User 05697590e8
27-11-2014 09:31:49
Recently I have created with JChemManager a "molecules" type database with default standarization parameters and I've found that uploading certain structures using Importer object gets high CPU/memory demands, it doesn't end and such thread can't be stopped nor killed, such code is integrated inside a web service so the webapp becomes inoperable after certain time I have launched such import.
I've also tried to launch it inside an Executors.newSingleThreadExecutor() to be able to interrupt it if it takes too long to process such molecule but Importer.cancel() and ExecutorService.shutdownNow() does not stop it.
I post such code.
importer.setConnectionHandler(ch);
importer.setInput(getJmolXYZ(webappFolder,geometryFilePath));
importer.setTableName(PropertiesLoad.getProperty("chemaxon.database.table"));
importer.setStoreImportedIDs(true);
importer.setHaltOnError(false);
logger.info("Importing structures from " + geometryFilePath + " ...");
final ExecutorService service = Executors.newSingleThreadExecutor();
try{
final Future<?> f = service.submit(importer);
logger.info(f.get(10, TimeUnit.SECONDS));
}
catch (final TimeoutException e){
logger.error("Chemaxon plugin took to long (+10s) to index final geometry of calculation id = " + String.valueOf(calc_id.intValue()) + ", skipping");
importer.cancel();
return;
}
catch (final Exception e){
importer.cancel();
throw new RuntimeException(e);
}
finally
{
service.shutdown();
ch.close();
}
During import process, an uncatchable exception is raised:
WARNING: Timeout reached in ringsearch.
Nov 27, 2014 9:44:57 AM chemaxon.jchem.base.persister.MoleculePersister writeMolecule
WARNING: Exception caught while trying persistency method: MoleculeToCxSmilesPersistencyMethod (see below for the problematic molecule)
java.lang.IllegalArgumentException: chemaxon.formats.MolFormatException: Ring (4) formed from two neighboring atoms at smiles [Ag]123456[Ag@]78[Ag]119%10%11%12[Ag]%13%14%15%16%17%18%19%20%21%22[Ag]%23%24%25%26%27%28%29[Ag]%30%31%32%33[Ag@@]%23%23[Ag@@]%24%24[Ag]%25%25%34%35[Ag]%36%37%38%39[Ag]%40%41%42%43%44[Ag]%13%13%45%46%47%48%49%50%51%52[Ag]%53%54%55%56%57%58[Ag]2%14%132%13%14%59%60[Ag]%61%62%63%64%65[Ag]%53%53%66[Ag]%54%54%67%68[Ag]%69%70%71%72%73%74%75%76[Ag]%77%78%79%80%81%82%83%84%85%86[Ag]%87%88%89%90%91[Ag]%77%77%92%93%94[Ag]%78%78%95%96%97[Ag]%69%69%98[Ag]%70%70%99%100[Ag]%101%102%103%104[Ag]%71%79%87%71%79%87%105[Ag]%72%70%101([Ag]%99%102)[Ag]%40%45%54%73%71%40%45[Ag]%36%41%46%55%67([Ag]%37%42)[Ag]%15%26%24%25%38%47%56%15[Ag]%16%34%39%43%48%16%24[Ag]%44%49%25%26[Ag]%50%80%88%79%40%34%36%37[Ag]32%61%8123%38%39%40[Ag]%82%89%77%41%42([Ag@]%43%44[Ag]%92%78%41[Ag]%62%83%952%42%43([Ag]%63%53%74%84%96%69[Ag]%51%57%13%64%66%68%75%85%45%343)[Ag]4%65%38%44)[Ag]%90%36%39[Ag]51%17%52%14%25%37%40[Ag]9%18%16%261[Ag]%102[Ag]%11%19%27%303([Ag]%20%28%35%2412)[Ag@@]7%31[Ag]68%12%21%32%593[Ag]%22%29%33%23%58%60%15.[Ag]%76%86%93%97%98%100%103%87[Ag]%91%94%104%105.C1CCCCC1 |r|
at chemaxon.jchem.base.persister.method.SmilesToMolecule.apply(SmilesToMolecule.java:43)
at chemaxon.jchem.base.persister.method.SmilesToMolecule.apply(SmilesToMolecule.java:27)
at chemaxon.jchem.base.persister.method.FunctionBasedPersistencyMethod.read(FunctionBasedPersistencyMethod.java:45)
at chemaxon.jchem.base.persister.method.ValidatingChemicalStructurePersistencyMethod.write(ValidatingChemicalStructurePersistencyMethod.java:48)
at chemaxon.jchem.base.persister.method.ValidatingChemicalStructurePersistencyMethod.write(ValidatingChemicalStructurePersistencyMethod.java:26)
at chemaxon.jchem.base.persister.MoleculePersister.writeMolecule(MoleculePersister.java:95)
at chemaxon.jchem.base.persister.MoleculePersister.<init>(MoleculePersister.java:76)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.init(StructureRecordMaker.java:520)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.initRecord(StructureRecordMaker.java:467)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.initStructureAndMolecule(StructureRecordMaker.java:343)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.createRecord(StructureRecordMaker.java:296)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.insertRecord(StructureRecordMaker.java:160)
at chemaxon.jchem.db.UpdateHandler.createRowData0(UpdateHandler.java:1549)
at chemaxon.jchem.db.ParallelStructTableUpdater$UpdateHandlerAdapter.process(ParallelStructTableUpdater.java:119)
at chemaxon.util.concurrent.util.AbstractWorkUnit.call(AbstractWorkUnit.java:33)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:58)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:50)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(WorkUnitWorker.java:51)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work(WorkUnitWorker.java:36)
