[Cdk-commits] CVS: cdk-taverna/src/org/openscience/cdk/applications/taverna/charges PartialChargesCalculator.java,1.3,1.4

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk-taverna/src/org/openscience/cdk/applications/taverna/charges
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9685/src/org/openscience/cdk/applications/taverna/charges

Modified Files:
	PartialChargesCalculator.java 
Log Message:
Added two other methods for calculating partial charges.

Index: PartialChargesCalculator.java
===================================================================
RCS file: /cvsroot/cdk/cdk-taverna/src/org/openscience/cdk/applications/taverna/charges/PartialChargesCalculator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- PartialChargesCalculator.java	16 Oct 2005 16:06:12 -0000	1.3
+++ PartialChargesCalculator.java	17 Oct 2005 19:57:42 -0000	1.4
@@ -27,12 +27,17 @@
 
 import org.openscience.cdk.applications.taverna.CMLChemFile;
 import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
+import org.openscience.cdk.charges.InductivePartialCharges;
+import org.openscience.cdk.charges.MMFF94PartialCharges;
+import org.openscience.cdk.interfaces.Atom;
 import org.openscience.cdk.interfaces.AtomContainer;
 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
 
 public class PartialChargesCalculator {
 
 	private static GasteigerMarsiliPartialCharges gmCalculator;
+	private static InductivePartialCharges indCalculator;
+	private static MMFF94PartialCharges mmff94Calculator;
 	
 	/**
 	 * Calculates Gasteiger-Marsili partial charges.
@@ -57,5 +62,63 @@
 		return file.toCML();
 	}
 
+	/**
+	 * Calculates inductive partial charges..
+	 * 
+	 * @taverna.consume
+	 */
+	public static String calculateInductivePartialCharges(String cmlString) throws Exception {
+		if (indCalculator == null) indCalculator = new InductivePartialCharges();
+		
+		CMLChemFile file = new CMLChemFile(cmlString);
+		
+		AtomContainer[] molecules = ChemFileManipulator.getAllAtomContainers(file);
+		for (int i=0; i<molecules.length; i++) {
+			try {
+				indCalculator.assignInductivePartialCharges(molecules[i]);
+				Atom[] atoms = molecules[i].getAtoms();
+				for (int j=0; j<atoms.length; j++) {
+					Object object = atoms[i].getProperty("InductivePartialCharge");
+					if (object != null && object instanceof Double) {
+						atoms[j].setCharge(((Double)object).doubleValue());
+					}
+				}
+			} catch (Exception exception) {
+				// this is going to happen a lot :(
+				// what to do about it??
+			}
+		}
+		
+		return file.toCML();
+	}
 	
+	/**
+	 * Calculates MMFF94 partial charges..
+	 * 
+	 * @taverna.consume
+	 */
+	public static String calculateMMFF94PartialCharges(String cmlString) throws Exception {
+		if (mmff94Calculator == null) mmff94Calculator = new MMFF94PartialCharges();
+		
+		CMLChemFile file = new CMLChemFile(cmlString);
+		
+		AtomContainer[] molecules = ChemFileManipulator.getAllAtomContainers(file);
+		for (int i=0; i<molecules.length; i++) {
+			try {
+				mmff94Calculator.assignMMFF94PartialCharges(molecules[i]);
+				Atom[] atoms = molecules[i].getAtoms();
+				for (int j=0; j<atoms.length; j++) {
+					Object object = atoms[i].getProperty("MMFF94charge");
+					if (object != null && object instanceof Double) {
+						atoms[j].setCharge(((Double)object).doubleValue());
+					}
+				}
+			} catch (Exception exception) {
+				// this is going to happen a lot :(
+				// what to do about it??
+			}
+		}
+		
+		return file.toCML();
+	}
 }