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

really subtle mismatching

User 870ab5b546

18-06-2014 21:10:57

Using JChem 6.2.1. This structure:


<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<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" elementType="C C C C C C C C C C C C C C O O O C C C H C H" x2="-6.591760000000001 -7.9253066666666685 -9.259040000000002 -9.259040000000002 -7.9253066666666685 -6.591760000000001 -3.924293333333334 -3.924293333333334 -2.5905600000000004 -2.5905600000000004 -1.2568266666666668 -1.2568266666666668 -5.530186666666667 -7.221946666666668 -8.761946666666669 -6.823413333333335 -4.760186666666668 -5.549600000000001 -4.966453333333334 -5.131653333333333 -4.361653333333334 -6.133120000000001 -7.620666666666667" y2="1.9950933333333336 2.7650933333333336 1.9950933333333336 0.45509333333333335 -0.31490666666666667 0.45509333333333335 1.9950933333333336 0.45509333333333335 2.7650933333333336 -0.3150933333333334 0.45490666666666674 1.9950933333333336 5.681760000000001 4.122346666666667 4.122346666666667 5.609893333333334 7.0153066666666675 -0.14 2.648426666666667 4.194213333333334 5.527946666666667 3.0333333333333337 3.431866666666667"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="2"/>

        <bond id="b2" atomRefs2="a1 a6" order="1"/>

        <bond id="b3" atomRefs2="a1 a19" order="1"/>

        <bond id="b4" atomRefs2="a2 a3" order="1"/>

        <bond id="b5" atomRefs2="a3 a4" order="2"/>

        <bond id="b6" atomRefs2="a4 a5" order="1"/>

        <bond id="b7" atomRefs2="a5 a6" order="2"/>

        <bond id="b8" atomRefs2="a18 a6" order="1"/>

        <bond id="b9" atomRefs2="a18 a8" order="1"/>

        <bond id="b10" atomRefs2="a7 a19" order="1"/>

        <bond id="b11" atomRefs2="a9 a7" order="2"/>

        <bond id="b12" atomRefs2="a8 a7" order="1"/>

        <bond id="b13" atomRefs2="a8 a10" order="2"/>

        <bond id="b14" atomRefs2="a9 a12" order="1"/>

        <bond id="b15" atomRefs2="a10 a11" order="1"/>

        <bond id="b16" atomRefs2="a11 a12" order="2"/>

        <bond id="b17" atomRefs2="a18 a22" order="1"/>

        <bond id="b18" atomRefs2="a19 a20" order="1"/>

        <bond id="b19" atomRefs2="a22 a20" order="1"/>

        <bond id="b20" atomRefs2="a20 a13" order="1"/>

        <bond id="b21" atomRefs2="a22 a14" order="1"/>

        <bond id="b22" atomRefs2="a14 a16" order="1"/>

        <bond id="b23" atomRefs2="a16 a13" order="1"/>

        <bond id="b24" atomRefs2="a13 a17" order="2"/>

        <bond id="b25" atomRefs2="a14 a15" order="2"/>

        <bond id="b26" atomRefs2="a20 a21" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a22 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

matches to this one:


<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<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" elementType="C C C C C C C C C C C C C C C C C C O O O H H" x2="-5.438125133514404 -6.771794474562663 -6.771794474562663 -5.438125133514404 -4.104455792466146 -4.104455792466146 -2.7707864514178873 -2.7707864514178873 -1.437117110369629 -1.437117110369629 -0.10344776932137068 -0.10344776932137068 1.2302215717268876 1.2302215717268876 0.2512422213989596 -0.22084944744652413 -1.7816474512263558 -2.1185218170329367 -0.6539743771130421 -3.452200938860972 1.5849213432269953 1.3191505823557983 -3.69282560507496" y2="2.502533857276223 1.7325169167171826 0.19248303559910152 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 -3.3687500953674308 -1.2566337878080764 -1.876871350630629 -4.138754006997239 -4.61461642438446 -4.908754006997239 -4.13875009536743 -1.497258632836 -2.3099961122120494"/>

