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.ugly;
  
  import com.actelion.research.chem.*;
  
  import java.util.ArrayList;
  
  public class NastyFunctionDetector {
  	public static final String[] cNastyFunctionsUnknown = null;
  
  	public static final String sNastyFunction[][] = {
  		{ "gGP@LdbKT`]RMdmGJFCPpWN@PBJpd@", "polar activated DB" },
  		{ "gGP@DjVePNlFJXhypB@Q\\xA@HjlPd@", "twice activated DB" },
  		{ "eM@HvCjFtQ[N@PBDiBHqJrlD@", "acyl-halogenide type" },
  		{ "eFBJHcAbc\\@axABIVVQFIV@", "Cl,Br,I on N,O,P,S,Se,I" },
  		{ "gC`HADIKRAuHubL", "allyl/benzyl chloride" },
  		{ "eM@HzCBKUFTqJp", "prim. alkyl-bromide/iodide" },
  		{ "gC`@H}PFrbcLfIV@", "sec./tert. alkyl-bromide/iodide" },
  		{ "gC`hH`DIVtAuL`", "alkyl sulfonate/sulfate type" },
  		{ "gJQ`@bdjt`P", "anhydride" },
  		{ "gJXA@IczhB", "quart. ammonium" },
  		{ "gChA@Icm@P", "tert. immonium" },
  		{ "fHT`P", "carbenium" },
  		{ "gCh`hEIWILtAuM@", "aromatic nitro" },
  		{ "gCd@Adeb@p`}M@", "1,2-diamino-aryl" },
  		{ "gJT@@TeXHCA@`", "1,3-diamino-aryl" },
  		{ "gGT@ATeV@`LDJ", "1,4-diamino-aryl" },
  		{ "gCd@ADiZDEsA@", "azo" },
  		{ "gJU@h`NdiLsPdh", "azoxy" },
  		{ "eMPRIncTH", "diazo" },
  		{ "eMPRI^cxH", "diazo" },
  		{ "gJT@@Te^lB", "1,1-dinitrile" },
  		{ "eMHAIhLDhsW@H^@Pb@", "formaldehyde aduct" },
  		{ "eO@HyjCYJLipB@", "oxiran/aziridine" },
  		{ "eMPBchLDkR", "hydrazine" },
  		{ "eM`AITLYs`D@`", "isocyanate type" },
  		{ "fH@MjM~@p\\@aHZA`x^@QDYAQbU`", "unwanted atom" },
  		{ "fHw`dB", "phosphonium" },
  		{ "gCi@hAteIi`H", "nitrone" },
  		{ "eMhHRVCZP", "nitroso" },
  		{ "gCa`@lduPD", "orthoester/acid" },
  		{ "eFDBcA@", "peroxo" },
  		{ "gGY@HDiViPMdmEGN@PBKg@HA@", "N-acyloxy-amide" },
  		{ "gC`@H{PFJVQFIV[HcDk@", "1,1-dihalo-alkene" },
  		{ "gC`@DiZDEbedQbUfrHqJp", "1,2-dihalo-alkene" },
  		{ "fIRPNj@", "pyrylium" },
  		{ "gCaHHGAIZPMXb@", "silylenol-ether" },
  		{ "gCd@ADie@y``", "dimethylene-hydrazine" },
  		{ "eMPARZCJg}T@", "methanediamine" },
  		{ "daFD`Bs`BLdTTIUSRpA@", "limit! methylene-thiazolidine-2,4-dione" },
  		{ "gOtHLPDISOkSM@XP`", "limit! thiazol-2-ylamine" },
  		{ "gGU@DPdsmRAeDx", "acyl-hydrazone" },
  		{ "gCh@@eKP`lIIROFIFC`@", "imine/hydrazone of aldehyde" },
  		{ "deUD@BxIrJJKPlKTmL@ZqP`", "2,3-diamino-quinone" },
  		{ "difL@DBarJIPhfZif@LHh", "limit! 4-acyl-3-azoline-2-one-3-ol" },
  		{ "gGT`EPTfyi`H", "limit! oxal-diamide" },
  		{ "daED@DpFRYUJfjV@H", "limit! 5-methylene-imidazolidine-2,4-dione" },
  		{ "gJQ@@dls@XpyDXeX", "2-halo-enone" },
  		{ "gJQ@@djsBJqarHqJp", "3-halo-enone" },
  		{ "gCd`i`iJyIf`H", "N-nitro" },
  		{ "gChHD@aIf`LYdXN@", "thio-amide/urea" } };
  