at chemaxon.util.concurrent.worker.Worker$1.call(Worker.java:45)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: chemaxon.formats.MolFormatException: Ring (4) formed from two neighboring atoms at smiles [Ag]123456[Ag@]78[Ag]119%10%11%12[Ag]%13%14%15%16%17%18%19%20%21%22[Ag]%23%24%25%26%27%28%29[Ag]%30%31%32%33[Ag@@]%23%23[Ag@@]%24%24[Ag]%25%25%34%35[Ag]%36%37%38%39[Ag]%40%41%42%43%44[Ag]%13%13%45%46%47%48%49%50%51%52[Ag]%53%54%55%56%57%58[Ag]2%14%132%13%14%59%60[Ag]%61%62%63%64%65[Ag]%53%53%66[Ag]%54%54%67%68[Ag]%69%70%71%72%73%74%75%76[Ag]%77%78%79%80%81%82%83%84%85%86[Ag]%87%88%89%90%91[Ag]%77%77%92%93%94[Ag]%78%78%95%96%97[Ag]%69%69%98[Ag]%70%70%99%100[Ag]%101%102%103%104[Ag]%71%79%87%71%79%87%105[Ag]%72%70%101([Ag]%99%102)[Ag]%40%45%54%73%71%40%45[Ag]%36%41%46%55%67([Ag]%37%42)[Ag]%15%26%24%25%38%47%56%15[Ag]%16%34%39%43%48%16%24[Ag]%44%49%25%26[Ag]%50%80%88%79%40%34%36%37[Ag]32%61%8123%38%39%40[Ag]%82%89%77%41%42([Ag@]%43%44[Ag]%92%78%41[Ag]%62%83%952%42%43([Ag]%63%53%74%84%96%69[Ag]%51%57%13%64%66%68%75%85%45%343)[Ag]4%65%38%44)[Ag]%90%36%39[Ag]51%17%52%14%25%37%40[Ag]9%18%16%261[Ag]%102[Ag]%11%19%27%303([Ag]%20%28%35%2412)[Ag@@]7%31[Ag]68%12%21%32%593[Ag]%22%29%33%23%58%60%15.[Ag]%76%86%93%97%98%100%103%87[Ag]%91%94%104%105.C1CCCCC1 |r|
at chemaxon.marvin.io.formats.smiles.SmilesImport.readRingNumber(SmilesImport.java:1539)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol0(SmilesImport.java:913)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:622)
at chemaxon.marvin.io.formats.smiles.CxsmilesImport.readMol(CxsmilesImport.java:186)
at chemaxon.jchem.base.persister.method.SmilesToMolecule.apply(SmilesToMolecule.java:41)
... 26 more
Nov 27, 2014 9:44:57 AM chemaxon.jchem.base.persister.MoleculePersister logMolecule
WARNING: <?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_11_17.xsd" version="ChemAxon file format v14.11.17, generated by v14.11.24.0">
<MDocument><MChemicalStruct><molecule molID="m1"><propertyList><property dictRef="mrv_H_3d_coordinates" title="mrv_H_3d_coordinates"><scalar dataType="xsd:ENTITY"><![CDATA[MProp:MHCoords3D:
55 1 -0.660188 2.9848068 14.902826
54 1 -0.65186113 5.4823065 14.90586
59 1 3.6621203 2.974906 14.914598
58 1 3.6706555 5.4728155 14.916926
57 1 1.4958946 1.731153 14.913388
56 1 1.5142885 6.725948 14.906544]]></scalar></property></propertyList><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 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55 a56 a57 a58 a59 a60" elementType="Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag C C C C C C" x3="0.0023661256 -1.4610555 -2.9244332 2.9362197 1.4727981 0.009420395 5.8701615 4.4067397 2.943362 1.4681097 0.0047321464 -1.4586895 4.402052 2.9386742 1.4752525 7.335906 5.872528 4.4091067 -2.0924375E-7 -1.4633778 5.8748503 2.9338534 1.4704758 0.0070543583 5.867795 4.4044175 2.9409957 0.0023658117 -1.4610559 -2.9244335 2.9362195 1.4727978 0.009420081 5.870161 4.406739 2.9433618 1.4680719 0.006217777 -1.4580727 4.4014373 2.9371243 1.4752192 7.33641 5.872467 4.40839 -3.1565467E-4 -1.4666563 5.8749976 2.9341626 1.4703711 -5.4292503E-4 5.867696 4.4074864 2.9489205 0.29217082 0.28829938 1.5105342 1.4999393 2.722666 2.7181091" y3="1.6952252 4.2381396 6.7809777 1.6952252 4.2381396 6.7809777 1.6952252 4.2381396 6.7809777 0.84761244 3.3904502 5.9333644 0.84761244 3.3904502 5.9333644 0.84761244 3.3904502 5.9333644 -3.6183715E-7 2.5428374 5.085751 -3.6183715E-7 2.5428374 5.085751 -3.6183715E-7 2.5428374 5.085751 1.6952246 4.238139 6.7809772 1.6952246 4.238139 6.7809772 1.6952246 4.238139 6.7809772 0.8483948 3.3913314 5.9329867 0.8473047 3.3913333 5.931612 0.8472965 3.3911064 5.9329767 2.2810543E-4 2.5410414 5.0854325 2.6863243E-5 2.5337446 5.090128 0.0036852297 2.5410206 5.090384 4.9336505 3.5294325 5.632313 2.8245273 4.928048 3.5236769" z3="0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 9.564554 9.569213 9.564521 9.564334 9.569394 9.569256 9.56426 9.564315 9.564563 11.97038 11.970341 11.970415 11.970411 11.959252 11.95955 11.970332 11.970284 11.959183 14.913734 14.912585 14.914332 14.917064 14.918158 14.91961" /><bondArray><bond id="b1" atomRefs2="a1 a10" order="1" /><bond id="b2" atomRefs2="a1 a4" order="1" /><bond id="b3" atomRefs2="a1 a11" order="1" /><bond id="b4" atomRefs2="a1 a5" order="1" /><bond id="b5" atomRefs2="a2 a1" order="1" /><bond id="b6" atomRefs2="a2 a12" order="1" /><bond id="b7" atomRefs2="a2 a11" order="1" /><bond id="b8" atomRefs2="a2 a5" order="1" /><bond id="b9" atomRefs2="a2 a6" order="1" /><bond id="b10" atomRefs2="a3 a2" order="1" /><bond id="b11" atomRefs2="a3 a12" order="1" /><bond