+            flush = 0
+            bonded_index = 0
+            bonded = ['', '', '', '']
+
+            # Loop over the bonded atoms.
+            for i in xrange(len(array[5:])):
+                # End of the array, hence create the CONECT record in this 
iteration.
+                if i == len(array[5:])-1:
+                    flush = 1
+
+                # Only four covalently bonded atoms allowed in one CONECT 
record.
+                if bonded_index == 3:
+                    flush = 1
+
+                # Get the bonded atom name.
+                bonded[bonded_index] = array[i+5]
+
+                # Increment the bonded_index value.
+                bonded_index = bonded_index + 1
+
+                # Generate the CONECT record and increment the counter.
+                if flush:
+                    # Write the CONECT record.
+                    file.write("%-6s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" % 
('CONECT', atom_num, bonded[0], bonded[1], bonded[2], bonded[3], '', '', '', 
'', '', ''))
+
+                    # Increment the CONECT record count.
+                    connect_count = connect_count + 1
+
+                    # Reset the flush flag, the bonded atom count, and the 
bonded atom names.
+                    flush = 0
+                    bonded_index = 0
+                    bonded = ['', '', '', '']
+
 
         # 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(self.atomic_data), 1, connect_count, 
0))