      <bondArray>

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

        <bond id="b2" atomRefs2="a1 a6" order="2"/>

        <bond id="b3" atomRefs2="a2 a3" order="2"/>

        <bond id="b4" atomRefs2="a3 a4" order="1"/>

        <bond id="b5" atomRefs2="a4 a5" order="2"/>

        <bond id="b6" atomRefs2="a5 a6" order="1"/>

        <bond id="b7" atomRefs2="a8 a9" order="1"/>

        <bond id="b8" atomRefs2="a9 a10" order="1"/>

        <bond id="b9" atomRefs2="a7 a10" order="1"/>

        <bond id="b10" atomRefs2="a5 a8" order="1"/>

        <bond id="b11" atomRefs2="a7 a6" order="1"/>

        <bond id="b12" atomRefs2="a12 a13" order="1"/>

        <bond id="b13" atomRefs2="a13 a14" order="2"/>

        <bond id="b14" atomRefs2="a11 a14" order="1"/>

        <bond id="b15" atomRefs2="a9 a12" order="2"/>

        <bond id="b16" atomRefs2="a11 a10" order="2"/>

        <bond id="b17" atomRefs2="a15 a16" order="1"/>

        <bond id="b18" atomRefs2="a15 a19" order="1"/>

        <bond id="b19" atomRefs2="a16 a17" order="1"/>

        <bond id="b20" atomRefs2="a17 a18" order="1"/>

        <bond id="b21" atomRefs2="a18 a19" order="1"/>

        <bond id="b22" atomRefs2="a8 a17" order="1"/>

        <bond id="b23" atomRefs2="a7 a16" order="1"/>

        <bond id="b24" atomRefs2="a18 a20" order="2"/>

        <bond id="b25" atomRefs2="a15 a21" order="2"/>

        <bond id="b26" atomRefs2="a16 a22" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a17 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

but not to this one:


<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<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" elementType="C C C C C C C C C C C C C C C C C C O O O H H" x2="-5.438125133514404 -6.771794474562663 -6.771794474562663 -5.438125133514404 -4.104455792466146 -4.104455792466146 -2.7707864514178873 -2.7707864514178873 -1.437117110369629 -1.437117110369629 -0.10344776932137068 -0.10344776932137068 1.2302215717268876 1.2302215717268876 0.2512422213989596 -0.6058493485028137 -2.1185218170329354 -2.1185218170329367 -0.6539743771130421 -3.452200938860972 1.5849213432269953 0.9341506514971863 -3.4522009388609707" y2="2.502533857276223 1.7325169167171826 0.19248303559910152 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 -3.3687500953674308 -1.9303836519094864 -2.5987461837376236 -4.138754006997239 -4.61461642438446 -4.908754006997239 -4.13875009536743 -1.9303836519094864 -1.828746183737623"/>

