axial stereochemistry and local/global models

In your documentation, you say,

Global stereo model is credited exclusively during Axial stereo search tasks.

But consider the following four searches comparing the same query and target.  All are FULL searches in STEREO_SPECIFIC mode.  Searches 1 and 2 ignore axial stereochemistry, whereas searches 3 and 4 consider it; and searches 1 and 3 use the local stereochemistry model, whereas searches 2 and 4 use the global stereochemistry model.  The stereochemistry model appears to have no effect on the search results: true in the first two cases, and false in the second two.  So what does your statement mean?

Sep 21, 2011 3:42:40 PM org.apache.catalina.core.StandardWrapperValve invoke

INFO: JChemCompare.jsp: searchType = 4

JChemCompare.jsp: setStereoSearch = 0

JChemCompare.jsp: considerDoubleBondStereoMatching = true

JChemCompare.jsp: considerOddCumuleneStereoMatching = true

JChemCompare.jsp: considerAxialStereoMatching = false

JChemCompare.jsp: considerSynAntiStereoMatching = true

JChemCompare.jsp: stereoMatchingModel = 0

JChemCompare.jsp: chargeType = 1

JChemCompare.jsp: radicalType = 1

JChemCompare.jsp: isotopeType = 1

JChemCompare.jsp: valenceType = true

JChemCompare.jsp: bondVagueness = 0

JChemCompare.jsp: orderSensitive = false

JChemCompare.jsp: listAllMatches = false

JChemCompare.jsp: target = C(=[C@@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: query = C(=[C@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: searchResult = true



Sep 21, 2011 3:42:44 PM org.apache.catalina.core.StandardWrapperValve invoke

INFO: JChemCompare.jsp: searchType = 4

JChemCompare.jsp: setStereoSearch = 0

JChemCompare.jsp: considerDoubleBondStereoMatching = true

JChemCompare.jsp: considerOddCumuleneStereoMatching = true

JChemCompare.jsp: considerAxialStereoMatching = false

JChemCompare.jsp: considerSynAntiStereoMatching = true

JChemCompare.jsp: stereoMatchingModel = 2

JChemCompare.jsp: chargeType = 1

JChemCompare.jsp: radicalType = 1

JChemCompare.jsp: isotopeType = 1

JChemCompare.jsp: valenceType = true

JChemCompare.jsp: bondVagueness = 0

JChemCompare.jsp: orderSensitive = false

JChemCompare.jsp: listAllMatches = false

JChemCompare.jsp: target = C(=[C@@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: query = C(=[C@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: searchResult = true



Sep 21, 2011 3:43:21 PM org.apache.catalina.core.StandardWrapperValve invoke

INFO: JChemCompare.jsp: searchType = 4

JChemCompare.jsp: setStereoSearch = 0

JChemCompare.jsp: considerDoubleBondStereoMatching = true

JChemCompare.jsp: considerOddCumuleneStereoMatching = true

JChemCompare.jsp: considerAxialStereoMatching = true

JChemCompare.jsp: considerSynAntiStereoMatching = true

JChemCompare.jsp: stereoMatchingModel = 0

JChemCompare.jsp: chargeType = 1

JChemCompare.jsp: radicalType = 1

JChemCompare.jsp: isotopeType = 1

JChemCompare.jsp: valenceType = true

JChemCompare.jsp: bondVagueness = 0

JChemCompare.jsp: orderSensitive = false

JChemCompare.jsp: listAllMatches = false

JChemCompare.jsp: target = C(=[C@@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: query = C(=[C@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: searchResult = false



Sep 21, 2011 3:43:25 PM org.apache.catalina.core.StandardWrapperValve invoke

INFO: JChemCompare.jsp: searchType = 4

JChemCompare.jsp: setStereoSearch = 0

JChemCompare.jsp: considerDoubleBondStereoMatching = true

JChemCompare.jsp: considerOddCumuleneStereoMatching = true

JChemCompare.jsp: considerAxialStereoMatching = true

JChemCompare.jsp: considerSynAntiStereoMatching = true

JChemCompare.jsp: stereoMatchingModel = 2

JChemCompare.jsp: chargeType = 1

JChemCompare.jsp: radicalType = 1

JChemCompare.jsp: isotopeType = 1

JChemCompare.jsp: valenceType = true

JChemCompare.jsp: bondVagueness = 0

JChemCompare.jsp: orderSensitive = false

JChemCompare.jsp: listAllMatches = false

JChemCompare.jsp: target = C(=[C@@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: query = C(=[C@]=CC1=CC=CC=C1)C1=CC=CC=C1 |r,c:5,7,12,14,t:3,10|

