/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
*
* Contact: cdk-devel@lists.sourceforge.net
*
* 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.
*
* 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.graph.invariant;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
/**
* Tool for calculating Morgan numbers {@cdk.cite MOR65}.
*
* @cdk.module standard
* @cdk.githash
*
* @author shk3
* @cdk.created 2003-06-30
* @cdk.keyword Morgan number
*/
@TestClass("org.openscience.cdk.graph.invariant.MorganNumbersToolsTest")
public class MorganNumbersTools {
/**
* Makes an array containing the morgan numbers of the atoms of atomContainer.
*
* @param atomContainer The atomContainer to analyse.
* @return The morgan numbers value.
*/
@TestMethod("testGetMorganNumbers_IAtomContainer")
public static long[] getMorganNumbers(IAtomContainer atomContainer) {
long[] morganMatrix;
long[] tempMorganMatrix;
int N = atomContainer.getAtomCount();
morganMatrix = new long[N];
tempMorganMatrix = new long[N];
java.util.List<IAtom> atoms;
for (int f = 0; f < N; f++) {
morganMatrix[f] = atomContainer.getConnectedBondsCount(f);
tempMorganMatrix[f] = atomContainer.getConnectedBondsCount(f);
}
for (int e = 0; e < N; e++) {
for (int f = 0; f < N; f++) {
morganMatrix[f] = 0;
atoms = atomContainer.getConnectedAtomsList(atomContainer.getAtom(f));
for (IAtom atom : atoms) {
morganMatrix[f] += tempMorganMatrix[atomContainer.getAtomNumber(atom)];
}
}
System.arraycopy(morganMatrix, 0, tempMorganMatrix, 0, N);
}
return tempMorganMatrix;
}
/**
* Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer. This method
* puts the element symbol before the morgan number, useful for finding out how many different rests are connected to an atom.
*
* @param atomContainer The atomContainer to analyse.
* @return The morgan numbers value.
*/
@TestMethod("testPhenylamine")
public static String[] getMorganNumbersWithElementSymbol(IAtomContainer atomContainer) {
long[] morgannumbers = getMorganNumbers(atomContainer);
String[] morgannumberswithelement = new String[morgannumbers.length];
for (int i = 0; i < morgannumbers.length; i++) {
morgannumberswithelement[i] = atomContainer.getAtom(i).getSymbol() + "-" + morgannumbers[i];
}
return (morgannumberswithelement);
}
}