ChemAxon Forum Archive » Storage & search: JChem Base and JChem Oracle Cartridge

infinite loop?

User 870ab5b546

03-02-2016 17:17:31

Hi,


The code:


final int EXACTLY = 0;

final int ATLEAST = 1;

final int oper = ATLEAST;



private boolean matchMapPattern(Molecule respMol, Molecule authMol)

        throws VerifyException {

    final String SELF = "MapProperty.matchMapPattern: ";

    try {

        final MolSearchOptions searchOpts = new MolSearchOptions(FULL);

        searchOpts.setStereoSearchType(STEREO_SPECIFIC);

                // checkEnant is irrelevant for map patterns

        searchOpts.setDoubleBondStereoMatchingMode(DBS_ALL);

        searchOpts.setExactBondMatching(true);

        searchOpts.setStereoModel(STEREO_MODEL_LOCAL);

                // required for diastereotopic atoms not to match

        searchOpts.setOrderSensitiveSearch(true); // want multiple results

        searchOpts.setIgnoreCumuleneOrRingCisTransStereo(false); // odd-numbered cumulenes

        searchOpts.setIgnoreAxialStereo(false); // allenes & biaryls

        searchOpts.setIgnoreSynAntiStereo(true);

        final MolSearch search = new MolSearch();

        search.setSearchOptions(searchOpts);

        search.setTarget(respMol);

        search.setQuery(authMol);

        final int MAX_MAP_NUMBER = 99;

        boolean haveMatch = false;

        while (true) {

            final int[] isomorphism = search.findNext(); // *** throws OutOfMemoryError

            if (isomorphism == null) {

                debugPrint(SELF + "no more isomorphisms found.");

                break;

            } else debugPrint(SELF + "looking at isomorphism: {",

                    Utils.join(isomorphism, 1), "}");

            final int[] maps = new int[MAX_MAP_NUMBER + 1]; // maps[respMap] = refMap

            final int[] mapsInvert = new int[MAX_MAP_NUMBER + 1]; // mapsInvert[refMap] = respMap

            haveMatch = true;

            for (int atomNum = 0; atomNum < isomorphism.length; atomNum++) {

                final MolAtom authAtom = authMol.getAtom(atomNum);

                final MolAtom respAtom = (isomorphism[atomNum] >= 0

                        ? respMol.getAtom(isomorphism[atomNum])

                        : new MolAtom(1));

                final int refMap = authAtom.getAtomMap();

                final int respMap = respAtom.getAtomMap();

                if (refMap == 0 && (respMap == 0 || oper == ATLEAST))

                    continue; // maps are OK; next atom in array

                if (respMap == 0 || (refMap == 0 && oper == EXACTLY)) {

                    haveMatch = false; // bad isomorphism; keep looking

                    break;

                } // if response atom is unmapped

                // both atoms are mapped; compare

                if (maps[respMap] == 0 && mapsInvert[refMap] == 0) {

                    // first encounter with respMap && refMap

                    maps[respMap] = refMap;

                    mapsInvert[refMap] = respMap;

                } // if maps[] and mapsInvert[]

                if (maps[respMap] != refMap) {

                    haveMatch = false;

                    break;

                }

            } // for each atom atomNum

            if (haveMatch) {

                debugPrint(SELF + "found a match!");

                break;

            } // if there's a match

        } // loop until match found or no more isomorphisms

        debugPrint(SELF + "returning ", haveMatch);

        return haveMatch;

    } catch (Exception e1) {

        e1.printStackTrace();

        throw new VerifyException("internal error in matchMapPattern");

    }

} // matchMapPattern(Molecule, Molecule)


respMol has MRV:


<?xml version="1.0" encoding="UTF-8"?>

<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_12_01.xsd" version="ChemAxon file format v14.12.01, generated by v15.11.23.0">

