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Open Source Chemistry Library
/*
* 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 com.actelion.research.chem.descriptor.AbstractDescriptorHandlerLongFP;
import java.nio.charset.StandardCharsets;
// TODO purge mMoleculeIndexInt,mFragmentIndexInt and related methods from this class. Long versions were introduced Aug 3, 2018
public class SSSearcherWithIndex {
public static final String cIndexVersion = "1.2.1";
// Outcommented and replaced idcodes are fragments, which originally used datatype==2 (wrongly encoded delocalized bond).
// They were replaced by fragments with bonds explicitly defined as delocalized, which should be compatible with original FFPs.
public static final String[] cKeyIDCode = {
"QM@HzAmdqjF@",
"RF@Q``",
"qC`@ISTAlQE`",
"`J@H",
"QM@HzAmdqbF@",
"qC`@ISTAlQEhqPp@",
"sJP@DiZhAmQEb",
"RF@QPvR@",
"QM@HzA@",
"qC`@ISTAlQEhpPp@",
"qC`@Qz`MbHl",
"sJP@DiZhAmQEcFZF@",
"RFPDXH",
"qC`@IVtAlQE`",
"QM@HvAmdqfF@",
"sGP@DiVj`FsDVM@",
"`L@H",
"sJP@DizhAmQEcFBF@",
"sJP@DjvhAmQEb",
"sFp@DiTt@@AlqEcP",
"sGP@LdbMU@MfHlZ",
"QMHAIhD",
"QM@HzAy@",
"sJP@DkVhAmQEb",
"sNp@DiUjj@[\\QXu`",
"sJP@DiZhAmQEcFBF@",
"sGP@DjVj`FsDVM@",
"RFPDTH",
"RG@DXOH@",
"sGP@Divj`FsDVMcAC@",
"sGP@Dj}j`FsDVM@",
"qC`@Qz`MbHmFRF@",
"sNp@LdbJjj@[\\QXu`",
"QMHAIhGe@",
"QM@HzAyd`",
"QM`AIhD",
"qC`@ISTA@",
"sGP@DkUj`FsDVM@",
"qC`@IVtAlQEhqPp@",
"sNp@DiUjj@[\\QXuqea`@",
"KAx@@IRjuUPAlHPfES\\",
"QM`BN`P",
"sJP@DjZhAmQEcFJF@",
"Hid@@DjU^nBBH@FtaBXUMp`",
"sNp@Diujj@[\\QXuq`a`@",
"sJP@DjvhAmQEcFZF@",
"sJP@DjZhAmQEcFFF@",
"sOp@DjWkB@@FwDVM\\YhX@",
"sNp@Dj}Zj@[\\QXu`",
"sNp@DiWjj@[\\QXuq`a`@",
"sOp@DjWkB@@D",
"KAx@@ITouUPAlHPfES\\",
"KAx@@YIDTjjh@vDHSBin@",
"sNp@DkUZj@[\\QXu`",
"RFPDXOH@",
"QM`BN`^L`",
"qC`@ISTAy@",
"sGP@LdbMU@MfHl[FVF@",
"qCb@AIZ`H",
"KAx@@IRjuUPAlHPfES]FFa`@",
"KAx@@ITnuUPAlHPfES\\",
"HiD@@DiUVjj`AmHPfES\\H",
"sNp@DjUjj@[\\QXu`",
"sJP@DkVhAmQEcFJF@",
"sGP@DjVj`FsDVMcCC@",
"qC`@Qz`MbHmFBF@",
"sJP@DkfhAmQEb",
"qC`@IVtAlQEhsPp@",
"sGP@Djuj`FsDVM@",
"sGP@Dj}j`FsDVMcMC@",
"sJP@DiZhA@",
"KAx@@ISjuUPAlHPfES]F@a`@",
"sJP@DjZhAmQEcFRF@",
"KAx@@IRnuUPAlHPfES]F@a`@",
"HiD@@DjWvjj`AmHPfES\\H",
"QMHAIhGd@",
"sNp@DiUjj@[\\QXuq`a`@",
"KAx@@IVjmUPAlHPfES\\",
"sGP@DjVj`FsDVMcMC@",
"QM`AIhGe@",
