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.
  *
  */
  
  package com.actelion.research.chem.descriptor;
  
  import com.actelion.research.chem.IDCodeParser;
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  
  public class DescriptorHelper implements DescriptorConstants {
  	
  	public static final String TAG_SIMILARITY = " Similarity";
  	
      public static int getDescriptorType(String shortName) {
          DescriptorInfo descriptorInfo = getDescriptorInfo(unifyShortName(shortName));
          return (descriptorInfo == null) ? DESCRIPTOR_TYPE_UNKNOWN
                                          : descriptorInfo.type;
      }
  
      public static DescriptorInfo getDescriptorInfo(String shortName) {
          for (int i=0; i<DESCRIPTOR_EXTENDED_LIST.length; i++)
              if (DESCRIPTOR_EXTENDED_LIST[i].shortName.equals(unifyShortName(shortName)))
                  return DESCRIPTOR_EXTENDED_LIST[i];
          return null;
      }
  
      public static boolean isBinaryFingerprint(String shortName) {
          DescriptorInfo descriptorInfo = getDescriptorInfo(unifyShortName(shortName));
          return (descriptorInfo == null) ? false
                                          : descriptorInfo.isBinary;
      }
  
      public static boolean isDescriptorShortName(String shortName) {
          for (int i=0; i<DESCRIPTOR_EXTENDED_LIST.length; i++)
              if (DESCRIPTOR_EXTENDED_LIST[i].shortName.equals(unifyShortName(shortName)))
                  return true;
          return false;
      }
  
      public static String shortNameToName(String shortName) {
  		for (int i=0; i<DESCRIPTOR_EXTENDED_LIST.length; i++)
  			if (DESCRIPTOR_EXTENDED_LIST[i].shortName.equals(shortName))
  				return DESCRIPTOR_EXTENDED_LIST[i].name;
  		return null;
  	}
  
  	public static String nameToShortName(String name) {
  		for (int i=0; i<DESCRIPTOR_EXTENDED_LIST.length; i++)
  			if (DESCRIPTOR_EXTENDED_LIST[i].name.equals(name))
  				return DESCRIPTOR_EXTENDED_LIST[i].shortName;
  		return null;
  	}
  
  	private static String unifyShortName(String shortname) {
          return "PP3DMM2".equals(shortname) ? "Flexophore" : shortname;
      }
  
  	/**
  	 * Creates a header tag name from the descriptor short name.
  	 * The tag is used to store virtual screening scores. 
  	 * @param shortName
  	 * @return
  	 */
  	public static String getTagDescriptorSimilarity(String shortName) {
  		return shortName + TAG_SIMILARITY;
  		}
  	public static String getTagDescriptorSimilarity(ISimilarityCalculator<?> dh) {
  		return getTagDescriptorSimilarity(dh.getInfo().shortName);
  	}
  
  	public static String getTagDescriptorSimilarity(SimilarityCalculatorInfo info) {
  		return getTagDescriptorSimilarity(info.shortName);
  		}
  
  	public static String getTagDescriptorSimilarity(DescriptorInfo dh){
  		return getTagDescriptorSimilarity(dh.shortName);
  		}
  
  	public static<T> T create(DescriptorHandler<T, StereoMolecule> dh, String idcode){
  		IDCodeParser parser = new IDCodeParser();
  		StereoMolecule mol = parser.getCompactMolecule(idcode);
  		mol.ensureHelperArrays(Molecule.cHelperRings);
  		return dh.createDescriptor(mol);
  	}
  
  }
  