[Cdk-commits] CVS: cdk/org/openscience/cdk/tools ElementFactory.java,1.5,1.6 IsotopeFactory.java,1.5,1.6

[Christoph S. <ste...@us...>]

Update of /cvsroot/cdk/cdk/org/openscience/cdk/tools
In directory usw-pr-cvs1:/tmp/cvs-serv8022/tools

Modified Files:
	ElementFactory.java IsotopeFactory.java 
Log Message:
Added a SMILES parser which can parse the SSMILES subset. Contains
some non-functional code for parsing atom specifications in brackets

Index: ElementFactory.java
===================================================================
RCS file: /cvsroot/cdk/cdk/org/openscience/cdk/tools/ElementFactory.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** ElementFactory.java	6 Apr 2002 15:26:45 -0000	1.5
--- ElementFactory.java	29 Apr 2002 19:43:08 -0000	1.6
***************
*** 59,66 ****
--- 59,80 ----
  	}
  
+ 	public Element getElement(int atomicNumber)
+ 	{
+ 		Isotope i = getMajorIsotope(atomicNumber);
+ 		
+ 		return (Element)i;
+ 	}
+ 
+ 
  	public Atom configure(Atom atom)
  	{
  		Isotope isotope = getMajorIsotope(atom.getSymbol());
+ 		return configure(atom, isotope);
+ 	}
+ 
+ 	public Atom configure(Atom atom, Isotope isotope)
+ 	{
  		atom.setAtomicMass(isotope.getAtomicMass());
+ 		atom.setSymbol(isotope.getSymbol());
  		atom.setExactMass(isotope.getExactMass());
  		atom.setAtomicNumber(isotope.getAtomicNumber());
***************
*** 68,71 ****
--- 82,86 ----
  		return atom;
  	}
+ 
  	
  	public void configureAtoms(AtomContainer ac) 

Index: IsotopeFactory.java
===================================================================
RCS file: /cvsroot/cdk/cdk/org/openscience/cdk/tools/IsotopeFactory.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -r1.5 -r1.6
*** IsotopeFactory.java	19 Oct 2001 10:32:10 -0000	1.5
--- IsotopeFactory.java	29 Apr 2002 19:43:08 -0000	1.6
***************
*** 118,121 ****
--- 118,144 ----
  		return (Isotope[]) al.toArray();
  	}
+ 
+ 	
+ 	/**
+ 	 *  Returns the major isotope with a given atomic number
+ 	 *
+ 	 * @param  atomicNumber The atomicNumber for which an isotope is to be returned
+ 	 * @return  The isotope corresponding to the given atomic number
+ 	 * @since
+ 	 */
+ 	public Isotope getMajorIsotope(int atomicNumber)
+ 	{
+ 		for (int f = 0; f < isotopes.size(); f++)
+ 		{
+ 			if (((Isotope) isotopes.elementAt(f)).getAtomicNumber() == atomicNumber)
+ 			{
+ 				if ((((Isotope)	isotopes.elementAt(f))).getNaturalAbundance() == ((double)100))
+ 				{
+ 					return (Isotope) ((Isotope) isotopes.elementAt(f)).clone();
+ 				}
+ 			}
+ 		}
+ 		return null;
+ 	}
  }