id="b12" atomRefs2="a3 a6" order="1" /><bond id="b13" atomRefs2="a4 a14" order="1" /><bond id="b14" atomRefs2="a4 a13" order="1" /><bond id="b15" atomRefs2="a4 a7" order="1" /><bond id="b16" atomRefs2="a4 a8" order="1" /><bond id="b17" atomRefs2="a5 a4" order="1" /><bond id="b18" atomRefs2="a5 a14" order="1" /><bond id="b19" atomRefs2="a5 a15" order="1" /><bond id="b20" atomRefs2="a5 a9" order="1" /><bond id="b21" atomRefs2="a5 a8" order="1" /><bond id="b22" atomRefs2="a6 a5" order="1" /><bond id="b23" atomRefs2="a6 a15" order="1" /><bond id="b24" atomRefs2="a6 a9" order="1" /><bond id="b25" atomRefs2="a7 a16" order="1" /><bond id="b26" atomRefs2="a7 a17" order="1" /><bond id="b27" atomRefs2="a8 a17" order="1" /><bond id="b28" atomRefs2="a8 a7" order="1" /><bond id="b29" atomRefs2="a8 a18" order="1" /><bond id="b30" atomRefs2="a9 a8" order="1" /><bond id="b31" atomRefs2="a9 a18" order="1" /><bond id="b32" atomRefs2="a10 a22" order="1" /><bond id="b33" atomRefs2="a10 a23" order="1" /><bond id="b34" atomRefs2="a10 a4" order="1" /><bond id="b35" atomRefs2="a10 a14" order="1" /><bond id="b36" atomRefs2="a10 a13" order="1" /><bond id="b37" atomRefs2="a11 a10" order="1" /><bond id="b38" atomRefs2="a11 a23" order="1" /><bond id="b39" atomRefs2="a11 a24" order="1" /><bond id="b40" atomRefs2="a11 a14" order="1" /><bond id="b41" atomRefs2="a11 a5" order="1" /><bond id="b42" atomRefs2="a11 a15" order="1" /><bond id="b43" atomRefs2="a12 a11" order="1" /><bond id="b44" atomRefs2="a12 a24" order="1" /><bond id="b45" atomRefs2="a12 a6" order="1" /><bond id="b46" atomRefs2="a12 a15" order="1" /><bond id="b47" atomRefs2="a13 a26" order="1" /><bond id="b48" atomRefs2="a13 a25" order="1" /><bond id="b49" atomRefs2="a13 a16" order="1" /><bond id="b50" atomRefs2="a13 a17" order="1" /><bond id="b51" atomRefs2="a13 a7" order="1" /><bond id="b52" atomRefs2="a14 a27" order="1" /><bond id="b53" atomRefs2="a14 a13" order="1" /><bond id="b54" atomRefs2="a14 a26" order="1" /><bond id="b55" atomRefs2="a14 a17" order="1" /><bond id="b56" atomRefs2="a14 a8" order="1" /><bond id="b57" atomRefs2="a14 a18" order="1" /><bond id="b58" atomRefs2="a15 a14" order="1" /><bond id="b59" atomRefs2="a15 a27" order="1" /><bond id="b60" atomRefs2="a15 a9" order="1" /><bond id="b61" atomRefs2="a15 a18" order="1" /><bond id="b62" atomRefs2="a17 a16" order="1" /><bond id="b63" atomRefs2="a17 a21" order="1" /><bond id="b64" atomRefs2="a18 a17" order="1" /><bond id="b65" atomRefs2="a18 a21" order="1" /><bond id="b66" atomRefs2="a19 a28" order="1" /><bond id="b67" atomRefs2="a19 a10" order="1" /><bond id="b68" atomRefs2="a19 a22" order="1" /><bond id="b69" atomRefs2="a19 a23" order="1" /><bond id="b70" atomRefs2="a20 a19" order="1" /><bond id="b71" atomRefs2="a20 a28" order="1" /><bond id="b72" atomRefs2="a20 a23" order="1" /><bond id="b73" atomRefs2="a20 a29" order="1" /><bond id="b74" atomRefs2="a20 a11" order="1" /><bond id="b75" atomRefs2="a20 a24" order="1" /><bond id="b76" atomRefs2="a22 a31" order="1" /><bond id="b77" atomRefs2="a22 a13" order="1" /><bond id="b78" atomRefs2="a22 a26" order="1" /><bond id="b79" atomRefs2="a22 a25" order="1" /><bond id="b80" atomRefs2="a23 a22" order="1" /><bond id="b81" atomRefs2="a23 a31" order="1" /><bond id="b82" atomRefs2="a23 a14" order="1" /><bond id="b83" atomRefs2="a23 a27" order="1" /><bond id="b84" atomRefs2="a23 a32" order="1" /><bond id="b85" atomRefs2="a23 a26" order="1" /><bond id="b86" atomRefs2="a24 a23" order="1" /><bond id="b87" atomRefs2="a24 a27" order="1" /><bond id="b88" atomRefs2="a24 a32" order="1" /><bond id="b89" atomRefs2="a24 a33" order="1" /><bond id="b90" atomRefs2="a24 a15" order="1" /><bond id="b91" atomRefs2="a25 a16" order="1" /><bond id="b92" atomRefs2="a25 a34" order="1" /><bond id="b93" atomRefs2="a26 a25" order="1" /><bond id="b94" atomRefs2="a26 a34" order="1" /><bond id="b95" atomRefs2="a26 a17" order="1" /><bond id="b96" atomRefs2="a26 a35" order="1" /><bond id="b97" atomRefs2="a26 a21" order="1" /><bond id="b98" atomRefs2="a27 a36" order="1" /><bond id="b99" atomRefs2="a27 a26" order="1" /><bond id="b100" atomRefs2="a27 a35" order="1" /><bond id="b101" atomRefs2="a27 a21" order="1" /><bond id="b102" atomRefs2="a27 a18" order="1" /><bond id="b103" atomRefs2="a28 a37" order="1" /><bond id="b104" atomRefs2="a28 a23" order="1" /><bond id="b105" atomRefs2="a28 a31" order="1" /><bond id="b106" atomRefs2="a28 a38" order="1" /><bond id="b107" atomRefs2="a28 a32" order="1" /><bond id="b108" atomRefs2="a29 a28" order="1" /><bond id="b109" atomRefs2="a29 a39" order="1" /><bond id="b110" atomRefs2="a29 a38" order="1" /><bond id="b111" atomRefs2="a29 a24" order="1" /><bond id="b112" atomRefs2="a29 