      <bondArray>

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

        <bond id="b2" atomRefs2="a1 a6" order="2"/>

        <bond id="b3" atomRefs2="a2 a3" order="2"/>

        <bond id="b4" atomRefs2="a3 a4" order="1"/>

        <bond id="b5" atomRefs2="a4 a5" order="2"/>

        <bond id="b6" atomRefs2="a5 a6" order="1"/>

        <bond id="b7" atomRefs2="a8 a9" order="1"/>

        <bond id="b8" atomRefs2="a9 a10" order="1"/>

        <bond id="b9" atomRefs2="a7 a10" order="1"/>

        <bond id="b10" atomRefs2="a5 a8" order="1"/>

        <bond id="b11" atomRefs2="a7 a6" order="1"/>

        <bond id="b12" atomRefs2="a12 a13" order="1"/>

        <bond id="b13" atomRefs2="a13 a14" order="2"/>

        <bond id="b14" atomRefs2="a11 a14" order="1"/>

        <bond id="b15" atomRefs2="a9 a12" order="2"/>

        <bond id="b16" atomRefs2="a11 a10" order="2"/>

        <bond id="b17" atomRefs2="a15 a16" order="1"/>

        <bond id="b18" atomRefs2="a15 a19" order="1"/>

        <bond id="b19" atomRefs2="a16 a17" order="1"/>

        <bond id="b20" atomRefs2="a17 a18" order="1"/>

        <bond id="b21" atomRefs2="a18 a19" order="1"/>

        <bond id="b22" atomRefs2="a8 a17" order="1"/>

        <bond id="b23" atomRefs2="a7 a16" order="1"/>

        <bond id="b24" atomRefs2="a18 a20" order="2"/>

        <bond id="b25" atomRefs2="a15 a21" order="2"/>

        <bond id="b26" atomRefs2="a16 a22" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a17 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

the only difference being a slight movement of a few atoms. Why?


I am doing a full match with specific matching of tetrahedral stereochemistry, considering axial stereochemistry and odd-numbered cumulenes but not sun/anti, local stereo matching model. Not sure whether any of these parameters makes a difference, but it shouldn't. 

ChemAxon d4fff15f08

19-06-2014 08:17:05

Hi Bob,


 


Good question!


We tried to reproduce the described behaviour, but we could not. In our environment both of them were hits with the mentioned options. We think, that both should be hit, no matter that little movement in the atom position.


Could you give us some more information like:


 - what JChem version are you using


 - how do you initiate the search (command line? API - maybe a code fragment cold help us, etc)


 - could you give us all the search options you are using 


 - in what type of table are your structures stored (any, molecules, etc)?


 


 Thanks in advance,


 Norbert

User 870ab5b546

19-06-2014 13:17:19

Hi, if you go to this page, you can reproduce the behavior. I'm attaching the page's code so you can see what options the user can set and what we leave as default. We're using JChem 6.2.1. I'm also attaching two screen shots that show the results of the two comparisons. The MRV for the target that matches the query is reproduced below (again). Just move the C-H bond on the right a little to the left, and the target fails to match the query. 


<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<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" elementType="C C C C C C C C C C C C C C C C C C O O O H H" x2="1.8545145889278798 0.5208452478796222 0.5208452478796222 1.8545145889278798 3.1881839299761383 3.1881839299761383 4.521853271024397 4.521853271024397 5.855522612072655 5.855522612072655 7.189191953120913 7.189191953120913 8.522861294169171 8.522861294169171 7.543881943841244 6.865756091493562 5.510992271215928 5.174117905409347 6.638665345329242 3.8404387835813125 8.87756106566928 8.405756121295886 3.599814117367324" y2="5.8888549375539 5.118837996994859 3.5788041158767783 2.8087871753177374 3.5788041158767783 5.118837996994859 5.8888549375539 2.8087871753177374 3.5788041158767783 5.118837996994859 5.8888549375539 2.8087871753177374 3.5788041158767783 5.118837996994859 0.01757098491024589 2.2121007274519 1.5094497296470477 -0.7524329267195622 -1.2282953441067832 -1.5224329267195627 -0.7524290150897537 1.9714758824239764 1.0763249680656273"/>