"HiD@@LdbJRjjh@[RDIaTwB",
"qCp@AIZ`H",
"sGP@LdbMU@MfHl[FFF@",
"QMDARVA@",
"sNp@LdbJjj@[\\QXuqba`@",
"sNp@LdbJjj@[\\QXuqca`@",
"sGP@Dkej`FsDVM@",
"qCb@AIZ`OI@",
"HaD@@DjUZxHH@AlHPfES]FLa`@",
"sGP@DkYj`FsDVM@",
"qCb@AIV`H",
"sNp@LdbJjj@[\\QXuqea`@",
"sGP@DkUj`FsDVMcEC@",
"sFp@DiTt@@Axa@",
"Hmt@@DjU_ZxHHj@AmhPfES\\Lj",
"QM`BN`^P",
"qCb@AIZ`OH`",
"sFp@DiTt@@AxaP",
"sGP@Djuj`FsDVMcEC@",
"sGP@Djuj`FsDVMcIC@",
"sGP@DkUj`FsDVMcKC@",
"sJP@DkfhAmQEcFRF@",
"sGP@DjVj`FsDVMcIC@",
"HaD@@DjUZxHH@AlHPfES]FFa`@",
"qC`@IRtDVqDV@",
"sNp@Dj}Zj@[\\QXuqfa`@",
"KAx@@ITnuUPAlHPfES]FFa`@",
"HiD@@DkUUjj`AmHPfES\\H",
"sJQ@@dkU@H",
"qC`@Qz`H",
"KAx@@IUkmUPAlHPfES\\",
"KAx@@ITouUPAlHPfES]FJa`@",
"sJP@H~j@[TQX`",
"sGP@DjZj`FsDVM@",
"sJP@DkVhAmQEcFFF@",
"sJX@@eKU@H",
"sJP@DizhAy@",
"QMHAIhGbP",
"KAx@@ITouUPAlHPfES]FNa`@",
"HaD@@DjUZxHD@AlHPfES\\",
"HaD@@DjUZxHH@A@",
"sNp@LdbJjj@[\\QXuqaa`@",
"Hed@@LdbRQUUUP@vTHSBinFP",
"KAx@@ITouUPAlHPfES]FLa`@",
"sNp@DkUZj@[\\QXuqba`@",
"KAx@@ITjuUPAlHPfES]FNa`@",
"KAx@@YIDTjjh@vDHSBincGPp@",
"HaD@@DjYvxH`@AlHPfES]FLa`@",
"RF@QP`",
"qCb@AIj`H",
"sNp@DjUjj@[\\QXuqaa`@",
"sNp@DkVZj@[\\QXu`",
"KAx@@YIDUJjh@vDHSBin@",
"sGP@DkYj`FsDVMcIC@",
"sGP@DjVj`FsDVMcAC@",
"sGP@DiVj`D",
"sJP@DkVhAmQEcFZF@",
"sNp@LdbLjj@[\\QXu`",
"QM@HvAmdqbF@",
"HaD@@DjWjXHB@AlHPfES\\",
"sNp@DjwZj@[\\QXuqba`@",
"sNp@LdbJjj@[\\QXuqda`@",
"sFp@DiTt@@Axa`",
"HiD@@Djuujj`AmHPfES\\H",
"sNp@DkUZj@[\\QXuqca`@",
"sJP@DiZhAy@",
"KAx@@YIDTjjh@vDHSBincCPp@",
"KAx@@IWNmUPAlHPfES\\",
"KAx@@IVkMUPAlHPfES\\",
"sJQ@@dju@H",
"qCb@AIZ`OH@",
"qC`@ISTAxa@",
"sNp@DjyZj@[\\QXu`",
"Hid@@DjUfaBB`@FtaBXUMp`",
"HiD@@DiUVjj`AmHPfES\\LXBF@",
"KAx@@IUjmUPAlHPfES\\",
"HiD@@DjWvjj`AmHPfES\\LXjF@",
"sJP@DjVhAmQEb",
"qCb@AIV`OH`",
"HiD@@LdbJRjjh@[RDIaTwCFDa`@",
"KAx@@YIDTjjh@vDHSBinc@Pp@",
"sNp@DjUjj@[\\QXuqda`@",
"qC`@Qz`OED",
"sJP@DkfhAmQEcFZF@",
"KAx@@YIDbjjh@vDHSBincDPp@",
"sGP@Djyj`FsDVMcMC@",
"KAx@@IVrmUPAlHPfES\\",
"qCp@AIZ`OI@",
"sJX@@dkU@H",
"sJQ@@dkU@OH`",
"sNp@Di]ZjBBvxbqk@",
"Hkl@@DjU_Uk``bj`@[VDIaTwCJzX",
"sGP@DjZj`FsDVMcEC@",
"Hid@@DjU^nBBH@FtaBXUMpqcHX@",
"sNp@DkeZj@[\\QXu`",
"sNp@DjYjj@[\\QXuqca`@",
"sGQ@@djuT@`",
"HiD@@LdbJTjjh@[RDIaTwB",
"sOp@DjWkB@@Gd`",
"HeT@@LdbbRKBDQD@CYPaLJfxY@",
"qCr@XIKTA@",
"HiD@@DjW^jj`AmHPfES\\LXJF@",
"HeT@@DjU]k``b`@[JDIaTwCH",
