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• 2024.9.3
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• DescriptorHandlerAllFragmentsFP.java

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com.actelion.research.chem.descriptor.DescriptorHandlerAllFragmentsFP Maven / Gradle / Ivy

/*
 * Copyright (c) 1997 - 2016
 * Actelion Pharmaceuticals Ltd.
 * Gewerbestrasse 16
 * CH-4123 Allschwil, Switzerland
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 3. Neither the name of the the copyright holder nor the
 *    names of its contributors may be used to endorse or promote products
 *    derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 */

package com.actelion.research.chem.descriptor;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.SSSearcherWithIndex;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.util.SortedList;

public class DescriptorHandlerAllFragmentsFP extends AbstractDescriptorHandlerLongFP {
	private static final double CORRECTION_FACTOR = 0.68;

	public static boolean skipIDCodes;

	private static DescriptorHandlerAllFragmentsFP sDefaultInstance;

	private static final int MAX_BOND_COUNT = 6;
	private static final int HASH_BITS = 11;
	private static final int DESCRIPTOR_SIZE = (1 << HASH_BITS);
	private static final int DESCRIPTOR_LEN = DESCRIPTOR_SIZE / Long.SIZE;

	private StereoMolecule mMol;
	private boolean[] mIsAtomMember,mIsBondMember;
	private int[] mMemberBond,mMemberAtom;
	private long[] mDescriptor;
	private SortedList mBondSets;
	private SimpleFragmentGraph mFragmentGraph;

	public static DescriptorHandlerAllFragmentsFP getDefaultInstance() {
		synchronized(DescriptorHandlerAllFragmentsFP.class) {
			if (sDefaultInstance == null) {
				sDefaultInstance = new DescriptorHandlerAllFragmentsFP();
			}
		}
		return sDefaultInstance;
	}

	@Override
	public DescriptorInfo getInfo() {
		return DescriptorConstants.DESCRIPTOR_ALLFRAG;
	}

	@Override
	public String getVersion() {
		return DescriptorConstants.DESCRIPTOR_ALLFRAG.version;
	}

	private StereoMolecule preprocessStructure(StereoMolecule mol) {
		if (mol.isFragment()) {
			mol.ensureHelperArrays(Molecule.cHelperNeighbours);

			boolean[] isBlockedAtom = new boolean[mol.getAtoms()];
			for (int atom = 0; atom();
		mIsAtomMember = new boolean[mMol.getAtoms()];
		mIsBondMember = new boolean[mMol.getBonds()];
		mDescriptor = new long[DESCRIPTOR_LEN];
		mMemberAtom = new int[mMol.getAtoms()];
		mMemberBond = new int[mMol.getBonds()];

		for (int rootBond=0; rootBond= 1.0f ? 1.0f
				: (float)(1.0-Math.pow(1-Math.pow(value, CORRECTION_FACTOR) ,1.0/CORRECTION_FACTOR));
	}

	@Override
	public DescriptorHandler getThreadSafeCopy() {
		return new DescriptorHandlerAllFragmentsFP();
	}
}

class BondSet implements Comparable {
	private int[] mMask;

	public BondSet(int[] bond, int usedBonds, int bondCount) {
		mMask = new int[(bondCount + 31) / 32];
		for (int i=0; i