r25390 - /trunk/lib/periodic_table.py -- August 28, 2014 - 16:46

Author: bugman
Date: Thu Aug 28 16:46:23 2014
New Revision: 25390

URL: http://svn.gna.org/viewcvs/relax?rev=25390&view=rev
Log:
Created the lib.periodic_table.process_symbol() function.

This will take an atomic symbol and return a copy of it with an uppercase 
first letter and lowercase
second letter.  This is used by the Periodic_table methods atomic_mass() and 
atomic_weight() to
allow for non-standard symbol input, for example if the element name comes 
directly from the all
uppercase PDB file format without translation.


Modified:
    trunk/lib/periodic_table.py

Modified: trunk/lib/periodic_table.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/periodic_table.py?rev=25390&r1=25389&r2=25390&view=diff
==============================================================================
--- trunk/lib/periodic_table.py (original)
+++ trunk/lib/periodic_table.py Thu Aug 28 16:46:23 2014
@@ -34,6 +34,7 @@
 # Python module imports.
 from numpy import array, average, float64
 from re import search, split
+from string import lower, upper
 
 # relax module imports.
 from lib.errors import RelaxError
@@ -63,6 +64,24 @@
 
         # Convert to a float and return the value.
         return float(val)
+
+
+def process_symbol(symbol):
+    """Make sure the symbol is in the correct format.
+
+    @param symbol:  The atomic symbol.
+    @type symbol:   str
+    @return:        The corrected atomic symbol.
+    @rtype:         str
+    """
+
+    # The format is uppercase first letter, lowercase second.
+    new_symbol = upper(symbol[0])
+    if len(symbol) == 2:
+        new_symbol += lower(symbol[1])
+
+    # Return the corrected atomic symbol.
+    return new_symbol
 
 
 
@@ -198,7 +217,7 @@
             A = int(split('[A-Z]', id)[0])
 
             # The atomic symbol.
-            symbol = split('[0-9]', id)[-1]
+            symbol = process_symbol(split('[0-9]', id)[-1])
 
             # Get the isotope container.
             isotope = self._get_isotope(symbol=symbol, A=A)
@@ -220,6 +239,9 @@
         @rtype:             float
         """
 
+        # Process the symbol.
+        symbol = process_symbol(symbol)
+
         # Checks.
         if symbol not in self:
             raise RelaxError("The atomic symbol '%s' cannot be found in the 
periodic table." % symbol)