Author: bugman
Date: Tue Oct 21 14:17:49 2014
New Revision: 26324
URL: http://svn.gna.org/viewcvs/relax?rev=26324&view=rev
Log:
Modified the internal structural object backend for the structure.read_pdb user
function.
The MolContainer._det_pdb_element() method for handling PDB files with missing
element information
has been updated to use the Periodic_table.has_element() method to check if the
PDB atom name
corresponds to any atoms in the periodic table. This allows for far greater
support for HETATOMS
and all of the metals.
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=26324&r1=26323&r2=26324&view=diff
==============================================================================
--- trunk/lib/structure/internal/molecules.py (original)
+++ trunk/lib/structure/internal/molecules.py Tue Oct 21 14:17:49 2014
@@ -147,11 +147,8 @@
element = key
break
- # Allowed element list.
- elements = ['H', 'C', 'N', 'O', 'F', 'P', 'S']
-
- # Return the element, if in the list.
- if element in elements:
+ # Return the element if it is in the periodic table.
+ if periodic_table.has_element(symbol=element):
return element
# Else, throw a warning.
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