net.bioclipse.cdk.ui.sdfeditor.CDKFingerPrintPropertyCalculator.java Source code

Introduction

Here is the source code for net.bioclipse.cdk.ui.sdfeditor.CDKFingerPrintPropertyCalculator.java

Source

/*******************************************************************************
 * Copyright (c) 2009  Arvid Berg <goglepox@users.sourceforge.net>
 *
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * <http://www.eclipse.org/legal/epl-v10.html>
 *
 * Contact: http://www.bioclipse.net/
 ******************************************************************************/
package net.bioclipse.cdk.ui.sdfeditor;

import java.util.BitSet;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.cdk.ui.sdfeditor.business.IPropertyCalculator;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.util.LogUtils;

import org.apache.commons.codec.binary.Base64;
import org.apache.log4j.Logger;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.nonotify.NNAtomContainer;

/**
 * @author arvid
 *
 */
public class CDKFingerPrintPropertyCalculator implements IPropertyCalculator<BitSet> {

    public BitSet calculate(ICDKMolecule molecule) {

        Fingerprinter fp = new Fingerprinter();
        try {
            IAtomContainer ac = new NNAtomContainer(molecule.getAtomContainer());
            BitSet fingerprint = fp.getFingerprint(ac);
            return fingerprint;
        } catch (Exception e) {
            LogUtils.handleException(new BioclipseException("Could not create fingerprint: " + e.getMessage()),
                    Logger.getLogger(CDKFingerPrintPropertyCalculator.class), "net.bioclipse.cdk.ui.sdfeditor");
            throw new RuntimeException("Could not create fingerprint. " + e.getMessage(), e);
        }
    }

    public String getPropertyName() {

        return "net.bioclipse.cdk.fingerprint";
    }

    public BitSet parse(String value) {
        // TODO check if this is right
        byte[] bytes = new Base64().decode(value.getBytes());
        BitSet set = new BitSet();
        for (int i = 0; i < bytes.length * 8; i++) {
            if ((bytes[bytes.length - i / 8 - 1] & (1 << (i % 8))) > 0) {
                set.set(i);
            }
        }
        return set;
    }

    public String toString(Object value) {
        // TODO check if this is right
        BitSet val = (BitSet) value;
        byte[] bytes = new byte[val.length() / 8 + 1];
        for (int i = 0; i < val.length(); i++) {
            if (val.get(i)) {
                bytes[bytes.length - i / 8 - 1] |= 1 << (i % 8);
            }
        }
        return new String(new Base64().encode(bytes));
    }

}