      <bondArray>

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

        <bond id="b2" atomRefs2="a1 a6" order="2"/>

        <bond id="b3" atomRefs2="a2 a3" order="2"/>

        <bond id="b4" atomRefs2="a3 a4" order="1"/>

        <bond id="b5" atomRefs2="a4 a5" order="2"/>

        <bond id="b6" atomRefs2="a5 a6" order="1"/>

        <bond id="b7" atomRefs2="a8 a9" order="1"/>

        <bond id="b8" atomRefs2="a9 a10" order="1"/>

        <bond id="b9" atomRefs2="a7 a10" order="1"/>

        <bond id="b10" atomRefs2="a5 a8" order="1"/>

        <bond id="b11" atomRefs2="a7 a6" order="1"/>

        <bond id="b12" atomRefs2="a12 a13" order="1"/>

        <bond id="b13" atomRefs2="a13 a14" order="2"/>

        <bond id="b14" atomRefs2="a11 a14" order="1"/>

        <bond id="b15" atomRefs2="a9 a12" order="2"/>

        <bond id="b16" atomRefs2="a11 a10" order="2"/>

        <bond id="b17" atomRefs2="a15 a16" order="1"/>

        <bond id="b18" atomRefs2="a15 a19" order="1"/>

        <bond id="b19" atomRefs2="a16 a17" order="1"/>

        <bond id="b20" atomRefs2="a17 a18" order="1"/>

        <bond id="b21" atomRefs2="a18 a19" order="1"/>

        <bond id="b22" atomRefs2="a8 a17" order="1"/>

        <bond id="b23" atomRefs2="a7 a16" order="1"/>

        <bond id="b24" atomRefs2="a18 a20" order="2"/>

        <bond id="b25" atomRefs2="a15 a21" order="2"/>

        <bond id="b26" atomRefs2="a16 a22" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a17 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

Here's the query again:


<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<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" elementType="C C C C C C C C C C C C C C O O O C C C H C H" x2="-10.551760514984132 -11.885307181650798 -13.219040514984133 -13.219040514984133 -11.885307181650798 -10.551760514984132 -7.884293848317465 -7.884293848317465 -6.550560514984131 -6.550560514984131 -5.216827181650798 -5.216827181650798 -9.490187181650798 -11.181947181650798 -12.7219471816508 -10.783413848317466 -8.720187181650799 -9.509600514984133 -8.926453848317465 -9.091653848317463 -8.321653848317464 -10.093120514984133 -11.580667181650798" y2="1.8300933714803063 2.6000933714803063 1.8300933714803063 0.290093371480306 -0.479906628519694 0.290093371480306 1.8300933714803063 0.290093371480306 2.6000933714803063 -0.48009329518636074 0.28990670481363945 1.8300933714803063 5.516760038146973 3.9573467048136397 3.9573467048136397 5.4448933714803065 6.85030670481364 -0.30499996185302736 2.4834267048136396 4.0292133714803064 5.362946704813639 2.8683333714803063 3.2668667048136397"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="2"/>

        <bond id="b2" atomRefs2="a1 a6" order="1"/>

        <bond id="b3" atomRefs2="a1 a19" order="1"/>

        <bond id="b4" atomRefs2="a2 a3" order="1"/>

        <bond id="b5" atomRefs2="a3 a4" order="2"/>

        <bond id="b6" atomRefs2="a4 a5" order="1"/>

        <bond id="b7" atomRefs2="a5 a6" order="2"/>

        <bond id="b8" atomRefs2="a18 a6" order="1"/>

        <bond id="b9" atomRefs2="a18 a8" order="1"/>

        <bond id="b10" atomRefs2="a7 a19" order="1"/>

        <bond id="b11" atomRefs2="a9 a7" order="2"/>

        <bond id="b12" atomRefs2="a8 a7" order="1"/>

        <bond id="b13" atomRefs2="a8 a10" order="2"/>

        <bond id="b14" atomRefs2="a9 a12" order="1"/>

        <bond id="b15" atomRefs2="a10 a11" order="1"/>

        <bond id="b16" atomRefs2="a11 a12" order="2"/>

        <bond id="b17" atomRefs2="a18 a22" order="1"/>

        <bond id="b18" atomRefs2="a19 a20" order="1"/>

        <bond id="b19" atomRefs2="a22 a20" order="1"/>

        <bond id="b20" atomRefs2="a20 a13" order="1"/>

        <bond id="b21" atomRefs2="a22 a14" order="1"/>

        <bond id="b22" atomRefs2="a14 a16" order="1"/>

        <bond id="b23" atomRefs2="a16 a13" order="1"/>

        <bond id="b24" atomRefs2="a13 a17" order="2"/>

        <bond id="b25" atomRefs2="a14 a15" order="2"/>

        <bond id="b26" atomRefs2="a20 a21" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a22 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

ChemAxon abe887c64e

23-06-2014 14:38:52

Hi Bob,


We could reproduce the strange hit/non-hit cases even in our environment. Unfortunately, It seems there is bug in our code around the identification of the allene stereo configuration. Now we register this issue, and will plan when to fix it.