"sGP@Djuj`FsDVMcCC@",
"`IH`B",
"sOp@DjWkB@@GdX",
"sJQ@@eKU@H",
"KAx@@YIDUJjh@vDHSBincBPp@",
"sJX@@eKU@OH@",
"KAx@@YIDTjjh@vDHSBincAPp@",
"sOq@@drm\\@@@`",
"KAx@@IUkMUPAlHPfES\\",
"qCp@AIj`H",
"Hed@@DjUUjjj@FraBXUMpr",
"sGX@@eJuT@`",
"sGP@DkUj`FsDVMcCC@",
"HiD@@Dj}Ujj`AmHPfES\\LXrF@",
"KAx@@ITouUPAlHPfES]FHa`@",
"Hed@@DjWujjj@FraBXUMpsFIa`@",
"sGP@DiUj``mfHlZ",
"sFp@DiTvjhAlqEcP",
"Hid@@DjU^nBBH@FtaBXUMpq`XX@",
"sJP@DkVdAmQEb",
"qCp@AIZ`OH`",
"QMhDRVA@",
"qC`@ISJAlQE`",
"qCp@BOTAyhl",
"sJX@@eOU@ODB",
"sFp@DiTt@@AyaB",
"sGP@DkUj`FsDVMcMC@",
"Hid@@DjYUaBH`@FtaBXUMpqcHX@",
"qC`@Qz`OH@",
"HiD@@DjUVjj`AmHPfES\\LXZF@",
"sJP@H~j@[TQXqda`@",
"sJX@@eKU@OI@",
"sNp@Djejj@[\\QXu`",
"sJQ@@dsU@H",
"sJQ@@dkU@OI`",
"KAx@@YIMDVjh@vDHSBin@",
"Hid@@DjU^nBBD@FtaBXUMp`",
"sNp@DkgZj@[\\QXuqca`@",
"qC`@IRtDVqDVcEC@",
"Hed@@LdbRQeUUP@vTHSBinFP",
"sNp@DiUjj@P",
"qC`@IRtDT",
"sNp@DkYZj@[\\QXuqca`@",
"KAx@@IUkmUPAlHPfES]FDa`@",
"KAx@@IVjmUPAlHPfES]FNa`@",
"sOx@@drm\\@@@`",
"KAx@@ITjuUPAlHPfES]FBa`@",
"QMDARVAyH",
"sJP`@dfvhA@",
"HeT@@DjU_k``b`@[JDIaTwCLXfF@",
"KAx@@IToUUPAlHPfES]FJa`@",
"sGP@DkYj`FsDVMcEC@",
"qCb@AIZ`ODH",
"`I@`B",
"KAx@@IUzmUPAlHPfES]FFa`@",
"sNp@DkfZj@[\\QXu`",
"KAx@@ITnuUPAlHPfES]F@a`@",
"HiD@@LddURjjh@[RDIaTwB",
"sNp@Dj~Zj@[\\QXuqfa`@",
"Hed@@Dj{uZjj@FraBXUMpr",
"KAx@@ITsUUPAlHPfES\\",
"Hid@@LdbRQk``b@AmHPfES\\LXrF@",
"sOp@DjWkB@@GdH",
"sJQ@@dkU@OH@",
"Hid@@DjU^nBBH@FtaBXUMpqahX@",
"sGP@DiYj``mfHlZ",
"KAx@@IToUUPAlHPfES]FLa`@",
"qCp@AJZ`ODH",
"Hmt@@DjU]ZxHHj@AmhPfES\\Lj",
"sGP@DkUjPFsDVM@",
"qC`@IVtA@",
"Hed@@LdbJReUUP@vTHSBinFP",
"sNp@DjuZj@[\\QXuqea`@",
"KAx@@IUkmUPAlHPfES]FNa`@",
"HiD@@DkVUjj`AmHPfES\\H",
"Hed@@DkUeZjj@FraBXUMpr",
"sNp@DkVZj@[\\QXuqea`@",
"sJP@DiVhHKZbKFLLL@",
"HiD@@Djuyjj`AmHPfES\\H",
"sNp@DjUjj@[\\QXuq`a`@",
"HeT@@DjYUXPbH`@[JDIaTwCH",
"HiD@@DjwUjj`AmHPfES\\LXRF@",
"sNq@@djmUPB",
"KAx@@YIEEZjh@vDHSBincCPp@",
"sGP@Di^V`dmfHlZ",
"Hid@@DjYUaBHP@FtaBXUMp`",
"sNp@DjYjj@[\\QXuqba`@",
"sGP@Dkej`FsDVMcKC@",
"HeT@@DjU^k``b`@[JDIaTwCH",
"qC`@Qv`MbHmFBF@",
"sGQ@@djmT@`",
"qCr@XIKTAyH",
"qC`@IVtAlQEhpPp@",
"Hid@@LdbbQxXF@@AmHPfES\\LXjF@",
"sGP@DkYj`FsDVMcCC@",
"KAx@@IVsMUPAlHPfES\\",
"qCp@AIj`ODl",
"HiD@@DkeUjj`AmHPfES\\H",
"deT@@DjU[k``b`@vTHSBinFP"/* "HeT@@DjU[kjjjh@ZLDXSSYPaLJfxY@" */,
"sJP@DkVdAmQEcFRF@",
