exception

We are throwing the following exception upon doing a MolSearch:





MechArrow:: unknown exception: No valid license key has been found.


Please contact sales _at_ chemaxon.com to obtain a license key.


Students and academic researchers can obtain license keys


for free through our Academic Package, for more information


please visit: http://www.chemaxon.com.


chemaxon.marvin.modules.LicenseException: No valid license key has been found.


Please contact sales _at_ chemaxon.com to obtain a license key.


Students and academic researchers can obtain license keys


for free through our Academic Package, for more information


please visit: http://www.chemaxon.com.


at chemaxon.enumeration.supergraph.Supergraph.<init>(Supergraph.java:134)


at chemaxon.sss.search.MarkushSGSearch.createSupergraphIfNeeded(MarkushSGSearch.java:88)


at chemaxon.sss.search.MarkushSGSearch.findFirst0(MarkushSGSearch.java:80)


at chemaxon.sss.search.StructureSearch.isMatching0(StructureSearch.java:5544)


at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:5536)


at chemaxon.sss.search.MolSearch.isEnumInitializedOk(MolSearch.java:1022)


at chemaxon.sss.search.MolSearch.findNextFiltered(MolSearch.java:968)


at chemaxon.sss.search.MolSearch.findFirst(MolSearch.java:883)


at com.prenhall.epoch.mechanisms.MechSet.fragInList(MechSet.java:121)





Our licenses are in the appropriate file in the appropriate place. What gives? Does it have anything to do with the fact that the target contains this feature:

Code:

<molecule id="sg2" role="SuperatomSgroup" title="Ph" molID="m3">         <atomArray             atomID="a28 a29 a30 a31 a32 a33"             elementType="C C C C C C"             residueType="UNK UNK UNK UNK UNK UNK"             residueId="r1 r1 r1 r1 r1 r1"             residueAtomName="0 0 0 0 0 0"             attachmentPoint="1 0 0 0 0 0"             x2="1.9833333333333336 2.753333333333334 4.293333333333334 5.0633333333333335 4.293333333333334 2.753333333333334"             y2="-3.4053600000000004 -4.739093333333335 -4.739093333333335 -3.405173333333334 -2.071813333333334 -2.071813333333334"             />         <bondArray>           <bond atomRefs2="a28 a29" order="2" />           <bond atomRefs2="a28 a33" order="1" />           <bond atomRefs2="a29 a30" order="1" />           <bond atomRefs2="a30 a31" order="2" />           <bond atomRefs2="a31 a32" order="1" />           <bond atomRefs2="a32 a33" order="2" />         </bondArray>       </molecule>

How does one go about generating a structure that has this feature, anyway?

Hi Bob,





This seems to be a problem similar to the one coming up for the other topic:





http://www.chemaxon.com/forum/ftopic1774.html&highlight=licenseexception+valid+licence+license+key





This time the target molecule is a Markush structure. (Although, I could not see any Markush features in the code fragment you included.)





You can switch off Markush searching in MolSearch using this option:

Code:

molsearch.setOption(SearchConstants.OPTION_MARKUSH_ENABLED,                     SearchConstants.MARKUSH_DISABLED);

Best regards,


Szabolcs

bobgr wrote:

How does one go about generating a structure that has this feature, anyway?

If you are referring to the residue... fields, probably they came from a PDB file?





Szabolcs

Yes, I was referring to the residue... lines. The snippet was from a file that could only have been drawn in MarvinSketch. It could not have come from a PDB file. That's why I was asking how one can generate such a file in MarvinSketch.

Here is the entire file on which we're doing the search. What features are Markush features? And how would a MarvinSketch user generate such a feature?

Code:

