r18875 - /trunk/generic_fns/structure/internal.py -- March 19, 2013 - 13:55

Author: bugman
Date: Tue Mar 19 13:55:15 2013
New Revision: 18875

URL: http://svn.gna.org/viewcvs/relax?rev=18875&view=rev
Log:
SHEET PDB records are now read, stored, and written out by the internal 
structural object.

This affects the structure.read_pdb and structure.write_pdb user functions.  
The sheet is stored as
a metadata type object - its elements do not correspond to the atoms in the 
structural object.


Modified:
    trunk/generic_fns/structure/internal.py

Modified: trunk/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/internal.py?rev=18875&r1=18874&r2=18875&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Tue Mar 19 13:55:15 2013
@@ -454,6 +454,16 @@
                 if not hasattr(self, 'helices'):
                     self.helices = []
                 self.helices.append([helix_id, init_chain_id, init_res_name, 
init_seq_num, end_chain_id, end_res_name, end_seq_num, helix_class, length])
+
+            # A sheet.
+            if lines[i][:5] == 'SHEET':
+                # Parse the record.
+                record_type, strand, sheet_id, num_strands, init_res_name, 
init_chain_id, init_seq_num, init_icode, end_res_name, end_chain_id, 
end_seq_num, end_icode, sense, cur_atom, cur_res_name, cur_chain_id, 
cur_res_seq, cur_icode, prev_atom, prev_res_name, prev_chain_id, 
prev_res_seq, prev_icode = pdb_read.sheet(lines[i])
+
+                # Store the data.
+                if not hasattr(self, 'sheets'):
+                    self.sheets = []
+                self.sheets.append([strand, sheet_id, num_strands, 
init_res_name, init_chain_id, init_seq_num, init_icode, end_res_name, 
end_chain_id, end_seq_num, end_icode, sense, cur_atom, cur_res_name, 
cur_chain_id, cur_res_seq, cur_icode, prev_atom, prev_res_name, 
prev_chain_id, prev_res_seq, prev_icode])
 
         # Return the remaining lines.
         return lines[i:]
@@ -1877,6 +1887,18 @@
             pdb_write.helix(file, ser_num=index, helix_id=helix_id, 
init_chain_id=init_chain_id, init_res_name=init_res_name, 
init_seq_num=init_seq_num, end_chain_id=end_chain_id, 
end_res_name=end_res_name, end_seq_num=end_seq_num, helix_class=helix_class, 
length=length)
             index += 1
 
+        # The SHEET records.
+        ####################
+
+        # Printout.
+        print("SHEET")
+
+        # Loop over and unpack the helix data.
+        index = 1
+        for strand, sheet_id, num_strands, init_res_name, init_chain_id, 
init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode, 
sense, cur_atom, cur_res_name, cur_chain_id, cur_res_seq, cur_icode, 
prev_atom, prev_res_name, prev_chain_id, prev_res_seq, prev_icode in 
self.sheets:
+            pdb_write.sheet(file, strand=strand, sheet_id=sheet_id, 
num_strands=num_strands, init_res_name=init_res_name, 
init_chain_id=init_chain_id, init_seq_num=init_seq_num, 
init_icode=init_icode, end_res_name=end_res_name, end_chain_id=end_chain_id, 
end_seq_num=end_seq_num, end_icode=end_icode, sense=sense, cur_atom=cur_atom, 
cur_res_name=cur_res_name, cur_chain_id=cur_chain_id, 
cur_res_seq=cur_res_seq, cur_icode=cur_icode, prev_atom=prev_atom, 
prev_res_name=prev_res_name, prev_chain_id=prev_chain_id, 
prev_res_seq=prev_res_seq, prev_icode=prev_icode)
+            index += 1
+
 
         ######################
         # Coordinate section #