Thank you for drawing our attention to this problem.


Best regards,


Krisztina

User 870ab5b546

23-06-2014 15:56:24

You said the bug has to do with identification of the allene stereo configuration, but I don't see an allene in my example. Is there any search flag I can turn off that will cause the bug not to manifest itself?

ChemAxon abe887c64e

24-06-2014 09:48:14

Yes, you are right, these structures do not contain allene groups, however, switching off/on the ignoreAlleneStereo (named as 'consider stereochemistry of odd-numbered cumulenes' in your JChemCompare.jsp) and ignoreSynAntiStereo ('consider syn/anti stereochemistry') search options changes the search result non-hit/hit.


Krisztina


 

User 870ab5b546

01-07-2014 00:26:47

Here's an even simpler example of a compound that fails to match to itself when axial stereochemistry is considered:


<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9" elementType="C C C C C C C C O" x2="-2.7431249618530273 -4.076794302901286 -4.076794302901286 -2.7431249618530273 -1.409455620804769 -1.409455620804769 -5.4104783150385165 -6.744157436866551 -0.07577649897673333" y2="2.406283859660409 1.6362669191013683 0.0962330379832873 -0.6737839025757533 0.0962330379832873 1.6362669191013683 -0.6737584916906038 0.09624150830939682 2.4062669191013684"/>

      <bondArray>

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

        <bond id="b2" atomRefs2="a1 a6" order="1"/>

        <bond id="b3" atomRefs2="a2 a3" order="1"/>

        <bond id="b4" atomRefs2="a3 a4" order="1"/>

        <bond id="b5" atomRefs2="a4 a5" order="1"/>

        <bond id="b6" atomRefs2="a5 a6" order="1"/>

        <bond id="b7" atomRefs2="a3 a7" order="2"/>

        <bond id="b8" atomRefs2="a7 a8" order="1"/>

        <bond id="b9" atomRefs2="a6 a9" order="1"/>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

ChemAxon abe887c64e

01-07-2014 06:55:03

The missing hit with ignoreAxialStereo:n option is reproducible. We will investigate this issue as well. Thank you for the notification.

User 870ab5b546

29-07-2014 13:26:51

Hi, any progress on this bug's fix?

ChemAxon abe887c64e

29-07-2014 13:42:43

Hi Bob,


We have fixed this bug, and the latest JChem version (14.7.28), released today, contains the fix.


Best regards,


Krisztina

User 870ab5b546

30-07-2014 18:36:19

I'm not finding that this bug has been fixed. This target:


<?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/help/formats/schema/mrvSchema_14_7_14.xsd" version="ChemAxon file format v14.7.14, generated by v14.7.14.0">

<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" elementType="C C C C C C C C C C C C C C C C C C O O O H H" x2="-5.438125133514404 -6.771794474562663 -6.771794474562663 -5.438125133514404 -4.104455792466146 -4.104455792466146 -2.7707864514178873 -2.7707864514178873 -1.437117110369629 -1.437117110369629 -0.10344776932137068 -0.10344776932137068 1.2302215717268876 1.2302215717268876 0.2512422213989596 -0.6058493485028137 -2.1185218170329354 -2.1185218170329367 -0.6539743771130421 -3.452200938860972 1.5849213432269953 0.9341506514971863 -3.4522009388609707" y2="2.502533857276223 1.7325169167171826 0.19248303559910152 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 -3.3687500953674308 -1.9303836519094864 -2.5987461837376236 -4.138754006997239 -4.61461642438446 -4.908754006997239 -4.13875009536743 -1.9303836519094864 -1.828746183737623"/>