a32" order="1" /><bond id="b113" atomRefs2="a29 a33" order="1" /><bond id="b114" atomRefs2="a30 a29" order="1" /><bond id="b115" atomRefs2="a30 a39" order="1" /><bond id="b116" atomRefs2="a30 a33" order="1" /><bond id="b117" atomRefs2="a31 a41" order="1" /><bond id="b118" atomRefs2="a31 a40" order="1" /><bond id="b119" atomRefs2="a31 a26" order="1" /><bond id="b120" atomRefs2="a31 a34" order="1" /><bond id="b121" atomRefs2="a31 a35" order="1" /><bond id="b122" atomRefs2="a32 a31" order="1" /><bond id="b123" atomRefs2="a32 a41" order="1" /><bond id="b124" atomRefs2="a32 a27" order="1" /><bond id="b125" atomRefs2="a32 a42" order="1" /><bond id="b126" atomRefs2="a32 a36" order="1" /><bond id="b127" atomRefs2="a32 a35" order="1" /><bond id="b128" atomRefs2="a33 a32" order="1" /><bond id="b129" atomRefs2="a33 a42" order="1" /><bond id="b130" atomRefs2="a33 a36" order="1" /><bond id="b131" atomRefs2="a34 a43" order="1" /><bond id="b132" atomRefs2="a34 a44" order="1" /><bond id="b133" atomRefs2="a35 a34" order="1" /><bond id="b134" atomRefs2="a35 a44" order="1" /><bond id="b135" atomRefs2="a35 a45" order="1" /><bond id="b136" atomRefs2="a35 a21" order="1" /><bond id="b137" atomRefs2="a36 a35" order="1" /><bond id="b138" atomRefs2="a36 a45" order="1" /><bond id="b139" atomRefs2="a37 a50" order="1" /><bond id="b140" atomRefs2="a37 a49" order="1" /><bond id="b141" atomRefs2="a37 a31" order="1" /><bond id="b142" atomRefs2="a37 a41" order="1" /><bond id="b143" atomRefs2="a37 a40" order="1" /><bond id="b144" atomRefs2="a38 a37" order="1" /><bond id="b145" atomRefs2="a38 a50" order="1" /><bond id="b146" atomRefs2="a38 a41" order="1" /><bond id="b147" atomRefs2="a38 a32" order="1" /><bond id="b148" atomRefs2="a38 a42" order="1" /><bond id="b149" atomRefs2="a39 a38" order="1" /><bond id="b150" atomRefs2="a39 a51" order="1" /><bond id="b151" atomRefs2="a39 a42" order="1" /><bond id="b152" atomRefs2="a39 a33" order="1" /><bond id="b153" atomRefs2="a40 a53" order="1" /><bond id="b154" atomRefs2="a40 a43" order="1" /><bond id="b155" atomRefs2="a40 a34" order="1" /><bond id="b156" atomRefs2="a40 a44" order="1" /><bond id="b157" atomRefs2="a40 a52" order="1" /><bond id="b158" atomRefs2="a41 a54" order="1" /><bond id="b159" atomRefs2="a41 a40" order="1" /><bond id="b160" atomRefs2="a41 a53" order="1" /><bond id="b161" atomRefs2="a41 a44" order="1" /><bond id="b162" atomRefs2="a41 a35" order="1" /><bond id="b163" atomRefs2="a41 a45" order="1" /><bond id="b164" atomRefs2="a42 a41" order="1" /><bond id="b165" atomRefs2="a42 a54" order="1" /><bond id="b166" atomRefs2="a42 a36" order="1" /><bond id="b167" atomRefs2="a42 a45" order="1" /><bond id="b168" atomRefs2="a44 a43" order="1" /><bond id="b169" atomRefs2="a44 a48" order="1" /><bond id="b170" atomRefs2="a45 a44" order="1" /><bond id="b171" atomRefs2="a45 a48" order="1" /><bond id="b172" atomRefs2="a46 a37" order="1" /><bond id="b173" atomRefs2="a46 a50" order="1" /><bond id="b174" atomRefs2="a46 a49" order="1" /><bond id="b175" atomRefs2="a47 a50" order="1" /><bond id="b176" atomRefs2="a47 a46" order="1" /><bond id="b177" atomRefs2="a47 a38" order="1" /><bond id="b178" atomRefs2="a47 a51" order="1" /><bond id="b179" atomRefs2="a49 a40" order="1" /><bond id="b180" atomRefs2="a49 a53" order="1" /><bond id="b181" atomRefs2="a49 a52" order="1" /><bond id="b182" atomRefs2="a50 a49" order="1" /><bond id="b183" atomRefs2="a50 a41" order="1" /><bond id="b184" atomRefs2="a50 a54" order="1" /><bond id="b185" atomRefs2="a50 a53" order="1" /><bond id="b186" atomRefs2="a51 a50" order="1" /><bond id="b187" atomRefs2="a51 a38" order="1" /><bond id="b188" atomRefs2="a51 a54" order="1" /><bond id="b189" atomRefs2="a51 a42" order="1" /><bond id="b190" atomRefs2="a52 a43" order="1" /><bond id="b191" atomRefs2="a53 a44" order="1" /><bond id="b192" atomRefs2="a53 a52" order="1" /><bond id="b193" atomRefs2="a53 a48" order="1" /><bond id="b194" atomRefs2="a54 a53" order="1" /><bond id="b195" atomRefs2="a54 a45" order="1" /><bond id="b196" atomRefs2="a54 a48" order="1" /><bond id="b197" atomRefs2="a55 a57" order="1" /><bond id="b198" atomRefs2="a56 a58" order="1" /><bond id="b199" atomRefs2="a56 a55" order="1" /><bond id="b200" atomRefs2="a57 a59" order="1" /><bond id="b201" atomRefs2="a58 a60" order="1" /><bond id="b202" atomRefs2="a60 a59" order="1" /></bondArray></molecule></MChemicalStruct></MDocument>
</cml>
Nov 27, 2014 9:44:57 AM chemaxon.jchem.base.persister.MoleculePersister writeMolecule
WARNING: Exception caught while trying persistency method: MoleculeToSmartsPersistencyMethod (see below for the problematic molecule)