JChemCompare.jsp: searchResult = false

Here is the MRV of the target.  The query is the same, except for a wedged bond instead of a hashed one.

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray>

        <atom id="a1" elementType="C"

              x2="-2.406250000000000" y2="0.8662499785423279" />

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

              x2="-0.866250000000000" y2="0.8662499785423279" />

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

              x2="0.6737500000000001" y2="0.8662499785423279" />

        <atom id="a4" elementType="R" sgroupRef="sg1"

              x2="-3.495194443027283" y2="-0.22269446448495533" />

        <atom id="a5" elementType="R" sgroupRef="sg2"

              x2="2.007429121828036" y2="0.09624997854232797" />

      </atomArray>

      <bondArray>

        <bond atomRefs2="a1 a2" order="2" />

        <bond atomRefs2="a2 a3" order="2" />

        <bond atomRefs2="a1 a4" order="1" />

        <bond atomRefs2="a3 a5" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

      <molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2">

        <atomArray

            atomID="a6 a7 a8 a9 a10 a11"

            elementType="C C C C C C"

            attachmentPoint="1 0 0 0 0 0"

            sgroupAttachmentPoint="1 0 0 0 0 0"

            x2="-2.8188916800499815 -1.485212558221944 -1.4852125582219466 -2.8188916800499833 -4.152570801878018 -4.152570801878017"

            y2="4.619999961853029 3.849999961853025 2.309999961853025 1.5399999618530273 2.3099999618530296 3.8499999618530296"

            />

        <bondArray>

          <bond atomRefs2="a6 a7" order="2" />

          <bond atomRefs2="a6 a11" order="1" />

          <bond atomRefs2="a7 a8" order="1" />

          <bond atomRefs2="a8 a9" order="2" />

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

          <bond atomRefs2="a10 a11" order="2" />

        </bondArray>

      </molecule>

      <molecule id="sg2" role="SuperatomSgroup" title="Ph" molID="m3">

        <atomArray

            atomID="a12 a13 a14 a15 a16 a17"

            elementType="C C C C C C"

            attachmentPoint="1 0 0 0 0 0"

            sgroupAttachmentPoint="1 0 0 0 0 0"

            x2="4.3036082627295595 5.637287384557597 5.637287384557595 4.303608262729558 2.969929140901523 2.969929140901524"

            y2="4.908750014305117 4.138750014305113 2.5987500143051125 1.8287500143051147 2.598750014305117 4.138750014305117"

            />

        <bondArray>

          <bond atomRefs2="a12 a13" order="2" />

          <bond atomRefs2="a12 a17" order="1" />

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

          <bond atomRefs2="a14 a15" order="2" />

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

          <bond atomRefs2="a16 a17" order="2" />

        </bondArray>

      </molecule>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

Hi Bob,

The sentence will say that axial, allene stereochemistry is always calculated according to global stereo model regardless of the model set. 

The attached query (...Q) will always match match the target (...T) in substructure search as there isn't yet an axial stereo chemistry calculation according to local model. 

Bye,

Robert

Ah, I see.  I suggest you change the wording of your documentation to,

The global stereo model is used exclusively during Axial stereo search tasks, even if a different model has been selected for the search. 

Hi,

Thanks Bob for the suggestion!

I'm forwarding it to the responsible person.

Bye,

Robi

The global stereo model is used exclusively during Axial stereo search tasks, even if a different model has been selected for the search. 

Hi Bob,

We've modified the documentation according to your suggestion. It will be readable on our website simultaneously with the next release of JChem.

Best regards,

Krisztina