more stereochemistry problems

I'm sure I must be missing something obvious here, but I can't figure out what it could be.

I am comparing the sigma-bond networks of two compounds.  I want "exact" stereo searching, that is, a query nonstereo bond matches to a target bond with any stereochemistry.

The code:

        debugPrint("matchSigmaNetwork: response after "

                + "adding H atoms and sigmanormalizing: \n"

                + respMol.toFormat("mrv"));

        debugPrint("matchSigmaNetwork: author structure after "

                + "adding H atoms and sigmanormalizing: \n"

                + authMol.toFormat("mrv"));

        MolSearch search = new MolSearch();

        MolSearchOptions searchOpts = new MolSearchOptions();

        searchOpts.setSearchType(SearchConstants.EXACT);

        searchOpts.setExactBondMatching(false);

        searchOpts.setChargeMatching(SearchConstants.CHARGE_MATCHING_IGNORE);

        searchOpts.setRadicalMatching(SearchConstants.RADICAL_MATCHING_IGNORE);

        searchOpts.setIsotopeMatching(SearchConstants.ISOTOPE_MATCHING_EXACT);

        searchOpts.setValenceMatching(false);

        searchOpts.setStereoSearchType(SearchConstants.STEREO_SPECIFIC);

        searchOpts.setStereoModel(SearchConstants.STEREO_MODEL_GLOBAL);

        search.setSearchOptions(searchOpts);

        search.setTarget(authMol);

        search.setQuery(respMol);

        try {

            debugPrint("MolFunctions.matchSigmaNetwork: without "

                    + "explicit H comparator, match = "

                    + search.isMatching());

            search.addComparator(new ExplicitHMatcher());

            boolean match = search.isMatching();

            debugPrint("MolFunctions.matchSigmaNetwork: returning " + match);

            return match;

The debug output:

matchSigmaNetwork: response after adding H atoms and sigmanormalizing: 

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray>

        <atom id="a1" elementType="O"

              x2="-2.0693750381469727" y2="1.9356172690826714" />

        <atom id="a2" elementType="C"

              x2="-3.315241367164001" y2="1.0304006705706712" />

        <atom id="a3" elementType="C"

              x2="-2.839378949776778" y2="-0.4341467693492209" />

        <atom id="a4" elementType="O"

              x2="-1.2993711265171655" y2="-0.4341467693492209" />

        <atom id="a5" elementType="C"

              x2="-0.8235087091299444" y2="1.0304006705706712" />

        <atom id="a6" elementType="C"

              x2="-3.928323392804061" y2="-1.5230912123765041" />

        <atom id="a7" elementType="O"

              x2="-5.262002514632096" y2="-0.7530912123765036" />

        <atom id="a8" elementType="C"

              x2="0.6640170633552206" y2="0.6318193411127893" />

        <atom id="a9" elementType="C"

              x2="-0.05350870912994421" y2="2.364079792398707" />

        <atom id="a10" elementType="O" formalCharge="1"

              x2="-0.452090038587826" y2="3.8516055648838723" />

        <atom id="a11" elementType="C" formalCharge="-1"

              x2="1.4864912908700558" y2="2.364079792398707" />

        <atom id="a12" elementType="C"

              x2="1.0625983928131038" y2="-0.8557064313723761" />

        <atom id="a13" elementType="H"

              x2="-4.357646249447952" y2="2.16397557387022" />

        <atom id="a14" elementType="H"

              x2="-4.82485617388603" y2="0.7259944693762628" />

        <atom id="a15" elementType="H"

              x2="-2.4720378794394415" y2="-1.9296936720050422" />

        <atom id="a16" elementType="H"

              x2="-3.727313056785182" y2="-3.049916298892172" />

        <atom id="a17" elementType="H"

              x2="2.1367263875382956" y2="1.0820717663858035" />

        <atom id="a18" elementType="H"

              x2="1.893915748828051" y2="1.5586144767669434" />

        <atom id="a19" elementType="H"

              x2="0.6368544044394577" y2="4.940550007911155" />

        <atom id="a20" elementType="H"

              x2="2.630934322105242" y2="1.3336186586060648" />

        <atom id="a21" elementType="H"

              x2="2.2564912908700565" y2="3.697758914226742" />

        <atom id="a22" elementType="H"

              x2="-0.4249273796720612" y2="-1.2542877608302592" />

        <atom id="a23" elementType="H"

              x2="1.4611797222709866" y2="-2.343232203857541" />

        <atom id="a24" elementType="H"

              x2="2.5501241652982687" y2="-0.4571251019144933" />

      </atomArray>

      <bondArray>

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

        <bond atomRefs2="a1 a5" order="1" />

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

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

        <bond atomRefs2="a3 a6" order="1">

          <bondStereo>W</bondStereo>

        </bond>

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

        <bond atomRefs2="a5 a9" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond atomRefs2="a5 a8" order="1">