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28" elementType="C C C C C C C C C C C C C C C C C C C C C C C C C C C O" mrvMap="2 2 1 2 0 0 1 1 2 1 2 2 1 0 2 2 0 1 3 2 2 2 0 3 3 3 0 0" lonePair="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2" x2="-4.427499771118164 -5.761169112166423 -5.761169112166423 -4.427499771118164 -3.0938304300699055 -3.0938304300699055 -1.760161089021647 -1.760161089021647 -0.42649174797338874 -0.42649174797338874 -0.42649174797338874 -1.760161089021647 0.9071775930748696 0.9071775930748696 2.3717158407834664 3.27693703783083 2.371825489897502 2.8477760950171014 1.514096973189066 4.181455216845137 5.515134338673173 6.8488134605012085 8.182492582329244 9.51617170415728 8.182492582329244 0.9071775930748697 -3.0938304300699055 -7.094848233994458" y2="1.5881588799259883 0.8181419393669477 -0.7218919417511335 -1.491908882310174 -0.7218919417511335 0.8181419393669477 1.5881588799259883 -1.491908882310174 -0.7218919417511335 0.8181419393669477 3.89820970160311 3.1281927610440694 1.5881588799259885 3.1281927610440694 1.112268172876402 2.3581408309426073 3.6039808406771088 5.068586938399731 5.8385869383997315 5.838586938399731 5.068586938399731 5.838586938399731 5.068586938399731 5.838586938399731 3.528586938399731 4.66819276104407 2.3581419393669476 -1.491891941751134"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="1"/>

        <bond id="b2" atomRefs2="a2 a3" order="1"/>

        <bond id="b3" atomRefs2="a3 a4" order="1"/>

        <bond id="b4" atomRefs2="a4 a5" order="1"/>

        <bond id="b5" atomRefs2="a1 a6" order="1"/>

        <bond id="b6" atomRefs2="a7 a6" order="1"/>

        <bond id="b7" atomRefs2="a6 a5" order="1"/>

        <bond id="b8" atomRefs2="a5 a8" order="2"/>

        <bond id="b9" atomRefs2="a8 a9" order="1"/>

        <bond id="b10" atomRefs2="a9 a10" order="1"/>

        <bond id="b11" atomRefs2="a10 a13" order="1"/>

        <bond id="b12" atomRefs2="a7 a10" order="1"/>

        <bond id="b13" atomRefs2="a12 a7" order="1"/>

        <bond id="b14" atomRefs2="a11 a12" order="1"/>

        <bond id="b15" atomRefs2="a11 a14" order="1"/>

        <bond id="b16" atomRefs2="a13 a15" order="1"/>

        <bond id="b17" atomRefs2="a14 a13" order="1"/>

        <bond id="b18" atomRefs2="a14 a17" order="1"/>

        <bond id="b19" atomRefs2="a15 a16" order="1"/>

        <bond id="b20" atomRefs2="a16 a17" order="1"/>

        <bond id="b21" atomRefs2="a17 a18" order="1"/>

        <bond id="b22" atomRefs2="a18 a19" order="1"/>

        <bond id="b23" atomRefs2="a18 a20" order="1"/>

        <bond id="b24" atomRefs2="a20 a21" order="1"/>

        <bond id="b25" atomRefs2="a21 a22" order="1"/>

        <bond id="b26" atomRefs2="a22 a23" order="1"/>

        <bond id="b27" atomRefs2="a23 a24" order="1"/>

        <bond id="b28" atomRefs2="a23 a25" order="1"/>

        <bond id="b29" atomRefs2="a14 a26" order="1"/>

        <bond id="b30" atomRefs2="a6 a27" order="1"/>

        <bond id="b31" atomRefs2="a3 a28" order="1"/>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

authMol has MRV:


<?xml version="1.0" encoding="UTF-8"?>

<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_12_01.xsd" version="ChemAxon file format v14.12.01, generated by v15.11.23.0">