java.lang.IllegalArgumentException: chemaxon.formats.MolFormatException: Ring (4) formed from two neighboring atoms at smiles [Ag]123456[Ag@]78[Ag]119%10%11%12[Ag]%13%14%15%16%17%18%19%20%21%22[Ag]%23%24%25%26%27%28%29[Ag]%30%31%32%33[Ag@@]%23%23[Ag@@]%24%24[Ag]%25%25%34%35[Ag]%36%37%38%39[Ag]%40%41%42%43%44[Ag]%13%13%45%46%47%48%49%50%51%52[Ag]%53%54%55%56%57%58[Ag]2%14%132%13%14%59%60[Ag]%61%62%63%64%65[Ag]%53%53%66[Ag]%54%54%67%68[Ag]%69%70%71%72%73%74%75%76[Ag]%77%78%79%80%81%82%83%84%85%86[Ag]%87%88%89%90%91[Ag]%77%77%92%93%94[Ag]%78%78%95%96%97[Ag]%69%69%98[Ag]%70%70%99%100[Ag]%101%102%103%104[Ag]%71%79%87%71%79%87%105[Ag]%72%70%101([Ag]%99%102)[Ag]%40%45%54%73%71%40%45[Ag]%36%41%46%55%67([Ag]%37%42)[Ag]%15%26%24%25%38%47%56%15[Ag]%16%34%39%43%48%16%24[Ag]%44%49%25%26[Ag]%50%80%88%79%40%34%36%37[Ag]32%61%8123%38%39%40[Ag]%82%89%77%41%42([Ag@]%43%44[Ag]%92%78%41[Ag]%62%83%952%42%43([Ag]%63%53%74%84%96%69[Ag]%51%57%13%64%66%68%75%85%45%343)[Ag]4%65%38%44)[Ag]%90%36%39[Ag]51%17%52%14%25%37%40[Ag]9%18%16%261[Ag]%102[Ag]%11%19%27%303([Ag]%20%28%35%2412)[Ag@@]7%31[Ag]68%12%21%32%593[Ag]%22%29%33%23%58%60%15.[Ag]%76%86%93%97%98%100%103%87[Ag]%91%94%104%105.[#6]-1-[#6]-[#6]-[#6]-[#6]-[#6]-1 |r|
at chemaxon.jchem.base.persister.method.SmartsToMolecule.apply(SmartsToMolecule.java:30)
at chemaxon.jchem.base.persister.method.SmartsToMolecule.apply(SmartsToMolecule.java:21)
at chemaxon.jchem.base.persister.method.FunctionBasedPersistencyMethod.read(FunctionBasedPersistencyMethod.java:45)
at chemaxon.jchem.base.persister.method.ValidatingChemicalStructurePersistencyMethod.write(ValidatingChemicalStructurePersistencyMethod.java:48)
at chemaxon.jchem.base.persister.method.ValidatingChemicalStructurePersistencyMethod.write(ValidatingChemicalStructurePersistencyMethod.java:26)
at chemaxon.jchem.base.persister.MoleculePersister.writeMolecule(MoleculePersister.java:95)
at chemaxon.jchem.base.persister.MoleculePersister.<init>(MoleculePersister.java:76)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.init(StructureRecordMaker.java:520)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.initRecord(StructureRecordMaker.java:467)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.initStructureAndMolecule(StructureRecordMaker.java:343)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.createRecord(StructureRecordMaker.java:296)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.insertRecord(StructureRecordMaker.java:160)
at chemaxon.jchem.db.UpdateHandler.createRowData0(UpdateHandler.java:1549)
at chemaxon.jchem.db.ParallelStructTableUpdater$UpdateHandlerAdapter.process(ParallelStructTableUpdater.java:119)
at chemaxon.util.concurrent.util.AbstractWorkUnit.call(AbstractWorkUnit.java:33)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:58)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:50)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(WorkUnitWorker.java:51)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work(WorkUnitWorker.java:36)
at chemaxon.util.concurrent.worker.Worker$1.call(Worker.java:45)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: chemaxon.formats.MolFormatException: Ring (4) formed from two neighboring atoms at smiles [Ag]123456[Ag@]78[Ag]119%10%11%12[Ag]%13%14%15%16%17%18%19%20%21%22[Ag]%23%24%25%26%27%28%29[Ag]%30%31%32%33[Ag@@]%23%23[Ag@@]%24%24[Ag]%25%25%34%35[Ag]%36%37%38%39[Ag]%40%41%42%43%44[Ag]%13%13%45%46%47%48%49%50%51%52[Ag]%53%54%55%56%57%58[Ag]2%14%132%13%14%59%60[Ag]%61%62%63%64%65[Ag]%53%53%66[Ag]%54%54%67%68[Ag]%69%70%71%72%73%74%75%76[Ag]%77%78%79%80%81%82%83%84%85%86[Ag]%87%88%89%90%91[Ag]%77%77%92%93%94[Ag]%78%78%95%96%97[Ag]%69%69%98[Ag]%70%70%99%100[Ag]%101%102%103%104[Ag]%71%79%87%71%79%87%105[Ag]%72%70%101([Ag]%99%102)[Ag]%40%45%54%73%71%40%45[Ag]%36%41%46%55%67([Ag]%37%42)[Ag]%15%26%24%25%38%47%56%15[Ag]%16%34%39%43%48%16%24[Ag]%44%49%25%26[Ag]%50%80%88%79%40%34%36%37[Ag]32%61%8123%38%39%40[Ag]%82%89%77%41%42([Ag@]%43%44[Ag]%92%78%41[Ag]%62%83%952%42%43([Ag]%63%53%74%84%96%69[Ag]%51%57%13%64%66%68%75%85%45%343)[Ag]4%65%38%44)[Ag]%90%36%39[Ag]51%17%52%14%25%37%40[Ag]9%18%16%261[Ag]%102[Ag]%11%19%27%303([Ag]%20%28%35%2412)[Ag@@]7%31[Ag]68%12%21%32%593[Ag]%22%29%33%23%58%60%15.[Ag]%76%86%93%97%98%100%103%87[Ag]%91%94%104%105.[#6]-1-[#6]-[#6]-[#6]-[#6]-[#6]-1 |r|
at chemaxon.marvin.io.formats.smiles.SmilesImport.readRingNumber(SmilesImport.java:1539)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol0(SmilesImport.java:913)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:622)
at chemaxon.marvin.io.formats.smiles.CxsmilesImport.readMol(CxsmilesImport.java:186)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:576)
at chemaxon.marvin.io.MRecordImporter.readStructure(MRecordImporter.java:784)
