content: /*
   * 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<Conformer> {
  	
  	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; i<confString.length;i++) {
  					Conformer conf = new Conformer(firstConformer);
  					try {
  						parser.parseCoordinates(confString[i].getBytes(StandardCharsets.UTF_8), 0, mol, conf.getCoordinates());
  						add(conf);
  					} catch (Exception e) {}
  				}
  			}
  		}
  	}
  
  	public ConformerSet(byte[] idcode, byte[] coords) {
  		super();
  		if (idcode != null && coords != null) {
  			IDCodeParserWithoutCoordinateInvention parser = new IDCodeParserWithoutCoordinateInvention();
  			StereoMolecule mol = parser.getCompactMolecule(idcode, coords);
  			Conformer firstConformer = new Conformer(mol);
  			add(firstConformer);
  
  			int index = ArrayUtils.indexOf(coords, (byte)32,0);
  			while (index != -1) {
  				Conformer conf = new Conformer(firstConformer);
  				try {
  					parser.parseCoordinates(coords, index+1, mol, conf.getCoordinates());
  					add(conf);
  				} catch (Exception e) {}
  			}
  		}
  	}
  
  	public ConformerSet getSubset(int size) {
  		ConformerSet treeSet = new ConformerSet();
  		this.stream().limit(size).forEach(c->treeSet.add(c));
  		return treeSet;
  		
  	}
  	
  	@Override
  	public String toString() {
  		StringBuilder sb = new StringBuilder();
  		if (!isEmpty()) {
  			Iterator<Conformer> 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();
  	}
  }
  