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/*
 * Copyright 2017 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
 *
 * This file is part of DataWarrior.
 * 
 * DataWarrior is free software: you can redistribute it and/or modify it under the terms of the
 * GNU General Public License as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 * 
 * DataWarrior is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
 * without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 * See the GNU General Public License for more details.
 * You should have received a copy of the GNU General Public License along with DataWarrior.
 * If not, see http://www.gnu.org/licenses/.
 *
 * @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