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• MoleculeShredder.java

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com.actelion.research.chem.shredder.MoleculeShredder Maven / Gradle / Ivy

/*
 * @(#)MoleculeShredder.java
 *
 * Copyright 1997-2001 Actelion Ltd., Inc. All Rights Reserved.
 *
 * This software is the proprietary information of Actelion Pharmaceuticals, Ltd.
 * Use is subject to license terms.
 *
 * @author Thomas Sander
 */

package com.actelion.research.chem.shredder;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;

import java.util.*;

public class MoleculeShredder {
	public static final int cModeSetAtomQFNoMoreNeighbours = 1;
	public static final int cModeExcludeCoreFragments = 64;

		// mode may contain one or none of those:
	public static final int cModeRetainSubstituentTypes = 2;
	public static final int cModeDiscardSubstitutionInfo = 128;

		// mode may contain one or none of these:
	public static final int cModeCoreFragmentsOnly = 4;
	public static final int cModeOneSpereAroundCoreOnly = 32;

		// mode may contain one or none of the 'Cut' options:
	public static final int cModeCutTerminalBondsAlso = 8;
	public static final int cModeCutSpacersOffRings = 16;

	public static final int cColorFragmentsInMolecule = 256;

	private static final int cMaxCoreFragments = 8;

	private final StereoMolecule mMol;
	private boolean[]			mIsCuttableBond;
	private boolean[][]			mAreNeighbours;
	private final int			mMode;
	private int					mCuttableBonds;
	private int					mCoreFragments;
	private int[]				mCoreFragmentNo;
	private ArrayList		mFragmentList;

	public MoleculeShredder(StereoMolecule mol, int mode) {
		mMol = mol;
		mMol.ensureHelperArrays(Molecule.cHelperRings);
		mMode = mode;
		locateCuttableBonds();
		locateCoreFragments();
		if ((mode & cModeCoreFragmentsOnly) == 0)
			createCoreNeighbourMatrix();
		createFragmentList();
		}


	public int getFragments() {
		return mFragmentList.size();
		}


	public int getCoreFragments() {
		return mCoreFragments;
		}


	public StereoMolecule getFragment(StereoMolecule theFragment, int fragmentNo) {
		boolean[] isMember = new boolean[mMol.getAtoms()];
		long fragmentBits = mFragmentList.get(fragmentNo);
		for (int coreFragment=0; coreFragment 1
				   && mMol.getConnAtoms(mMol.getBondAtom(1, bond)) > 1))) {
					mIsCuttableBond[bond] = true;
					mCuttableBonds++;
					}
				}
			}
		}


	private void locateCoreFragments() {
		mCoreFragmentNo = new int[mMol.getAtoms()];
		for (int atom=0; atom();

		if (mCoreFragments == 1)	// if the only fragment is the entire molecule then return no fragments
			return;

		if (mCoreFragments > 64)	// fragment combinations cannot be coded in long -> don't shredder
			return;

		if ((mMode & cModeCoreFragmentsOnly) == 0
		 && mCoreFragments > cMaxCoreFragments)	// do not create fragments of to flexible molecules
			return;

		for (int fragment=0; fragment centralCoreList = new ArrayList();
		for (int fragment=0; fragment