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Open Source Chemistry Library
/*
* 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.reaction;
import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import java.util.Arrays;
public class MoleculeAutoMapper implements AutoMapper {
private static final int MASK_ATOM_INDEX = 0x0000FFFF;
private static final int MASK_ATOM_TYPE = 0xFFFF0000;
private StereoMolecule mMol;
private Canonizer mCanonizer;
private int mCurrentMapNo;
private int[] mCounterAtom;
private boolean[] mMapNoInUse,mMatchHandled;
public MoleculeAutoMapper(StereoMolecule mol) {
mMol = mol;
}
public void autoMap() {
// Removes previously assigned auto-mapping numbers and recursively assigns
// new mapping numbers to all neighbors of manually assigned seed atoms.
// Expects existing mapping numbers to occur on two atoms sharing the same atomic number.
mMol.ensureHelperArrays(Molecule.cHelperRings);
// Init vars
mMapNoInUse = new boolean[mMol.getAtoms()+1];
mMatchHandled = new boolean[mMol.getAtoms()+1];
mCounterAtom = new int[mMol.getAtoms()];
mCurrentMapNo = 0;
for (int atom=0; atom= count2)
|| (atom2HasEqualNeighbors && count2 >= count1)) {
int count = Math.min(count1, count2);
for (int i=0; i