at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:724)
at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:687)
at chemaxon.marvin.io.MRecordImporter.readMol0(MRecordImporter.java:595)
at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:512)
at chemaxon.formats.MolImporter.readMol(MolImporter.java:883)
at chemaxon.formats.MolImporter.read(MolImporter.java:766)
at chemaxon.formats.MolImporter.importMol(MolImporter.java:1308)
at chemaxon.formats.MolImporter.importMol(MolImporter.java:1499)
at chemaxon.jchem.base.persister.method.SmartsToMolecule.apply(SmartsToMolecule.java:28)
... 26 more
Nov 27, 2014 9:44:57 AM chemaxon.jchem.base.persister.MoleculePersister logMolecule
WARNING: <?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_11_17.xsd" version="ChemAxon file format v14.11.17, generated by v14.11.24.0">
<MDocument><MChemicalStruct><molecule molID="m1"><propertyList><property dictRef="mrv_H_3d_coordinates" title="mrv_H_3d_coordinates"><scalar dataType="xsd:ENTITY"><![CDATA[MProp:MHCoords3D:
55 1 -0.660188 2.9848068 14.902826
54 1 -0.65186113 5.4823065 14.90586
59 1 3.6621203 2.974906 14.914598
58 1 3.6706555 5.4728155 14.916926
57 1 1.4958946 1.731153 14.913388
56 1 1.5142885 6.725948 14.906544]]></scalar></property></propertyList><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 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55 a56 a57 a58 a59 a60" elementType="Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag C C C C C C" x3="0.0023661256 -1.4610555 -2.9244332 2.9362197 1.4727981 0.009420395 5.8701615 4.4067397 2.943362 1.4681097 0.0047321464 -1.4586895 4.402052 2.9386742 1.4752525 7.335906 5.872528 4.4091067 -2.0924375E-7 -1.4633778 5.8748503 2.9338534 1.4704758 0.0070543583 5.867795 4.4044175 2.9409957 0.0023658117 -1.4610559 -2.9244335 2.9362195 1.4727978 0.009420081 5.870161 4.406739 2.9433618 1.4680719 0.006217777 -1.4580727 4.4014373 2.9371243 1.4752192 7.33641 5.872467 4.40839 -3.1565467E-4 -1.4666563 5.8749976 2.9341626 1.4703711 -5.4292503E-4 5.867696 4.4074864 2.9489205 0.29217082 0.28829938 1.5105342 1.4999393 2.722666 2.7181091" y3="1.6952252 4.2381396 6.7809777 1.6952252 4.2381396 6.7809777 1.6952252 4.2381396 6.7809777 0.84761244 3.3904502 5.9333644 0.84761244 3.3904502 5.9333644 0.84761244 3.3904502 5.9333644 -3.6183715E-7 2.5428374 5.085751 -3.6183715E-7 2.5428374 5.085751 -3.6183715E-7 2.5428374 5.085751 1.6952246 4.238139 6.7809772 1.6952246 4.238139 6.7809772 1.6952246 4.238139 6.7809772 0.8483948 3.3913314 5.9329867 0.8473047 3.3913333 5.931612 0.8472965 3.3911064 5.9329767 2.2810543E-4 2.5410414 5.0854325 2.6863243E-5 2.5337446 5.090128 0.0036852297 2.5410206 5.090384 4.9336505 3.5294325 5.632313 2.8245273 4.928048 3.5236769" z3="0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 2.393604 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 4.7869387 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 7.1805425 9.564554 9.569213 9.564521 9.564334 9.569394 9.569256 9.56426 9.564315 9.564563 11.97038 11.970341 11.970415 11.970411 11.959252 11.95955 11.970332 11.970284 11.959183 14.913734 14.912585 14.914332 14.917064 14.918158 14.91961" /><bondArray><bond id="b1" atomRefs2="a1 a10" order="1" /><bond id="b2" atomRefs2="a1 a4" order="1" /><bond id="b3" atomRefs2="a1 a11" order="1" /><bond id="b4" atomRefs2="a1 a5" order="1" /><bond id="b5" atomRefs2="a2 a1" order="1" /><bond id="b6" atomRefs2="a2 a12" order="1" /><bond id="b7" atomRefs2="a2 a11" order="1" /><bond id="b8" atomRefs2="a2 a5" order="1" /><bond id="b9" atomRefs2="a2 a6" order="1" /><bond id="b10" atomRefs2="a3 a2" order="1" /><bond id="b11" atomRefs2="a3 a12" order="1" /><bond id="b12" atomRefs2="a3 a6" order="1" /><bond id="b13" atomRefs2="a4 a14" order="1" /><bond id="b14" atomRefs2="a4 a13" order="1" /><bond id="b15" atomRefs2="a4 a7" order="1" /><bond id="b16" atomRefs2="a4 a8" order="1" /><bond id="b17" atomRefs2="a5 a4" order="1" /><bond id="b18" atomRefs2="a5 a14" order="1" /><bond id="b19" atomRefs2="a5 a15" order="1" /><bond id="b20" atomRefs2="a5 a9" order="1" /><bond id="b21" atomRefs2="a5 a8" order="1" /><bond id="b22" atomRefs2="a6 a5" order="1" /><bond id="b23" atomRefs2="a6 a15" order="1" /><bond id="b24" atomRefs2="a6 a9" order="1" /><bond id="b25" atomRefs2="a7 a16" order="1" /><bond id="b26" atomRefs2="a7 a17" order="1" /><bond id="b27" atomRefs2="a8 a17" order="1" /><bond id="b28" atomRefs2="a8 a7" order="1" /><bond id="b29" atomRefs2="a8 a18" order="1" /><bond id="b30" atomRefs2="a9 a8" order="1" /><bond id="b31" atomRefs2="a9 a18" order="1" /><bond id="b32" atomRefs2="a10 a22" order="1" /><bond id="b33" atomRefs2="a10 a23" order="1" /><bond id="b34" atomRefs2="a10 a4" order="1" /><bond