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• ScaffoldHelper.java

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com.actelion.research.chem.ScaffoldHelper 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.
 *
 * @author Thomas Sander
 */

package com.actelion.research.chem;

import java.util.Arrays;

public class ScaffoldHelper {

	/**
	 * Modifies mol in-place to represent the Murcko scaffold from the original mol.
	 * If skeletonOnly is true, then all bond types are reduced to non-stereo-single bonds
	 * and all atoms are converted to carbon atoms.
	 * @param mol may be an empty molecule if there are no ring systems
	 * @param skeletonOnly reduce to simple skeleton
	 */
	public static void createMurckoScaffold(StereoMolecule mol, boolean skeletonOnly) {
		boolean[] isScaffoldMember = findMurckoScaffold(mol);
		if (isScaffoldMember == null) {
			mol.deleteMolecule();
			return;
			}
		for (int atom=0; atom 2) {
					for (int i=0; i 1) {
							isMember[connAtom] = true;
							found |= (connAtom < atom);
							}
						}
					}
				}
			} while (found);

		return isMember;
		}

	private static void addShortestPathToMember(StereoMolecule mol, int atom1, int atom2, boolean[] isMember) {
		int[] parentAtom = new int[mol.getAtoms()];	// serves as indication of being a path member and allows backtracking the path
		int[] graphAtom = new int[mol.getAtoms()];
		Arrays.fill(parentAtom, -1);

		graphAtom[0] = atom2;
		parentAtom[atom1] = -2;	// != -1 to mark it being a part of the graph
		parentAtom[atom2] = atom1;
		int current = 0;
		int highest = 0;
		while (current <= highest) {
			for (int i=0; i (double)fragmentDistanceSum[i]/fragmentAtomCount[i]) {
				minSum = (double)fragmentDistanceSum[i]/fragmentAtomCount[i];
				minFragment = i;
				}
			}
		boolean[] isFragmentMember = new boolean[mol.getAtoms()];
		for (int atom=0; atom