"HiD@@LdbJTjjh@[RDIaTwCFDa`@",
"HiD@@DkYyjj`AmHPfES\\H",
"sJP@DjZhAyH",
"KAx@@IVkMUPAlHPfES]FDa`@",
"sJX@@dkU@OI@",
"Hed@@LdbRQUUUP@vTHSBinFXpLL@",
"Hed@@DjuUZjj@FraBXUMpr",
"sGP@Djfj`FsDVMcKC@",
"sNp@DkVZj@[\\QXuqba`@",
"sNp@DjyZj@[\\QXuqfa`@",
"qCb@AIj`OH@",
"sNp@DjUZj@[\\QXu`",
"KAx@@IWOMUPAlHPfES\\",
"Hid@@DjU^nBBH@D",
"Hed@@DjuvZjj@FraBXUMpr",
"sJP@DiVhHKZbKFLtL@",
"dmt@@DjU_ZxHHj@C[PaLJfxYVLKC@" /* "Hmt@@DjU_Zzjjj`AhpQaLmmBDpj[aeXplL@" */,
"sNp@DjuZj@[\\QXuqca`@",
"sJP@DkfhAmQEcFJF@",
"sNp@LdbJZj@[\\QXu`",
"HeT@@DjU_k``b`@[JDIaTwCLXFF@",
"KAx@@IVlmUPAlHPfES]FNa`@",
"HeT@@LdbbRKBDQD@CYPaLJfxYcEPp@",
"Hid@@DjUZnBBH@FtaBXUMpqcHX@",
"qCa@CIKTA@",
"HiD@@Dj~]jj`AmHPfES\\LXFF@",
"sKP@Di\\Zj@[TQX`",
"sGP@Djfj`FsDVMcEC@",
"HiD@@DkgYjj`AmHPfES\\H",
"sNp@DjuZj@[\\QXuqaa`@",
"KAx@@YIMDVjh@vDHSBincDPp@",
"sJP@DjVhHKZbKFLTL@",
"Hid@@LdbRQk``b@AmHPfES\\LXZF@",
"HiD@@Dj}Ujj`AmHPfES\\LXzF@",
"HeT@@DjU_k``bP@[JDIaTwCH",
"sNp@DkUZi@[\\QXu`",
"HiD@@DjYfjj`AmHPfES\\H",
"sGP@DjZj`FsDVMcAC@",
"Hmt@@DjU_jxHHj@AmhPfES\\Lj",
"Hid@@LdbRQk``R@AmHPfES\\H",
"KAx@@YIDUJjh@vDHSBincDPp@",
"qCr@XIKTAyD",
"sOq@@drm\\@@@|`@",
"Hed@@DjW^jjj@FraBXUMpsFBa`@",
"HeT@@DjY]zXFB@@[JDIaTwCH",
"Hkl@@DjU_Vk``bj`@[VDIaTwCJzX",
"Hid@@DjY}nBHH@FtaBXUMpqcHX@",
"sGX@@eKuT@|d@",
"sGP@Dj^Y`FsDVM@",
"HcL@@DjU_ZnBBJh@FqaBXUMprn`",
"sJP@DkVdAmQEcFJF@",
"sOq@@drm\\@@@|b@",
"sNp@DjyZj@[\\QXuqaa`@",
"HaD@@DjUZxHH@AyD@",
"qC`@Qv`H",
"dmt@@DjU_ZxHHj@C[PaLJfxYVLYC@" /* "Hmt@@DjU_Zzjjj`AhpQaLmmBDpj[aeXqdL@" */,
"sGP@Dkej`FsDVMcMC@",
"Hed@@DjUUjjj@FraBXUMpsFHa`@",
"HeT@@LdbbRkBDQD@CYPaLJfxY@",
"KAx@@IU{MUPAlHPfES]FLa`@",
"RG@DTH",
"sJY@DDeVhA@",
"KAx@@YIDUJjh@vDHSBinc@Pp@",
"sJX@@dkU@OI`",
"sJQ@@dju@OI`",
"HeT@@LdbbRKBDQD@CYPaLJfxYcFPp@",
"sFp@DiTvjhAlqEcXpPp@",
"HaD@@DjUZxHH@AyG@",
"sNx@@eJ}UPB",
"sNp@LddUjj@[\\QXuqca`@",
"HaDH@@RVU[j@@@D",
"sNp@DkgZi@[\\QXu`",
"sGY@LDeVj`D",
"sNp@LdbJfZBZvxbqk@",
"sJP`@dfvhAyL",
"sGX@AddQjhAxe`",
"Hmt@@DjU_ZxHHj@AmhPfES\\LkFIa`@",
"qCh@CIKTA@",
"sNp@LdbLjj@[\\QXuq`a`@",
"sOq@@drm\\@@@|a@",
"KAx@@IUzmUPAlHPfES]FJa`@",
"sNx@AddQUUPB",
"sGP@Di]jP`mfHlZ",
"sJP`@TeZhA@",
"KAx@@IRjmUPHKXPaLJfx",
"HeT@@LdbRTM\\DDT@CYPaLJfxY@",
"HaF@@@Rfu[j@@@D",
"Hid@@DjYUaBH`@FtaBXUMpqchX@",
"KAx@@IUjmTpAlHPfES\\",
"Hid@@DjU^nBBD@FtaBXUMpqcHX@",