id="b35" atomRefs2="a10 a14" order="1" /><bond id="b36" atomRefs2="a10 a13" order="1" /><bond id="b37" atomRefs2="a11 a10" order="1" /><bond id="b38" atomRefs2="a11 a23" order="1" /><bond id="b39" atomRefs2="a11 a24" order="1" /><bond id="b40" atomRefs2="a11 a14" order="1" /><bond id="b41" atomRefs2="a11 a5" order="1" /><bond id="b42" atomRefs2="a11 a15" order="1" /><bond id="b43" atomRefs2="a12 a11" order="1" /><bond id="b44" atomRefs2="a12 a24" order="1" /><bond id="b45" atomRefs2="a12 a6" order="1" /><bond id="b46" atomRefs2="a12 a15" order="1" /><bond id="b47" atomRefs2="a13 a26" order="1" /><bond id="b48" atomRefs2="a13 a25" order="1" /><bond id="b49" atomRefs2="a13 a16" order="1" /><bond id="b50" atomRefs2="a13 a17" order="1" /><bond id="b51" atomRefs2="a13 a7" order="1" /><bond id="b52" atomRefs2="a14 a27" order="1" /><bond id="b53" atomRefs2="a14 a13" order="1" /><bond id="b54" atomRefs2="a14 a26" order="1" /><bond id="b55" atomRefs2="a14 a17" order="1" /><bond id="b56" atomRefs2="a14 a8" order="1" /><bond id="b57" atomRefs2="a14 a18" order="1" /><bond id="b58" atomRefs2="a15 a14" order="1" /><bond id="b59" atomRefs2="a15 a27" order="1" /><bond id="b60" atomRefs2="a15 a9" order="1" /><bond id="b61" atomRefs2="a15 a18" order="1" /><bond id="b62" atomRefs2="a17 a16" order="1" /><bond id="b63" atomRefs2="a17 a21" order="1" /><bond id="b64" atomRefs2="a18 a17" order="1" /><bond id="b65" atomRefs2="a18 a21" order="1" /><bond id="b66" atomRefs2="a19 a28" order="1" /><bond id="b67" atomRefs2="a19 a10" order="1" /><bond id="b68" atomRefs2="a19 a22" order="1" /><bond id="b69" atomRefs2="a19 a23" order="1" /><bond id="b70" atomRefs2="a20 a19" order="1" /><bond id="b71" atomRefs2="a20 a28" order="1" /><bond id="b72" atomRefs2="a20 a23" order="1" /><bond id="b73" atomRefs2="a20 a29" order="1" /><bond id="b74" atomRefs2="a20 a11" order="1" /><bond id="b75" atomRefs2="a20 a24" order="1" /><bond id="b76" atomRefs2="a22 a31" order="1" /><bond id="b77" atomRefs2="a22 a13" order="1" /><bond id="b78" atomRefs2="a22 a26" order="1" /><bond id="b79" atomRefs2="a22 a25" order="1" /><bond id="b80" atomRefs2="a23 a22" order="1" /><bond id="b81" atomRefs2="a23 a31" order="1" /><bond id="b82" atomRefs2="a23 a14" order="1" /><bond id="b83" atomRefs2="a23 a27" order="1" /><bond id="b84" atomRefs2="a23 a32" order="1" /><bond id="b85" atomRefs2="a23 a26" order="1" /><bond id="b86" atomRefs2="a24 a23" order="1" /><bond id="b87" atomRefs2="a24 a27" order="1" /><bond id="b88" atomRefs2="a24 a32" order="1" /><bond id="b89" atomRefs2="a24 a33" order="1" /><bond id="b90" atomRefs2="a24 a15" order="1" /><bond id="b91" atomRefs2="a25 a16" order="1" /><bond id="b92" atomRefs2="a25 a34" order="1" /><bond id="b93" atomRefs2="a26 a25" order="1" /><bond id="b94" atomRefs2="a26 a34" order="1" /><bond id="b95" atomRefs2="a26 a17" order="1" /><bond id="b96" atomRefs2="a26 a35" order="1" /><bond id="b97" atomRefs2="a26 a21" order="1" /><bond id="b98" atomRefs2="a27 a36" order="1" /><bond id="b99" atomRefs2="a27 a26" order="1" /><bond id="b100" atomRefs2="a27 a35" order="1" /><bond id="b101" atomRefs2="a27 a21" order="1" /><bond id="b102" atomRefs2="a27 a18" order="1" /><bond id="b103" atomRefs2="a28 a37" order="1" /><bond id="b104" atomRefs2="a28 a23" order="1" /><bond id="b105" atomRefs2="a28 a31" order="1" /><bond id="b106" atomRefs2="a28 a38" order="1" /><bond id="b107" atomRefs2="a28 a32" order="1" /><bond id="b108" atomRefs2="a29 a28" order="1" /><bond id="b109" atomRefs2="a29 a39" order="1" /><bond id="b110" atomRefs2="a29 a38" order="1" /><bond id="b111" atomRefs2="a29 a24" order="1" /><bond id="b112" atomRefs2="a29 a32" order="1" /><bond id="b113" atomRefs2="a29 a33" order="1" /><bond id="b114" atomRefs2="a30 a29" order="1" /><bond id="b115" atomRefs2="a30 a39" order="1" /><bond id="b116" atomRefs2="a30 a33" order="1" /><bond id="b117" atomRefs2="a31 a41" order="1" /><bond id="b118" atomRefs2="a31 a40" order="1" /><bond id="b119" atomRefs2="a31 a26" order="1" /><bond id="b120" atomRefs2="a31 a34" order="1" /><bond id="b121" atomRefs2="a31 a35" order="1" /><bond id="b122" atomRefs2="a32 a31" order="1" /><bond id="b123" atomRefs2="a32 a41" order="1" /><bond id="b124" atomRefs2="a32 a27" order="1" /><bond id="b125" atomRefs2="a32 a42" order="1" /><bond id="b126" atomRefs2="a32 a36" order="1" /><bond id="b127" atomRefs2="a32 a35" order="1" /><bond id="b128" atomRefs2="a33 a32" order="1" /><bond id="b129" atomRefs2="a33 a42" order="1" /><bond id="b130" atomRefs2="a33 a36" order="1" /><bond id="b131" atomRefs2="a34 a43" order="1" /><bond id="b132" atomRefs2="a34 a44" order="1" /><bond id="b133" atomRefs2="a35 a34" order="1" /><bond id="b134" atomRefs2="a35 