r26206 - in /branches/frame_order_cleanup: ./ lib/structure/pdb_write.py -- October 08, 2014 - 09:24

Author: bugman
Date: Wed Oct  8 09:24:19 2014
New Revision: 26206

URL: http://svn.gna.org/viewcvs/relax?rev=26206&view=rev
Log:
Merged revisions 26205 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk

........
  r26205 | bugman | 2014-10-08 09:22:04 +0200 (Wed, 08 Oct 2014) | 9 lines
  
  Improvements for PDB creation in the relax library for out of bounds 
structural coordinates.
  
  The lib.structure.pdb_write module atom() and hetatm() functions will now 
more gracefully handle
  atomic coordinates which are outside of the PDB limits of [-999.999, 
9999.999].  When such
  coordinates are encountered, instead of producing a too long PDB line which 
does not pass the
  validation step, the functions will set the coordinates to the boundary 
value.  This will at least
  allow a valid PDB file to be created, despite the warping of the 
coordinates.
........

Modified:
    branches/frame_order_cleanup/   (props changed)
    branches/frame_order_cleanup/lib/structure/pdb_write.py

Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Oct  8 09:24:19 2014
@@ -1 +1 @@
-/trunk:1-26203
+/trunk:1-26205

Modified: branches/frame_order_cleanup/lib/structure/pdb_write.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/pdb_write.py?rev=26206&r1=26205&r2=26206&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/pdb_write.py     (original)
+++ branches/frame_order_cleanup/lib/structure/pdb_write.py     Wed Oct  8 
09:24:19 2014
@@ -269,6 +269,16 @@
     @type charge:           int
     """
 
+    # Coordinate bounds.
+    pdb_min = -999.999
+    pdb_max = 9999.999
+    coord = [x, y, z]
+    for i in range(3):
+        if coord[i] != '' and coord[i] < pdb_min:
+            coord[i] = pdb_min
+        if coord[i] != '' and coord[i] > pdb_max:
+            coord[i] = pdb_max
+
     # The formatted record.
     text = "%-6s%5s %-4s%1s%3s %1s%4s%1s   %8.3f%8.3f%8.3f%6.2f%6.2f         
 %2s%2s" % (
         'ATOM',
@@ -279,9 +289,9 @@
         _handle_none(chain_id),
         _handle_none(res_seq),
         _handle_none(icode),
-        _handle_none(x),
-        _handle_none(y),
-        _handle_none(z),
+        _handle_none(coord[0]),
+        _handle_none(coord[1]),
+        _handle_none(coord[2]),
         _handle_none(occupancy),
         _handle_none(temp_factor),
         _handle_none(element),
@@ -1082,6 +1092,16 @@
     @type charge:           int
     """
 
+    # Coordinate bounds.
+    pdb_min = -999.999
+    pdb_max = 9999.999
+    coord = [x, y, z]
+    for i in range(3):
+        if coord[i] != '' and coord[i] < pdb_min:
+            coord[i] = pdb_min
+        if coord[i] != '' and coord[i] > pdb_max:
+            coord[i] = pdb_max
+
     # The formatted record.
     text = "%-6s%5s %4s%1s%3s %1s%4s%1s   %8.3f%8.3f%8.3f%6.2f%6.2f          
%2s%2s" % (
         'HETATM',
@@ -1092,9 +1112,9 @@
         _handle_none(chain_id),
         _handle_none(res_seq),
         _handle_none(icode),
-        _handle_none(x),
-        _handle_none(y),
-        _handle_none(z),
+        _handle_none(coord[0]),
+        _handle_none(coord[1]),
+        _handle_none(coord[2]),
         _handle_none(occupancy),
         _handle_none(temp_factor),
         _handle_none(element),