com.actelion.research.chem.NamedSubstituents Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
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 java.util.TreeMap;
public class NamedSubstituents {
private static final String[][] SUBSTITUENT_LIST = {
// if multiple options are given, then the first one is the preferred
{ "Acyl", "gCaHA`AIf`@" },
{ "Alloc", "gNph@l@ILzuR@@" },
{ "Allyl", "Al" },
{ "Benzyl;Bn", "daD@`F@DjUZxHH@@" },
{ "Boc", "daxD`@S@AIgijj@@" },
{ "BOM;BzOM", "deTH`@H@Re[TYj`@@@" },
{ "Bs", "dmtDpAdLS`aPAIe]jf`@e`@@" },
{ "Bt", "dew@`@aJ@DiY]paej`@@@" },
{ "Btm", "did@P@BJ@Die_ahH@@@" },
{ "Butyl;nButyl", "gJPHB@IRuP@" },
{ "Benzoyl;Bz", "didH`@p@RYm^Eh@@@@" },
{ "Bzh", "dg|@`N@LdbRbtJUB]aAP@@@@" },
{ "Cbz", "dmtD`@S@AIgYVUZh@@@@" },
{ "cButyl", "gKPHL@IThuT@@" },
{ "cHeptyl", "daD@`L@DjWVzjj`@" },
{ "cHexyl", "gOpHL@IToWUU@@" },
{ "cOctyl", "did@`L@DjWWajjj@@" },
{ "cPentyl", "gFpHL@ITimUP@" },
{ "cPropyl", "gBPHL@Qxjh@" },
{ "COOH", "gC`h@l@ILt@@ !Bb@K~@Hc}" },
{ "DEAE", "daz@`@x@RiUjj`@" },
{ "DEIPS", "diD@P@\\B@DjfVjj`@" },
{ "DMIPS", "gNpD@xD@RjZjh@" },
{ "DMPM", "dcLD`@kPCIEMDdcttDDT@@" },
{ "DMPS", "deT@P@\\B@LddTjPsU@@@@" },
{ "DMTr", "fak@b@@Mt@ISZ{SMjo{NQKfm@AU@@@E@@@@" },
{ "DNP", "dkmB`hdDt~@HeNfS{HihheCAUhBHX@@" },
{ "DNS;Dan", "fhi`a@KPP@HH@YIHYheEhYKQgKP@@QP@@@" },
{ "DPIPS", "fdyAA@H@\\B@FRRIQSQIHzp_Qjh@h@@@@@" },
{ "DPTBS", "fleAA@H@\\B@FRRIQSRIIWNbEMU@EP@@@@@" },
{ "DTBMS", "dmT@P@\\B@Djffjjjh@@" },
{ "Ethyl", "eMBD@ch@" },
{ "Fmoc", "fde@b@@Hp@IL{LrjxeVCzKUT@@@P@@@" },
{ "iAmyl", "gGPHJ@YIDZj@@" },
{ "iButyl", "gJPHB@ITuP@" },
{ "Im", "gFtHAj@IRnKSP@" },
{ "iPropyl", "gC`HL@Qz`@" },
{ "MDIPS", "diD@P@\\B@DjfZjj`@" },
{ "MDPS", "foA@A@@NA@CIIEEBdeeVLzj@@@@@@" },
{ "Methyl", "eFBH@c@@" },
{ "MEM", "gNphAR@IRoUT@@" },
{ "Mes", "deT@`J@DjY{[`bB`@@" },
{ "MMTr", "ffcAB@@Z@Dim]ifuWYrI\\uh@Jh@@@@@@" },
{ "MOM", "gCaHA`AJZ`@" },
{ "MPM;PMB", "deTH`@d@Rfuunh@J@@" },
{ "Ms", "gJPdH`DD@cuh@" },
{ "MTM", "gC`D@DX@Rfh@" },
{ "mTolyl", "daD@`N@DjWjXHB@@" },
{ "N3", "gClHaE`@RnReX@" },
{ "nAmyl;Amyl", "gGPHJ@IRmU@@" },
{ "neoAm", "gGPHJ@IUMU@@" },
{ "NO2,Nitro", "gChhhE`BRnRYh@" },
{ "Np", "deVDaHAI@HeNR[e_aZ@B@@" },
{ "nPropyl;Propyl", "gC`HL@IST@@" },
{ "oTolyl", "daD@`J@DjYvxH`@@" },
{ "Phenyl", "gOpHL@IToVD@@@" },
{ "Pht", "dcLL`@RU@Dfyed]ZBA`@@" },
{ "Piv;Pv", "gNqHA`AIffj`@" },
{ "PMBM", "dcLD`@T`AJUm]FZh@J@@" },
{ "PNB", "dcNLaHAEt@bTyInUvxV`@f@@" },
{ "Poc", "didD`@S@AIgexVjj`@" },
{ "PPi", "diDFsHSB[`|J|A@Lxn{lddqdZih@@" },
{ "pTolyl", "daD@`N@DjWzXHB@@" },