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28" elementType="C C C C C C C C C C C C C C C C C C C C C C C C C C C O" mrvMap="0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0" x2="-4.427499771118164 -5.761169112166423 -5.761169112166423 -4.427499771118164 -3.0938304300699055 -3.0938304300699055 -1.760161089021647 -1.760161089021647 -0.42649174797338874 -0.42649174797338874 -0.42649174797338874 -1.760161089021647 0.9071775930748696 0.9071775930748696 2.3717158407834664 3.27693703783083 2.371825489897502 2.8477760950171014 1.514096973189066 4.181455216845137 5.515134338673173 6.8488134605012085 8.182492582329244 9.51617170415728 8.182492582329244 0.9071775930748697 -3.0938304300699055 -7.094848233994458" y2="1.5881588799259883 0.8181419393669477 -0.7218919417511335 -1.491908882310174 -0.7218919417511335 0.8181419393669477 1.5881588799259883 -1.491908882310174 -0.7218919417511335 0.8181419393669477 3.89820970160311 3.1281927610440694 1.5881588799259885 3.1281927610440694 1.112268172876402 2.3581408309426073 3.6039808406771088 5.068586938399731 5.8385869383997315 5.838586938399731 5.068586938399731 5.838586938399731 5.068586938399731 5.838586938399731 3.528586938399731 4.66819276104407 2.3581419393669476 -1.491891941751134"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="1"/>

        <bond id="b2" atomRefs2="a2 a3" order="1"/>

        <bond id="b3" atomRefs2="a3 a4" order="1"/>

        <bond id="b4" atomRefs2="a4 a5" order="1"/>

        <bond id="b5" atomRefs2="a1 a6" order="1"/>

        <bond id="b6" atomRefs2="a7 a6" order="1"/>

        <bond id="b7" atomRefs2="a6 a5" order="1"/>

        <bond id="b8" atomRefs2="a5 a8" order="2"/>

        <bond id="b9" atomRefs2="a8 a9" order="1"/>

        <bond id="b10" atomRefs2="a9 a10" order="1"/>

        <bond id="b11" atomRefs2="a10 a13" order="1"/>

        <bond id="b12" atomRefs2="a7 a10" order="1"/>

        <bond id="b13" atomRefs2="a12 a7" order="1"/>

        <bond id="b14" atomRefs2="a11 a12" order="1"/>

        <bond id="b15" atomRefs2="a11 a14" order="1"/>

        <bond id="b16" atomRefs2="a13 a15" order="1"/>

        <bond id="b17" atomRefs2="a14 a13" order="1"/>

        <bond id="b18" atomRefs2="a14 a17" order="1"/>

        <bond id="b19" atomRefs2="a15 a16" order="1"/>

        <bond id="b20" atomRefs2="a16 a17" order="1"/>

        <bond id="b21" atomRefs2="a17 a18" order="1"/>

        <bond id="b22" atomRefs2="a18 a19" order="1"/>

        <bond id="b23" atomRefs2="a18 a20" order="1"/>

        <bond id="b24" atomRefs2="a20 a21" order="1"/>

        <bond id="b25" atomRefs2="a21 a22" order="1"/>

        <bond id="b26" atomRefs2="a22 a23" order="1"/>

        <bond id="b27" atomRefs2="a23 a24" order="1"/>

        <bond id="b28" atomRefs2="a23 a25" order="1"/>

        <bond id="b29" atomRefs2="a14 a26" order="1"/>

        <bond id="b30" atomRefs2="a6 a27" order="1"/>

        <bond id="b31" atomRefs2="a3 a28" order="1"/>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

The program goes into what seems like an infinite loop, eating up 100% of the CPU, and eventually throws this error:


INFO: java.lang.OutOfMemoryError: GC overhead limit exceeded

        at chemaxon.common.util.IntVector.<init>(IntVector.java:72)

        at chemaxon.common.util.IntVector.<init>(IntVector.java:59)

        at chemaxon.sss.search.SearchHitUtils.transformHit(SearchHitUtils.java:147)

        at chemaxon.sss.search.BaseMolSearchCore.getTransformedSearchHit(BaseMolSearchCore.java:406)

        at chemaxon.sss.search.BaseMolSearchCore.findNextHit(BaseMolSearchCore.java:225)

        at chemaxon.sss.search.pipeline.QueryEnumeratorElement.findNextHit(QueryEnumeratorElement.java:79)

        at chemaxon.sss.search.pipeline.AbstractDelegatorSearchElement.findNextHit(AbstractDelegatorSearchElement.java:56)

