r27626 - /trunk/lib/structure/internal/molecules.py -- February 11, 2015 - 10:48

Author: bugman
Date: Wed Feb 11 10:48:24 2015
New Revision: 27626

URL: http://svn.gna.org/viewcvs/relax?rev=27626&view=rev
Log:
Modified the structure.read_pdb user function backend to skip water molecules.

All residues with the name 'HOH' are now skipped when loading PDB files.  
This is implemented in the
MolContainer.fill_object_from_pdb() method, and a RelaxWarning is printed 
listing the residue
numbers of all skipped waters.


Modified:
    trunk/lib/structure/internal/molecules.py

Modified: trunk/lib/structure/internal/molecules.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/molecules.py?rev=27626&r1=27625&r2=27626&view=diff
==============================================================================
--- trunk/lib/structure/internal/molecules.py   (original)
+++ trunk/lib/structure/internal/molecules.py   Wed Feb 11 10:48:24 2015
@@ -388,6 +388,7 @@
         """
 
         # Loop over the records.
+        water = []
         for record in records:
             # Nothing to do.
             if not record or record == '\n':
@@ -401,6 +402,11 @@
                 if record[:6] == 'HETATM':
                     record_type, serial, name, alt_loc, res_name, chain_id, 
res_seq, icode, x, y, z, occupancy, temp_factor, element, charge = 
pdb_read.hetatm(record)
 
+                # Skip waters.
+                if res_name == 'HOH':
+                    water.append(res_seq)
+                    continue
+
                 # Handle the alternate locations.
                 if alt_loc != None:
                     # Don't know what to do.
@@ -435,6 +441,9 @@
 
                     # Make the connection.
                     self.atom_connect(index1=self._atom_index(serial), 
index2=self._atom_index(bonded))
+
+        if len(water):
+            warn(RelaxWarning("Skipping the water molecules HOH %s." % 
water))
 
 
     def fill_object_from_xyz(self, records):