{ "sAmyl", "gGPHL@YIDZj@@" },
{ "sButyl", "gJPHL@ITuP@" },
{ "SEM", "diDHPFApD@rRQUJjj`@" },
{ "SES", "dedDpHP@``AgCIICeHmUT@@" },
{ "SO3H", "gJQdHl@``D^m@@" },
{ "tAmyl", "gGPHB@IUMU@@" },
{ "TBDMS;TBS", "dax@P@\\B@Djfjjh@@" },
{ "TBDPS", "fdy@A@@NA@CIIEEEIde]XOhuPAT@@@@@" },
{ "TBMPS", "dg\\HPHApH@rRQJJPjg]UAT@@@" },
{ "tButyl,tBu", "gJPHB@Q}T@@" },
{ "TDS", "ded@P@\\B@LddTeeUUP@@" },
{ "Tf", "daxDhHP@``BiAiCiCIICHmU@@" },
{ "TFA", "gNqBJIARFdF@YEHYUL@@" },
{ "Thexyl", "gNpHB@IUMUT@@" },
{ "THF", "gFqH@PAJYujj@@" },
{ "THP", "gOqH@PAJYZzjh@" },
{ "TIPS", "dmT@P@\\B@DjfYjjjh@@" },
{ "TMS", "gJPD@xD@czh@" },
{ "Tosyl;Ts", "dmtDPHP@``CIICLeaeZ@B@@" },
{ "Troc", "diDDHJxHaHcH`PCHiBeJjf@@" },
{ "Trt", "fbm@B@A@FRQIRKQPiIZdoIcdHJ`@@@@@@" },
{ "Xyl", "did@`J@DjYynBHH@@" },
};
private static TreeMap sIDCodeMap = null;
private static void createMap() {
sIDCodeMap = new TreeMap<>();
for (String[] sp:SUBSTITUENT_LIST) {
String[] key = sp[0].split(";");
for (String k:key)
sIDCodeMap.put(normalize(k), sp[1]);
}
}
/**
* Checks, whether the given nameStart either exactly matches one of the dictionary names
* or whether exactly one dictionary name starts with the given nameStart.
* If one of these conditions occurr, then the full dictionary name is returned.
* @param nameStart
* @return null, "", or dictionary name if no, multiple, or exactly one name matches nameStart
*/
public static String identify(String nameStart) {
if (nameStart == null || nameStart.length() == 0)
return null;
String name = null;
nameStart = normalize(nameStart);
for (String[] sp:SUBSTITUENT_LIST) {
String[] key = sp[0].split(";");
for (String k:key) {
if (normalize(k).equals(nameStart))
return k;
if (normalize(k).startsWith(nameStart)) {
if (name == null)
name = k;
else
return "";
}
}
}
return name;
}
private static String normalize(String s) {
return s.toLowerCase().replace("-", "");
}
public static String getSubstituentIDCode(String name) {
if (sIDCodeMap == null)
createMap();
return sIDCodeMap.get(normalize(name));
}
public static StereoMolecule getSubstituent(String name) {
String idcode = getSubstituentIDCode(name);
return (idcode == null) ? null : new IDCodeParser(false).getCompactMolecule(idcode);
}
/**
* @param s
* @return whether appending some characters to s may lead to a known substituent name
*/
public static boolean isValidSubstituentNameStart(String s) {
if (sIDCodeMap == null)
createMap();
s = normalize(s);
for (String n:sIDCodeMap.keySet())
if (n.startsWith(s))
return true;
return false;
}
}