"sGP@DiUj``mfHl[FFF@",
"KAx@@IUvmUPAlHPfES]FLa`@",
"Hed@@LdbQTUUUP@vTHSBinFXqDL@",
"sJP@DkVhA@",
"sOx@@drm\\@@@|b@",
"KAx@@IUkMUPAlHPfES]FDa`@",
"HeT@@LdbRQU\\DDT@CYPaLJfxY@",
"HiD@@Dj}Yjj`AmHPfES\\LXrF@",
"HiD@@Dj{ujj`AmHPfES\\LXFF@",
"KAx@@IWNmUPAlHPfES]FFa`@",
"KAx@@IRkMUPHKXPaLJfx",
"sJP@DjYdAmQEcFZF@",
"sJY@LDeZhAyL",
"HaDH@@RVU[f@@@D",
"sJP`@deVhAyB",
"HaD@@DjWjZjj`AlHPfES\\",
"sGP@DkYj`FsDVMcMC@",
"sNp@DkgZj@[\\QXuqea`@",
"sJQ@@dlu@H",
"HeT@@DjU]k``b`@[JDIaTwCLXrF@",
"sJX@@dkU@OH`",
"RFDDQFCr`",
"sJP@DiYXIKZbKFLLL@",
"KAx@@YIHjjjh@vDHSBincGPp@",
"Hk\\@@DjU^ukmLHH@@@AmXPfES\\Lki`",
"sGQ@@djmT@|b@",
"Hid@@DjUfaBB`@FtaBXUMpqahX@",
"sNx@@eRmUPB",
"Hmt@@LdbRVak``ah@FvaBXUMprh",
"qCr@XIJtA@",
"KAx@@IWMmUPAlHPfES]FNa`@",
"HeT@@DjYYZPbJ@@[JDIaTwCH",
"sNp@DkfZj@[\\QXuqea`@",
"Hid@@DjU^nBAHAEVtaBXUMp`",
"dmt@@DjUgZDHJJ@C[PaLJfxYT" /* "Hmt@@DjYU^Vjjj`AhtISRmmBDpj[aeP" */,
"sGP@DkejPFsDVM@",
"sNx@@eJmUPB",
"qCb@AIf`H",
"HcL@@DjU_VnBBJh@FqaBXUMprnqcXX@",
"Hid@@DjUZnBBH@FtaBXUMpqahX@",
"sNp@LdbQZjBBvxbqkcGC@",
"sOx@@drm\\@@@|c@",
"sJP@H~j@^R@",
"KAx@@YIDcFjhDElHPfES\\",
"Hid@@DjUZnBAH@FtaBXUMp`",
"sNp@LddUji@[\\QXu`",
"sGP@DjfjPFsDVM@",
"HeT@@DjYUXPbD`@[JDIaTwCH",
"KAx@@IUoMUPAlHPfES]FDa`@",
"sFp@DiTt@@AyaD",
"Hed@@DjuuZjj@FraBXUMpsFIa`@",
"HeT@@DjUghP`h`@[JDIaTwCLXfF@",
"sOp@DjWkjj`FwDVM\\YhX@",
"sGP@Djfj`FsDVMcIC@",
"KAx@@IRkmUPHKXPaLJfzL]C@",
"sNx@@djmUPB",
"QM`AIdD",
"sOp@DjWkB@@Gbe@",
"sNp@DjyZj@[\\QXuqca`@",
"QM@HuAmd`",
"sNp@LddUjj@[\\QXuqea`@",
"daD@@DjUZxHD@CXPaLJfzLYC@" /* "HaD@@DkeVyjj`AhrXUMuaBDpj[hpDL@" */,
"qCb@AIZPH",
"HiD@@LdbJTjjh@[RDIaTwCF@a`@",
"Hmt@@DjU_ZxHHi@AmhPfES\\Lj",
"HaDH@@RYWih@H@D",
"HiD@@LdbJTjjh@[RDIaTwCFHa`@",
"sGX@@djuT@|a@",
"sNp@DkfZj@[\\QXuqaa`@",
"Hid@@DjU^nBBH@GdL",
"KAx@@IVkMUPAlHPfES]FJa`@",
"qCr@XIKTAy@",
"HmT@@Dj{uVjjh@[ZDIaTwCJqaXX@",
"dmt@@DjYWVDHbJ@C[PaLJfxYT" /* "Hmt@@DjYWVFjjj`AhpQe\\mmBDpj[aeP" */,
"Hif@@@RUe^Fh@@@P",
"HaDH@@Rfu[j@@@GdH",
"KAx@@IVsMUPAlHPfES]FDa`@",
"sKP@Di\\Zj@[TQXq`a`@",
"sJX@@eMU@OH@",
"HeT@@DjU^k``b`@[JDIaTwCLXFF@",
"Hmt@@LdbbRJXPbHh@FvaBXUMprh",
"sJP@DjvhAmQEcFBF@",
"dmt@@LdbbRNXPbHh@MmBDpj[aeXplL@" /* "Hmt@@LdbbRNXZjjj@FcAFUrvtHSBinFUcBpp@" */,
"sJP`@dfvhAyD",
"sGP@Di^V`dmfHl[FVF@",
"KAx@@IVsmUPAlHPfES]FBa`@",
"sOq@@drm\\@@@|PP",
"sJY@BDeZhA@",
