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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;
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 nastyFunctionList = new ArrayList();
SSSearcherWithIndex sss = new SSSearcherWithIndex(SSSearcher.cMatchAtomCharge);
sss.setMolecule(mol, index);
for (int i=0; i nastyFunctionList) {
RingCollection ringSet = mol.getRingSet();
for (int ring=0; ring 2) {
nastyFunctionList.add("polyhalo aromatic ring");
}
}
}
}
}