      <bondArray>

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

        <bond id="b2" atomRefs2="a1 a6" order="2"/>

        <bond id="b3" atomRefs2="a2 a3" order="2"/>

        <bond id="b4" atomRefs2="a3 a4" order="1"/>

        <bond id="b5" atomRefs2="a4 a5" order="2"/>

        <bond id="b6" atomRefs2="a5 a6" order="1"/>

        <bond id="b7" atomRefs2="a8 a9" order="1"/>

        <bond id="b8" atomRefs2="a9 a10" order="1"/>

        <bond id="b9" atomRefs2="a7 a10" order="1"/>

        <bond id="b10" atomRefs2="a5 a8" order="1"/>

        <bond id="b11" atomRefs2="a7 a6" order="1"/>

        <bond id="b12" atomRefs2="a12 a13" order="1"/>

        <bond id="b13" atomRefs2="a13 a14" order="2"/>

        <bond id="b14" atomRefs2="a11 a14" order="1"/>

        <bond id="b15" atomRefs2="a9 a12" order="2"/>

        <bond id="b16" atomRefs2="a11 a10" order="2"/>

        <bond id="b17" atomRefs2="a15 a16" order="1"/>

        <bond id="b18" atomRefs2="a15 a19" order="1"/>

        <bond id="b19" atomRefs2="a16 a17" order="1"/>

        <bond id="b20" atomRefs2="a17 a18" order="1"/>

        <bond id="b21" atomRefs2="a18 a19" order="1"/>

        <bond id="b22" atomRefs2="a8 a17" order="1"/>

        <bond id="b23" atomRefs2="a7 a16" order="1"/>

        <bond id="b24" atomRefs2="a18 a20" order="2"/>

        <bond id="b25" atomRefs2="a15 a21" order="2"/>

        <bond id="b26" atomRefs2="a16 a22" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a17 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

should match to this query, but does not:


<?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/help/formats/schema/mrvSchema_14_7_14.xsd" version="ChemAxon file format v14.7.14, generated by v14.7.14.0">

<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" elementType="C C C C C C C C C C C C C C O O O C C C H C H" x2="-6.591760000000001 -7.9253066666666685 -9.259040000000002 -9.259040000000002 -7.9253066666666685 -6.591760000000001 -3.924293333333334 -3.924293333333334 -2.5905600000000004 -2.5905600000000004 -1.2568266666666668 -1.2568266666666668 -5.530186666666667 -7.221946666666668 -8.761946666666669 -6.823413333333335 -4.760186666666668 -5.549600000000001 -4.966453333333334 -5.131653333333333 -4.361653333333334 -6.133120000000001 -7.620666666666667" y2="1.9950933333333336 2.7650933333333336 1.9950933333333336 0.45509333333333335 -0.31490666666666667 0.45509333333333335 1.9950933333333336 0.45509333333333335 2.7650933333333336 -0.3150933333333334 0.45490666666666674 1.9950933333333336 5.681760000000001 4.122346666666667 4.122346666666667 5.609893333333334 7.0153066666666675 -0.14 2.648426666666667 4.194213333333334 5.527946666666667 3.0333333333333337 3.431866666666667"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="2"/>