  private static StereoMolecule[]	sFragmentList;
  	private static long[][]			sIndexList;
  	private static boolean			sInitialized;
  
  	public NastyFunctionDetector() {
  		synchronized(NastyFunctionDetector.class) {
  			if (!sInitialized) {
  		        try {
  					sFragmentList = new StereoMolecule[sNastyFunction.length];
  					sIndexList = new long[sNastyFunction.length][];
  					SSSearcherWithIndex sss = new SSSearcherWithIndex(SSSearcher.cMatchAtomCharge);
  					for (int i=0; i<sNastyFunction.length; i++) {
  						sFragmentList[i] = new IDCodeParser(false).getCompactMolecule(sNastyFunction[i][0]);
  						sIndexList[i] = sss.createLongIndex(sFragmentList[i]);
  						}
  					sInitialized = true;
  					}
  				catch (Exception e) {
  		            System.out.println("Unable to initialize NastyFunctionDetector");
  					}
  				}
  			}
  		}
  
  	/**
  	 * @param mol
  	 * @param index FragFp descriptor
  	 * @return list of names of detected nasty function or null in case of initialization error
  	 */
  	public String[] getNastyFunctionList(StereoMolecule mol, long[] index) {
  		if (!sInitialized)
  			return cNastyFunctionsUnknown;
  
  		ArrayList<String> nastyFunctionList = new ArrayList<String>();
  
  		SSSearcherWithIndex sss = new SSSearcherWithIndex(SSSearcher.cMatchAtomCharge);
  		sss.setMolecule(mol, index);
  		for (int i=0; i<sNastyFunction.length; i++) {
  			sss.setFragment(sFragmentList[i], sIndexList[i]);
  			if (sss.isFragmentInMolecule())
  				nastyFunctionList.add(sNastyFunction[i][1]);
  			}
  
  		addPolyHaloAromaticRings(mol, nastyFunctionList);
  
  		return nastyFunctionList.toArray(new String[0]);
  		}
  
  	/**
  	 * @param mol
  	 * @param index FragFp descriptor
  	 * @return '; ' separated list of detected nasty function names
  	 */
  	public String getNastyFunctionString(StereoMolecule mol, long[] index) {
  		String[] nfl = getNastyFunctionList(mol, index);
  		if (nfl == null)
  			return "initialization error";
  		if (nfl.length == 0)
  			return "";
  		StringBuilder sb = new StringBuilder(nfl[0]);
  		for (int i=1; i<nfl.length; i++)
  			sb.append("; "+nfl[i]);
  		return sb.toString();
  		}
  
  	private void addPolyHaloAromaticRings(StereoMolecule mol, ArrayList<String> nastyFunctionList) {
  		RingCollection ringSet = mol.getRingSet();
  		for (int ring=0; ring<ringSet.getSize(); ring++) {
  			if (ringSet.isAromatic(ring)) {
  				int halogenes = 0;
  				int[] ringAtom = ringSet.getRingAtoms(ring);
  				for (int i=0; i<ringAtom.length; i++) {
  					for (int j=0; j<mol.getConnAtoms(ringAtom[i]); j++) {
  						int connAtom = mol.getConnAtom(ringAtom[i], j);
  						if (!mol.isRingAtom(connAtom)
  						 && (mol.getAtomicNo(connAtom) == 9
  						  || mol.getAtomicNo(connAtom) == 17
  						  || mol.getAtomicNo(connAtom) == 35
  						  || mol.getAtomicNo(connAtom) == 53))
  							halogenes++;
  						}
  					}
  
  				if (halogenes > 2) {
  					nastyFunctionList.add("polyhalo aromatic ring");
  					}
  				}
  			}
  		}
  	}
  