[Cdk-commits] SF.net SVN: cdk: [8635] trunk/cdk/src/org/openscience/cdk/tools/ CDKHydrogenAdder.java

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

Revision: 8635
          http://cdk.svn.sourceforge.net/cdk/?rev=8635&view=rev
Author:   egonw
Date:     2007-07-27 22:29:23 -0700 (Fri, 27 Jul 2007)

Log Message:
-----------
Added the NG implicit hydrogen adder: uses the new CDK atom type list to count missing hydrogens. If the atom typing failed, then this method fails too.

Added Paths:
-----------
    trunk/cdk/src/org/openscience/cdk/tools/CDKHydrogenAdder.java

Added: trunk/cdk/src/org/openscience/cdk/tools/CDKHydrogenAdder.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/tools/CDKHydrogenAdder.java	                        (rev 0)
+++ trunk/cdk/src/org/openscience/cdk/tools/CDKHydrogenAdder.java	2007-07-28 05:29:23 UTC (rev 8635)
@@ -0,0 +1,84 @@
+/* $Revision: 8399 $ $Author: rajarshi $ $Date: 2007-06-24 06:34:35 +0200 (Sun, 24 Jun 2007) $
+ *  
+ * Copyright (C) 2007  Egon Willighagen
+ *
+ * Contact: cdk...@li...
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.tools;
+
+import java.util.Iterator;
+
+import org.openscience.cdk.config.AtomTypeFactory;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+
+/**
+ * Assumes CDK atom types to be detected and adds missing hydrogens based on the
+ * atom typing.
+ * 
+ * @author egonw
+ */
+public class CDKHydrogenAdder {
+
+	private static AtomTypeFactory atomTypeList;
+	private final static String ATOM_TYPE_LIST = "org/openscience/cdk/config/data/cdk_atomtypes.xml";
+	
+	static {
+		atomTypeList = AtomTypeFactory.getInstance(ATOM_TYPE_LIST, NoNotificationChemObjectBuilder.getInstance());
+	}
+	
+	/**
+	 * Sets implicit hydrogen counts for all atoms in the given IAtomContainer.
+	 * 
+	 * @param  container
+	 * @throws CDKException Throws if insufficient information is present
+	 */
+	public void addImplicitHydrogens(IAtomContainer container) throws CDKException {
+		Iterator<IAtom> atoms = container.atoms();
+		while (atoms.hasNext()) {
+			addImplicitHydrogens(container, atoms.next());
+		}
+	}
+	
+	/**
+	 * Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.
+	 * 
+	 * @param  container
+	 * @param  atom         IAtom to set the implicit hydrogen count for
+	 * @throws CDKException Throws if insufficient information is present
+	 */
+	public void addImplicitHydrogens(IAtomContainer container, IAtom atom) throws CDKException {
+		if (atom.getAtomTypeName() == null)
+			throw new CDKException("IAtom is not typed!" + atom.getSymbol());
+		
+		IAtomType type =  atomTypeList.getAtomType(atom.getAtomTypeName());
+		if (type == null)
+			throw new CDKException("Atom type is not a recognized CDK atom type: " + atom.getAtomTypeName());
+		
+		// very simply counting: each missing explicit neighbor is a missing hydrogen
+		atom.setHydrogenCount(
+			type.getFormalNeighbourCount() - container.getConnectedAtomsCount(atom)
+		);
+	}
+}


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