        <bond id="b2" atomRefs2="a1 a6" order="1"/>

        <bond id="b3" atomRefs2="a1 a19" order="1"/>

        <bond id="b4" atomRefs2="a2 a3" order="1"/>

        <bond id="b5" atomRefs2="a3 a4" order="2"/>

        <bond id="b6" atomRefs2="a4 a5" order="1"/>

        <bond id="b7" atomRefs2="a5 a6" order="2"/>

        <bond id="b8" atomRefs2="a18 a6" order="1"/>

        <bond id="b9" atomRefs2="a18 a8" order="1"/>

        <bond id="b10" atomRefs2="a7 a19" order="1"/>

        <bond id="b11" atomRefs2="a9 a7" order="2"/>

        <bond id="b12" atomRefs2="a8 a7" order="1"/>

        <bond id="b13" atomRefs2="a8 a10" order="2"/>

        <bond id="b14" atomRefs2="a9 a12" order="1"/>

        <bond id="b15" atomRefs2="a10 a11" order="1"/>

        <bond id="b16" atomRefs2="a11 a12" order="2"/>

        <bond id="b17" atomRefs2="a18 a22" order="1"/>

        <bond id="b18" atomRefs2="a19 a20" order="1"/>

        <bond id="b19" atomRefs2="a22 a20" order="1"/>

        <bond id="b20" atomRefs2="a20 a13" order="1"/>

        <bond id="b21" atomRefs2="a22 a14" order="1"/>

        <bond id="b22" atomRefs2="a14 a16" order="1"/>

        <bond id="b23" atomRefs2="a16 a13" order="1"/>

        <bond id="b24" atomRefs2="a13 a17" order="2"/>

        <bond id="b25" atomRefs2="a14 a15" order="2"/>

        <bond id="b26" atomRefs2="a20 a21" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a22 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

This is true even when I turn off syn/anti and axial matching. However, they do match when I turn off odd-cumulene matching. So it appears that there is a bug in odd-cumulene matching that causes them not to match.

ChemAxon abe887c64e

31-07-2014 07:34:45

Hi Bob,


Sorry, there were two issues reported in this forum topic, and the second one - relating to ignoreAxialStereo option with the structure below - was fixed:




<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9" elementType="C C C C C C C C O" x2="-2.7431249618530273 -4.076794302901286 -4.076794302901286 -2.7431249618530273 -1.409455620804769 -1.409455620804769 -5.4104783150385165 -6.744157436866551 -0.07577649897673333" y2="2.406283859660409 1.6362669191013683 0.0962330379832873 -0.6737839025757533 0.0962330379832873 1.6362669191013683 -0.6737584916906038 0.09624150830939682 2.4062669191013684"/>

      <bondArray>

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

        <bond id="b2" atomRefs2="a1 a6" order="1"/>

        <bond id="b3" atomRefs2="a2 a3" order="1"/>

        <bond id="b4" atomRefs2="a3 a4" order="1"/>

        <bond id="b5" atomRefs2="a4 a5" order="1"/>

        <bond id="b6" atomRefs2="a5 a6" order="1"/>

        <bond id="b7" atomRefs2="a3 a7" order="2"/>

        <bond id="b8" atomRefs2="a7 a8" order="1"/>

        <bond id="b9" atomRefs2="a6 a9" order="1"/>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>


However, the question of the first issue hasn't been solved yet. At present, only settings ignoreSynAntiStereo:y and ignoreCumuleneOrRingCisTransStereo:y (or in case of older JChem versions: ignoreAlleneStereo:y) give the desired hit result.


Our syn-anti recognizer works in 2D on the basis of the perspective drawing of the structures as illustrated here. Your structures in question are more complicated and distorted, so their syn/anti property cannot be unequivocally identified. Do you think they are really identical from syn/anti point of view according to their drawn structure?


If we run Clean2D process on the not-found structure below (the target structure in your previous post), the search result is hit - even with the original search options:



<?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/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<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" elementType="C C C C C C C C C C C C C C C C C C O O O H H" x2="-5.438125133514404 -6.771794474562663 -6.771794474562663 -5.438125133514404 -4.104455792466146 -4.104455792466146 -2.7707864514178873 -2.7707864514178873 -1.437117110369629 -1.437117110369629 -0.10344776932137068 -0.10344776932137068 1.2302215717268876 1.2302215717268876 0.2512422213989596 -0.6058493485028137 -2.1185218170329354 -2.1185218170329367 -0.6539743771130421 -3.452200938860972 1.5849213432269953 0.9341506514971863 -3.4522009388609707" y2="2.502533857276223 1.7325169167171826 0.19248303559910152 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502533857276223 -0.5775339049599391 0.19248303559910152 1.7325169167171826 -3.3687500953674308 -1.9303836519094864 -2.5987461837376236 -4.138754006997239 -4.61461642438446 -4.908754006997239 -4.13875009536743 -1.9303836519094864 -1.828746183737623"/>