"HeT@@LdbRbmBDED@CYPaLJfxY@",
"Hed@@Djy[Zjj@FraBXUMpr",
"HeT@@DjU]k``b`@[JDIaTwCLXFF@",
"Hid@@DjUfaBB`@D",
"qCa@CIJtA@",
"QMPARVA@",
"Hid@@DjUfaBB`@FtaBXUMpqcHX@",
"sJY@BDfZhA@",
"HeT@@DjUghP`hP@[JDIaTwCH",
"Hed@@Dj{uZjj@FraBXUMpsFIa`@",
"dmt@@DjYUvDHbJ@C[PaLJfxYVLUC@" /* "Hmt@@LdbbRUXZjjj@FcAFUrvtHSBinFUcFPp@" */,
"sNp`@dfuZj@P",
"sJQ@@dmU@OH@",
"sJX@@dmU@H",
"HeT@@DjU]k``b`@[JDIaTwCLXZF@",
"HiD@@LdfbJZjh@[RDIaTwCFAa`@",
"sOx@@drm\\@@@|a@",
"deT@@DjUfhP`h`@vTHSBinFP" /* "HeT@@LdbbQgCUUU@CQhRfz[JDIaTwCH" */,
"dmt@@DjU]ZxHHj@C[PaLJfxYVLKC@" /* "Hmt@@DjU]Zzjjj`AhpQaLmmBDpj[aeXplL@" */,
"sOp@DjWkjj`FwDVM\\XHX@",
"HcL@@LdbbRNSBDQEP@McBDpj[ae]cFpp@",
"HiD@@Dj}Yji`AmHPfES\\H",
"HaDH@@RYe[hB@@D",
"Hid@@DjU^njjj@FtaBXUMpq`XX@",
"deT@@LdbbRKBDQB@FraBXUMpr" /* "HeT@@DkYeFVjjh@ZMaUpsYPaLJfxY@" */,
"QMPARZA@",
"sOq@@drm\\@@@|QX",
"HaD@@DjYvxH`@A@",
"HcL@@LdbbRNcBDQEP@McBDpj[ae]@",
"QMhDRZA@",
"RG@DXLHmP",
"QM`BN`XQYd",
"RG@DTLHmP",
"QMHAIXFEVd",
"QMDARVAaH",
"RFPDXLHmP",
"RF@Q`vRbdLEC@",
"RF@QpvR@",
"QO@HyjAmd`",
"`II@B",
"`II@CFspqJp",
"`II@CF[@hM@prB`",
"`H@[T[|B`XN@PdM@p|@bHrBcDk@",
"RG@DXMj}F@",
"QM`BN`[L~b@",
"RG@DTMj}D@",
"QMHAIXFt~j@",
"QMDARVA}L@",
"RFPDXMj}D@",
"sKP@Di\\YZ@[TQXqaa`@",
"eF`BHD" /* "RG@DXMH" */ };
private static StereoMolecule[] sKeyFragment;
private SSSearcher mSSSearcher;
private StereoMolecule mMolecule,mFragment;
private int[] mMoleculeIndexInt,mFragmentIndexInt;
private long[] mMoleculeIndexLong,mFragmentIndexLong;
private byte[] mMoleculeIDCode,mFragmentIDCode;
private AbstractDescriptorHandlerLongFP mDescriptorHandler;
public static int getNoOfKeys() {
return cKeyIDCode.length;
}
public SSSearcherWithIndex(AbstractDescriptorHandlerLongFP dh) {
mSSSearcher = new SSSearcher();
mDescriptorHandler = dh;
init();
}
public SSSearcherWithIndex() {
mSSSearcher = new SSSearcher();
init();
}
public SSSearcherWithIndex(int matchMode) {
mSSSearcher = new SSSearcher(matchMode);
init();
}
public static StereoMolecule getKeyFragment(int no) {
return sKeyFragment[no];
}
@Deprecated // Use long version of this method
public void setFragment(StereoMolecule fragment, int[] index) {
mFragmentIDCode = null;
mFragmentIndexLong = null;
mFragment = fragment;
if (index == null)
mFragmentIndexInt = createIndex(fragment);