<?xml version="1.0" ?> <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"           elementType="Cl Cl Cl C H O O Cl Cl Cl C C C R C R C Cl Cl C Cl"           radical="0 0 0 0 0 monovalent monovalent 0 0 0 monovalent 0 0 0 monovalent 0 0 0 0 0 0"           sgroupRef="0 0 0 0 0 0 0 0 0 0 0 0 0 sg1 0 sg2 0 0 0 0 0"           x2="-10.09176 -11.631760000000002 -10.09176 -10.09176 -8.55176 -7.116666666666668 -5.576666666666667 2.484906666666667 0.9449066666666668 2.484906666666667 2.484906666666667 6.125093333333334 6.895093333333334 8.435093333333334 0.44333333333333336 1.9833333333333336 -0.3266666666666667 -1.866666666666667 -3.406666666666667 -1.866666666666667 -1.866666666666667"           y2="5.915093333333334 4.375093333333334 2.8350933333333335 4.375093333333334 4.375093333333334 6.708426666666667 6.708426666666667 6.498426666666668 4.958426666666667 3.418426666666667 4.958426666666667 3.5584266666666675 4.8919733333333335 4.8919733333333335 -3.4053600000000004 -3.4053600000000004 -4.739093333333335 -3.199093333333334 -4.739093333333335 -4.739093333333335 -6.279093333333334"           />       <bondArray>         <bond atomRefs2="a4 a1" order="1" />         <bond atomRefs2="a4 a2" order="1" />         <bond atomRefs2="a4 a3" order="1" />         <bond atomRefs2="a4 a5" order="1" />         <bond atomRefs2="a6 a7" order="1" />         <bond atomRefs2="a11 a8" order="1" />         <bond atomRefs2="a11 a9" order="1" />         <bond atomRefs2="a11 a10" order="1" />         <bond atomRefs2="a12 a13" order="2" />         <bond atomRefs2="a17 a15" order="1" />         <bond atomRefs2="a17 a20" order="1" />         <bond atomRefs2="a20 a18" order="1" />         <bond atomRefs2="a20 a19" order="1" />         <bond atomRefs2="a20 a21" order="1" />         <bond atomRefs2="a15 a16" order="1" />         <bond atomRefs2="a13 a14" order="1" />       </bondArray>       <molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2">         <atomArray             atomID="a22 a23 a24 a25 a26 a27"             elementType="C C C C C C"             attachmentPoint="1 0 0 0 0 0"             x2="8.435093333333334 9.205093333333336 10.745093333333335 11.515093333333335 10.745093333333335 9.205093333333336"             y2="4.8919733333333335 3.5584266666666675 3.5584266666666675 4.891786666666667 6.225706666666667 6.225706666666667"             />         <bondArray>           <bond atomRefs2="a22 a23" order="2" />           <bond atomRefs2="a22 a27" order="1" />           <bond atomRefs2="a23 a24" order="1" />           <bond atomRefs2="a24 a25" order="2" />           <bond atomRefs2="a25 a26" order="1" />           <bond atomRefs2="a26 a27" order="2" />         </bondArray>       </molecule>       <molecule id="sg2" role="SuperatomSgroup" title="Ph" molID="m3">         <atomArray             atomID="a28 a29 a30 a31 a32 a33"             elementType="C C C C C C"             residueType="UNK UNK UNK UNK UNK UNK"             residueId="r1 r1 r1 r1 r1 r1"             residueAtomName="0 0 0 0 0 0"             attachmentPoint="1 0 0 0 0 0"             x2="1.9833333333333336 2.753333333333334 4.293333333333334 5.0633333333333335 4.293333333333334 2.753333333333334"             y2="-3.4053600000000004 -4.739093333333335 -4.739093333333335 -3.405173333333334 -2.071813333333334 -2.071813333333334"             />         <bondArray>           <bond atomRefs2="a28 a29" order="2" />           <bond atomRefs2="a28 a33" order="1" />           <bond atomRefs2="a29 a30" order="1" />           <bond atomRefs2="a30 a31" order="2" />           <bond atomRefs2="a31 a32" order="1" />           <bond atomRefs2="a32 a33" order="2" />         </bondArray>       </molecule>     </molecule>   </MChemicalStruct>   <MEFlow id="o2" color="#000000" arcAngle="-150.0" headSkip="0.25"           headFlags="2" headLength="0.5" headWidth="0.4" tailSkip="0.25">     <MAtomSetPoint atomRefs="m1.a6" />     <MAtomSetPoint atomRefs="m1.a5" />   </MEFlow>   <MEFlow id="o3" color="#000000" arcAngle="-254.995522631729"           headSkip="0.25" headFlags="2" headLength="0.5" headWidth="0.4"           tailSkip="0.15">     <MAtomSetPoint atomRefs="m1.a4 m1.a5" />     <MAtomSetPoint atomRefs="m1.a5" />   </MEFlow>   <MEFlow id="o4" color="#000000" arcAngle="150.0" headSkip="0.15"           headFlags="2" headLength="0.5" headWidth="0.4" tailSkip="0.25">     <MAtomSetPoint atomRefs="m1.a11" />     <MAtomSetPoint atomRefs="m1.a11 m1.a12" weights="0.25 0.75" />   </MEFlow>   <MEFlow id="o5" color="#000000" arcAngle="-182.17399554899995"           headSkip="0.15" headFlags="2" headLength="0.5" headWidth="0.4"           tailSkip="0.15">     <MAtomSetPoint atomRefs="m1.a12 m1.a13" />     <MAtomSetPoint atomRefs="m1.a13 m1.a14" />   </MEFlow> </MDocument>

bobgr wrote:

What features are Markush features?

R-groups, atom lists, bond lists("single or double", "any", etc.), link nodes.


(Some more will be introduced later, but you can't draw them in Marvin yet.)





See this presentation from the UGM: http://www.chemaxon.com/forum/viewpost6503.html#6503





Your molecule is definitely not a Markush molecule. I tried, it does not generate the exception without the license. Perhaps this one was used as the query and the other molecule (target) was the Markush. (Only Markush target requires a license. A "Markush molecule" on the query side is just a query, and these query features were already supported by earlier versions.)

Ah, I think I know what is happening. The other molecule is a calculated product of electron-flow arrows, and if a student breaks a single bond with a single one-electron electron-flow arrow, we use an ANY bond to represent the half-bond that results, and that must be the Markush structure that is causing us trouble. OK, we can use the option you mentioned to turn that search off. Thanks!