      <bondArray>

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

        <bond id="b2" atomRefs2="a1 a6" order="2"/>

        <bond id="b3" atomRefs2="a2 a3" order="2"/>

        <bond id="b4" atomRefs2="a3 a4" order="1"/>

        <bond id="b5" atomRefs2="a4 a5" order="2"/>

        <bond id="b6" atomRefs2="a5 a6" order="1"/>

        <bond id="b7" atomRefs2="a8 a9" order="1"/>

        <bond id="b8" atomRefs2="a9 a10" order="1"/>

        <bond id="b9" atomRefs2="a7 a10" order="1"/>

        <bond id="b10" atomRefs2="a5 a8" order="1"/>

        <bond id="b11" atomRefs2="a7 a6" order="1"/>

        <bond id="b12" atomRefs2="a12 a13" order="1"/>

        <bond id="b13" atomRefs2="a13 a14" order="2"/>

        <bond id="b14" atomRefs2="a11 a14" order="1"/>

        <bond id="b15" atomRefs2="a9 a12" order="2"/>

        <bond id="b16" atomRefs2="a11 a10" order="2"/>

        <bond id="b17" atomRefs2="a15 a16" order="1"/>

        <bond id="b18" atomRefs2="a15 a19" order="1"/>

        <bond id="b19" atomRefs2="a16 a17" order="1"/>

        <bond id="b20" atomRefs2="a17 a18" order="1"/>

        <bond id="b21" atomRefs2="a18 a19" order="1"/>

        <bond id="b22" atomRefs2="a8 a17" order="1"/>

        <bond id="b23" atomRefs2="a7 a16" order="1"/>

        <bond id="b24" atomRefs2="a18 a20" order="2"/>

        <bond id="b25" atomRefs2="a15 a21" order="2"/>

        <bond id="b26" atomRefs2="a16 a22" order="1">

          <bondStereo>W</bondStereo>

        </bond>

        <bond id="b27" atomRefs2="a17 a23" order="1">

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>


 

User 870ab5b546

31-07-2014 13:20:07










kvajda wrote:

Hi Bob,


However, the question of the first issue hasn't been solved yet. At present, only settings ignoreSynAntiStereo:y and ignoreCumuleneOrRingCisTransStereo:y (or in case of older JChem versions: ignoreAlleneStereo:y) give the desired hit result.


Our syn-anti recognizer works in 2D on the basis of the perspective drawing of the structures as illustrated here. Your structures in question are more complicated and distorted, so their syn/anti property cannot be unequivocally identified. Do you think they are really identical from syn/anti point of view according to their drawn structure?

For this very reason, I always run setIgnoreSynAntiStereo(true). I also run setIgnoreCumuleneOrRingCisTransStereo(false), because it should not affect the match behavior in cases like this one. But it does.


I cannot do a Clean2D on every submission, because it would be too computationally intensive, and useless most of the time, anyway.

ChemAxon abe887c64e

01-08-2014 07:25:52

We are trying to find and fix the bug which causes the missing hit in case of the query-target pair in question when setIgnoreCumuleneOrRingCisTransStereo(false) is applied.


Best regards,


Krisztina



User 870ab5b546

21-08-2014 19:13:44

Hi, any progress on this problem? I start classes again in a week, and I would like not to have to worry about this bug.

ChemAxon d4fff15f08

22-08-2014 11:30:54

Hi Bob,


It is in 'In Progress' status which means that we are waiting for other team to deliver the fix which can be implemented. They have promised it to be available in short time. This means that - unfortunately - in the upcoming release (next week) this fix will be not included. We will try to urge them.


 


Best regards,


Norbert

User 870ab5b546

04-09-2014 13:27:04

A couple of weeks later -- has your urging moved the process along?

ChemAxon abe887c64e

08-09-2014 14:44:45

Hi Bob,


The above bug of the setIgnoreCumuleneOrRingCisTransStereo search option has been fixed, and the fix will be included in the next JChem version, 14.9.8, planned to be released this week.


Thank you for your patience.


Krisztina