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)
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