        at chemaxon.sss.search.pipeline.AbstractDelegatorSearchElement.findNextHit(AbstractDelegatorSearchElement.java:56)

        at chemaxon.sss.search.pipeline.HitFilterElement.findNextHit(HitFilterElement.java:44)

        at chemaxon.sss.search.pipeline.AbstractDelegatorSearchElement.findNextHit(AbstractDelegatorSearchElement.java:56)

        at chemaxon.sss.search.pipeline.TrivialSearchCaseFilter.findNextHit(TrivialSearchCaseFilter.java:77)

        at chemaxon.sss.search.pipeline.TimeoutHandler.findNextHit(TimeoutHandler.java:34)

        at chemaxon.sss.search.BaseMolSearch$1.call(BaseMolSearch.java:176)

        at chemaxon.sss.search.BaseMolSearch$1.call(BaseMolSearch.java:172)

        at chemaxon.sss.search.SearchUtil.invokeSearchWithExceptionWrapping(SearchUtil.java:528)

        at chemaxon.sss.search.SearchUtil.invokeSearchWithExceptionWrapping(SearchUtil.java:522)

        at chemaxon.sss.search.BaseMolSearch.findNextCoreHit(BaseMolSearch.java:179)

        at chemaxon.sss.search.BaseMolSearch.findNextHit(BaseMolSearch.java:168)

        at chemaxon.sss.search.MolSearch$2.call(MolSearch.java:399)

        at chemaxon.sss.search.MolSearch$2.call(MolSearch.java:394)

        at chemaxon.sss.search.SearchUtil.invokeSearchWithExceptionWrapping(SearchUtil.java:528)

        at chemaxon.sss.search.MolSearch.findNextHit(MolSearch.java:404)

        at chemaxon.sss.search.Search.findNext(Search.java:168)

        at com.epoch.evals.impl.chemEvals.MapProperty.matchMapPattern(MapProperty.java:258)

        at com.epoch.evals.impl.chemEvals.MapProperty.isResponseMatching(MapProperty.java:162)

        at com.epoch.evals.Subevaluator.isResponseMatching(Subevaluator.java:120)

        at com.epoch.evals.Evaluator.matchResponse(Evaluator.java:249)

        at com.epoch.qBank.Question.evaluateResponse(Question.java:1195)

        at com.epoch.session.HWSession.submitResponse(HWSession.java:1124)

        at org.apache.jsp.homework.answerPreview_jsp._jspService(answerPreview_jsp.java:600)

        at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

It seems to me that just one isomorphism should be found, so I don't understand why it's going into an infinite loop. Can you help? The only difference between the two molecules is that one of them has many mapping numbers, and the other has only one (on a different C). My understanding was that map numbers were ignored by MolSearch; has this changed? (When we want to compare exact map numbers, we add a MolComparator, and it is not throwing exceptions.)

ChemAxon 822473489f

03-02-2016 18:01:42

Hi Bob, 


 


I have checked your code. As you set "searchOpts.setOrderSensitiveSearch(true);" there should be 2 hits. By modifying only the debug information, I get the following results on my laptop in less than a second:


looking at isomorphism: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]


looking at isomorphism: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 23, 25, 26, 27]


no more isomorphisms found.


returning: false


 


Which version are you using?


 


Best regards,
Moni 

User 870ab5b546

03-02-2016 19:44:55

Ah! I see what happened. Before we sent it to this method, we explicitized the H atoms and converted them to pseudoatoms. That't what led to all of the matches.


We had a good reason for explicitizing the H atoms and converting them to pseudoatoms. Can't remember what the reason is, now. But maybe I can restrict doing this only to cases where either molecule has mapped H atoms.

ChemAxon 822473489f

04-02-2016 10:16:31

Hi Bob,


 


thanks for your information. Let us know if you encounter any problem.


 


Best regards, 


Moni

ChemAxon 822473489f

04-02-2016 10:16:57

Hi Bob,


 


thanks for your information. Let us know if you encounter any problem.


 


Best regards, 


Moni