r8115 - /1.3/generic_fns/structure/mass.py -- December 03, 2008 - 22:30

Author: bugman
Date: Wed Dec  3 22:30:16 2008
New Revision: 8115

URL: http://svn.gna.org/viewcvs/relax?rev=8115&view=rev
Log:
The centre_of_mass() function now only throws warnings rather than 
RelaxErrors.

This allows the CoM to be calculated even if a few elements are unknown or if 
the element record is
missing.


Modified:
    1.3/generic_fns/structure/mass.py

Modified: 1.3/generic_fns/structure/mass.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/mass.py?rev=8115&r1=8114&r2=8115&view=diff
==============================================================================
--- 1.3/generic_fns/structure/mass.py (original)
+++ 1.3/generic_fns/structure/mass.py Wed Dec  3 22:30:16 2008
@@ -22,12 +22,14 @@
 
 # Python module imports.
 from numpy import float64, zeros
+from warnings import warn
 
 # relax module imports.
 from generic_fns.mol_res_spin import return_molecule, return_residue, 
return_spin
 from generic_fns import pipes
 from physical_constants import return_atomic_mass
 from relax_errors import RelaxError, RelaxNoPdbError
+from relax_warnings import RelaxWarning
 
 
 
@@ -90,10 +92,13 @@
 
         # No element?
         if element == None:
-            raise RelaxError, "The element corresponding to '%s' does not 
exist in the PDB file.  Cannot calculate the centre of mass." % id
+            warn(RelaxWarning("Skipping the atom '%s' as the element name 
does not exist in the PDB file." % id))
 
         # Atomic mass.
-        mass = return_atomic_mass(element)
+        try:
+            mass = return_atomic_mass(element)
+        except RelaxError:
+            warn(RelaxWarning("Skipping the atom '%s' as the element '%s' is 
unknown." % (id, element)))
 
         # Total mass.
         M = M + mass