else
mFragmentIndexInt = index;
}
@Deprecated // Use long version of this method
public void setFragment(String idcode, int[] index) {
setFragment(idcode.getBytes(StandardCharsets.UTF_8), index);
}
@Deprecated // Use long version of this method
public void setFragment(byte[] idcode, int[] index) {
mFragmentIDCode = idcode;
mFragmentIndexLong = null;
if (index == null) {
mFragment = (new IDCodeParser(false)).getCompactMolecule(idcode);
mFragmentIndexInt = createIndex(mFragment);
}
else {
mFragment = null;
mFragmentIndexInt = index;
}
}
@Deprecated // Use long version of this method
public void setMolecule(StereoMolecule molecule, int[] index) {
mMoleculeIDCode = null;
mMoleculeIndexLong = null;
mMolecule = molecule;
if (index == null)
mMoleculeIndexInt = createIndex(molecule);
else
mMoleculeIndexInt = index;
}
@Deprecated // Use long version of this method
public void setMolecule(String idcode, int[] index) {
setMolecule(idcode.getBytes(StandardCharsets.UTF_8), index);
}
@Deprecated // Use long version of this method
public void setMolecule(byte[] idcode, int[] index) {
mMoleculeIDCode = idcode;
mMoleculeIndexLong = null;
if (index == null) {
mMolecule = (new IDCodeParser(false)).getCompactMolecule(idcode);
mMoleculeIndexInt = createIndex(mMolecule);
}
else {
mMolecule = null;
mMoleculeIndexInt = index;
}
}
public void setFragment(StereoMolecule fragment, long[] index) {
mFragmentIDCode = null;
mFragmentIndexInt = null;
mFragment = fragment;
if (index == null)
mFragmentIndexLong = createLongIndex(fragment);
else
mFragmentIndexLong = index;
}
public void setFragment(String idcode, long[] index) {
setFragment(idcode.getBytes(StandardCharsets.UTF_8), index);
}
public void setFragment(byte[] idcode, long[] index) {
mFragmentIDCode = idcode;
mFragmentIndexInt = null;
if (index == null) {
mFragment = (new IDCodeParser(false)).getCompactMolecule(idcode);
mFragmentIndexLong = createLongIndex(mFragment);
}
else {
mFragment = null;
mFragmentIndexLong = index;
}
}
public void setMolecule(StereoMolecule molecule, long[] index) {
mMoleculeIDCode = null;
mMoleculeIndexInt = null;
mMolecule = molecule;
if (index == null)
mMoleculeIndexLong = createLongIndex(molecule);
else
mMoleculeIndexLong = index;
}
