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/*
 * 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.conf;

import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.util.ArrayUtils;

import java.nio.charset.StandardCharsets;
import java.util.Iterator;
import java.util.TreeSet;


public class ConformerSet extends TreeSet {
	
	public ConformerSet() {
		this(null);
	}
	
	public ConformerSet(String s) {
		super();
		if (s != null) {
			String[] confString = s.split(" ");
			if (confString.length >= 2) {
				IDCodeParserWithoutCoordinateInvention parser = new IDCodeParserWithoutCoordinateInvention();
				StereoMolecule mol = parser.getCompactMolecule(confString[0], confString[1]);
				Conformer firstConformer = new Conformer(mol);
				add(firstConformer);

				for(int i=2; itreeSet.add(c));
		return treeSet;
		
	}
	
	@Override
	public String toString() {
		StringBuilder sb = new StringBuilder();
		if (!isEmpty()) {
			Iterator iterator = iterator();
			StereoMolecule mol = iterator.next().toMolecule();
			Canonizer can = new Canonizer(mol, Canonizer.COORDS_ARE_3D);
			sb.append(can.getIDCode());
			sb.append(" ");
			sb.append(can.getEncodedCoordinates(true));
			while (iterator.hasNext()) {
				can.invalidateCoordinates();
				iterator.next().toMolecule(mol);
				sb.append(" ");
				sb.append(can.getEncodedCoordinates(true));
			}
		}
		return sb.toString();
	}
}