          <bondStereo>H</bondStereo>

        </bond>

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

        <bond atomRefs2="a12 a8" order="1" />

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

        <bond atomRefs2="a9 a11" order="1" />

        <bond atomRefs2="a2 a13" order="1" />

        <bond atomRefs2="a2 a14" order="1" />

        <bond atomRefs2="a3 a15" order="1">

          <bondStereo>H</bondStereo>

        </bond>

        <bond atomRefs2="a6 a16" order="1" />

        <bond atomRefs2="a8 a17" order="1" />

        <bond atomRefs2="a8 a18" order="1" />

        <bond atomRefs2="a10 a19" order="1" />

        <bond atomRefs2="a11 a20" order="1" />

        <bond atomRefs2="a11 a21" order="1" />

        <bond atomRefs2="a12 a22" order="1" />

        <bond atomRefs2="a12 a23" order="1" />

        <bond atomRefs2="a12 a24" order="1" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>



matchSigmaNetwork: author structure after adding H atoms and sigmanormalizing: 

<?xml version="1.0" ?>

<cml>

<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"

          elementType="O C C O C C O C C O C C H H H H H H H H H H H H"

          x2="-2.0693750381469727 -3.315241367164001 -2.839378949776778 -1.2993711265171655 -0.8235087091299444 -3.928323392804061 -5.262002514632096 0.6640170633552206 -0.05350870912994421 -0.452090038587826 1.4864912908700558 1.0625983928131038 -4.357646249447952 -4.82485617388603 -2.4720378794394415 -3.727313056785182 2.1367263875382956 1.893915748828051 0.6368544044394577 2.630934322105242 2.2564912908700565 -0.4249273796720612 1.4611797222709866 2.5501241652982687"

          y2="1.9356172690826714 1.0304006705706712 -0.4341467693492209 -0.4341467693492209 1.0304006705706712 -1.5230912123765041 -0.7530912123765036 0.6318193411127893 2.364079792398707 3.8516055648838723 2.364079792398707 -0.8557064313723761 2.16397557387022 0.7259944693762628 -1.9296936720050422 -3.049916298892172 1.0820717663858035 1.5586144767669434 4.940550007911155 1.3336186586060648 3.697758914226742 -1.2542877608302592 -2.343232203857541 -0.4571251019144933"

          />

      <bondArray>

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

        <bond atomRefs2="a1 a5" order="1" />

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

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

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

        <bond atomRefs2="a3 a6" order="1" />

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

        <bond atomRefs2="a5 a9" order="1" />

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

        <bond atomRefs2="a9 a11" order="1" />

        <bond atomRefs2="a5 a8" order="1" />

        <bond atomRefs2="a12 a8" order="1" />

        <bond atomRefs2="a2 a13" order="1" />

        <bond atomRefs2="a2 a14" order="1" />

        <bond atomRefs2="a3 a15" order="1" />

        <bond atomRefs2="a6 a16" order="1" />

        <bond atomRefs2="a8 a17" order="1" />

        <bond atomRefs2="a8 a18" order="1" />

        <bond atomRefs2="a10 a19" order="1" />

        <bond atomRefs2="a11 a20" order="1" />

        <bond atomRefs2="a11 a21" order="1" />

        <bond atomRefs2="a12 a22" order="1" />

        <bond atomRefs2="a12 a23" order="1" />

        <bond atomRefs2="a12 a24" order="1" />

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>



MolFunctions.matchSigmaNetwork: without explicit H comparator, match = false

MolFunctions.matchSigmaNetwork: returning false

The method ought to return true, but it doesn't.  Why not?

The code above is for JChem 5.1.5, but I see similar behavior in JChem 3.2.13.  (In the JChem 3.2.13, rather than setting charge and radical matching to IGNORE, we set the charge of every atom to 0 and turn off every radical flag.  But we still set search type to EXACT, stereosearch to true, and exact bond matching to false.)  

Hello Bob,

First I would like to clarify one thing: Exact stereo is the stereo option which requires all stereo information to match. e.g. not only stereo specific query's hits must be stereo specific, but a query atom without stereo information can only match stereo aspecific targets.

You wanted non-stereo match on stereo but (I assume) stereo query to match only on stereo target. This corresponds to the stereo specific option. (http://www.chemaxon.com/jchem/doc/user/query_stereochemistry.html) In fact your code is right because you set this stereo option.

Now about the non-matching:

From your degubbing output I could see that your query (respMol) is stereo specific and your target (authmol) is without stereo information. Stereo specific search type means that there is no hit in such a case. If you try changing the query and the target structures, then there is a hit (in exact stereo not - as noted earlier).

Hope this helps.

Bye,

Robert

I knew it was something obvious....

OK, here's a real one.  I got this in a log:

Cpd 1, C\C=C1/CC\C(CC1)=C/C, precisely matches cpd 3, C\C=C1/CC\C(CC1)=C\C

The code for precise matching is:

        MolSearch search = new MolSearch();

        MolSearchOptions searchOpts = new MolSearchOptions();

        searchOpts.setSearchType(SearchConstants.PERFECT);

        searchOpts.setVagueBondLevel(SearchConstants.VAGUE_BOND_OFF);

        searchOpts.setStereoModel(SearchConstants.STEREO_MODEL_GLOBAL);

                // required for comparing nonaromatized aromatic rings

        search.setSearchOptions(searchOpts);

        search.setTarget(respMol);

        search.setQuery(authMol);

And when will Marvin be able to recognize that allenes are chiral?

Hello Bob,

Indeed marvin can not specify the CIS/TRANS stereo info for such structures. We will consider the implementation of their recognition and see when we can schedule it.

Regards,

Robert