public void setMolecule(String idcode, long[] index) {
setMolecule(idcode.getBytes(StandardCharsets.UTF_8), index);
}
public void setMolecule(byte[] idcode, long[] index) {
mMoleculeIDCode = idcode;
mMoleculeIndexInt = null;
if (index == null) {
mMolecule = (new IDCodeParser(false)).getCompactMolecule(idcode);
mMoleculeIndexLong = createLongIndex(mMolecule);
}
else {
mMolecule = null;
mMoleculeIndexLong = index;
}
}
public int getFirstHittingLongIndexBlockNo() {
if (mMoleculeIndexLong != null) {
for (int i=0; i 16)
code -= 7;
index[j] <<= 4;
index[j] += code;
}
return index;
}
public static int[] getIndexFromHexString(byte[] bytes) {
if (bytes==null || bytes.length==0 || (bytes.length & 7) != 0)
return null;
int[] index = new int[bytes.length/8];
for (int i=0; i 16)
code -= 7;
index[j] <<= 4;
index[j] += code;
}
return index;
}
public static long[] getLongIndexFromHexString(String hex) {
if (hex.length() == 0 || (hex.length() & 15) != 0)
return null;
long[] index = new long[hex.length()/16];
for (int i=0; i 16)
code -= 7;
index[j] <<= 4;
index[j] += code;
}
return index;
}
public static long[] getLongIndexFromHexString(byte[] bytes) {
if (bytes==null || bytes.length==0 || (bytes.length & 15) != 0)
return null;
long[] index = new long[bytes.length/16];
for (int i=0; i 16)
code -= 7;
index[j] <<= 4;
index[j] += code;
}
return index;
}
public static String getHexStringFromIndex(int[] index) {
if (index == null)
return null;
byte[] bytes = new byte[index.length*8];
for (int i=0; i=0; j--) {
int code = value & 15;
if (code > 9)
code += 7;
bytes[i*8+j] = (byte)('0'+code);
value >>= 4;
}
}
return new String(bytes, StandardCharsets.UTF_8);
}
/* use Integer.bitCount() instead, which is supposed to use the POPCNT processor command on x86
public static int bitCount(int x) {
int temp;
temp = 0x55555555;
x = (x & temp) + (x >>> 1 & temp);
temp = 0x33333333;
x = (x & temp) + (x >>> 2 & temp);
temp = 0x07070707;
x = (x & temp) + (x >>> 4 & temp);
temp = 0x000F000F;
x = (x & temp) + (x >>> 8 & temp);
return (x & 0x1F) + (x >>> 16);
} */
private void init() {
synchronized(SSSearcherWithIndex.class) {
if (sKeyFragment == null) {
IDCodeParser theParser = new IDCodeParser(false);
sKeyFragment = new StereoMolecule[cKeyIDCode.length];
for (int i=0; i