a44" order="1" /><bond id="b135" atomRefs2="a35 a45" order="1" /><bond id="b136" atomRefs2="a35 a21" order="1" /><bond id="b137" atomRefs2="a36 a35" order="1" /><bond id="b138" atomRefs2="a36 a45" order="1" /><bond id="b139" atomRefs2="a37 a50" order="1" /><bond id="b140" atomRefs2="a37 a49" order="1" /><bond id="b141" atomRefs2="a37 a31" order="1" /><bond id="b142" atomRefs2="a37 a41" order="1" /><bond id="b143" atomRefs2="a37 a40" order="1" /><bond id="b144" atomRefs2="a38 a37" order="1" /><bond id="b145" atomRefs2="a38 a50" order="1" /><bond id="b146" atomRefs2="a38 a41" order="1" /><bond id="b147" atomRefs2="a38 a32" order="1" /><bond id="b148" atomRefs2="a38 a42" order="1" /><bond id="b149" atomRefs2="a39 a38" order="1" /><bond id="b150" atomRefs2="a39 a51" order="1" /><bond id="b151" atomRefs2="a39 a42" order="1" /><bond id="b152" atomRefs2="a39 a33" order="1" /><bond id="b153" atomRefs2="a40 a53" order="1" /><bond id="b154" atomRefs2="a40 a43" order="1" /><bond id="b155" atomRefs2="a40 a34" order="1" /><bond id="b156" atomRefs2="a40 a44" order="1" /><bond id="b157" atomRefs2="a40 a52" order="1" /><bond id="b158" atomRefs2="a41 a54" order="1" /><bond id="b159" atomRefs2="a41 a40" order="1" /><bond id="b160" atomRefs2="a41 a53" order="1" /><bond id="b161" atomRefs2="a41 a44" order="1" /><bond id="b162" atomRefs2="a41 a35" order="1" /><bond id="b163" atomRefs2="a41 a45" order="1" /><bond id="b164" atomRefs2="a42 a41" order="1" /><bond id="b165" atomRefs2="a42 a54" order="1" /><bond id="b166" atomRefs2="a42 a36" order="1" /><bond id="b167" atomRefs2="a42 a45" order="1" /><bond id="b168" atomRefs2="a44 a43" order="1" /><bond id="b169" atomRefs2="a44 a48" order="1" /><bond id="b170" atomRefs2="a45 a44" order="1" /><bond id="b171" atomRefs2="a45 a48" order="1" /><bond id="b172" atomRefs2="a46 a37" order="1" /><bond id="b173" atomRefs2="a46 a50" order="1" /><bond id="b174" atomRefs2="a46 a49" order="1" /><bond id="b175" atomRefs2="a47 a50" order="1" /><bond id="b176" atomRefs2="a47 a46" order="1" /><bond id="b177" atomRefs2="a47 a38" order="1" /><bond id="b178" atomRefs2="a47 a51" order="1" /><bond id="b179" atomRefs2="a49 a40" order="1" /><bond id="b180" atomRefs2="a49 a53" order="1" /><bond id="b181" atomRefs2="a49 a52" order="1" /><bond id="b182" atomRefs2="a50 a49" order="1" /><bond id="b183" atomRefs2="a50 a41" order="1" /><bond id="b184" atomRefs2="a50 a54" order="1" /><bond id="b185" atomRefs2="a50 a53" order="1" /><bond id="b186" atomRefs2="a51 a50" order="1" /><bond id="b187" atomRefs2="a51 a38" order="1" /><bond id="b188" atomRefs2="a51 a54" order="1" /><bond id="b189" atomRefs2="a51 a42" order="1" /><bond id="b190" atomRefs2="a52 a43" order="1" /><bond id="b191" atomRefs2="a53 a44" order="1" /><bond id="b192" atomRefs2="a53 a52" order="1" /><bond id="b193" atomRefs2="a53 a48" order="1" /><bond id="b194" atomRefs2="a54 a53" order="1" /><bond id="b195" atomRefs2="a54 a45" order="1" /><bond id="b196" atomRefs2="a54 a48" order="1" /><bond id="b197" atomRefs2="a55 a57" order="1" /><bond id="b198" atomRefs2="a56 a58" order="1" /><bond id="b199" atomRefs2="a56 a55" order="1" /><bond id="b200" atomRefs2="a57 a59" order="1" /><bond id="b201" atomRefs2="a58 a60" order="1" /><bond id="b202" atomRefs2="a60 a59" order="1" /></bondArray></molecule></MChemicalStruct></MDocument>
</cml>
Nov 27, 2014 9:44:57 AM chemaxon.jchem.base.persister.MoleculePersister writeMolecule
WARNING: Exception caught while trying persistency method: MoleculeTo2DSmilesPersistencyMethod (see below for the problematic molecule)
java.lang.IllegalArgumentException: chemaxon.formats.MolFormatException: Ring (4) formed from two neighboring atoms at smiles [Ag]123456[Ag@]78[Ag]119%10%11%12[Ag]%13%14%15%16%17%18%19%20%21%22[Ag]%23%24%25%26%27%28%29[Ag]%30%31%32%33[Ag@@]%23%23[Ag@@]%24%24[Ag]%25%25%34%35[Ag]%36%37%38%39[Ag]%40%41%42%43%44[Ag]%13%13%45%46%47%48%49%50%51%52[Ag]%53%54%55%56%57%58[Ag]2%14%132%13%14%59%60[Ag]%61%62%63%64%65[Ag]%53%53%66[Ag]%54%54%67%68[Ag]%69%70%71%72%73%74%75%76[Ag]%77%78%79%80%81%82%83%84%85%86[Ag]%87%88%89%90%91[Ag]%77%77%92%93%94[Ag]%78%78%95%96%97[Ag]%69%69%98[Ag]%70%70%99%100[Ag]%101%102%103%104[Ag]%71%79%87%71%79%87%105[Ag]%72%70%101([Ag]%99%102)[Ag]%40%45%54%73%71%40%45[Ag]%36%41%46%55%67([Ag]%37%42)[Ag]%15%26%24%25%38%47%56%15[Ag]%16%34%39%43%48%16%24[Ag]%44%49%25%26[Ag]%50%80%88%79%40%34%36%37[Ag]32%61%8123%38%39%40[Ag]%82%89%77%41%42([Ag@]%43%44[Ag]%92%78%41[Ag]%62%83%952%42%43([Ag]%63%53%74%84%96%69[Ag]%51%57%13%64%66%68%75%85%45%343)[Ag]4%65%38%44)[Ag]%90%36%39[Ag]51%17%52%14%25%37%40[Ag]9%18%16%261[Ag]%102[Ag]%11%19%27%303([Ag]%20%28%35%2412)[Ag@@]7%31[Ag]68%12%21%32%593[Ag]%22%29%33%23%58%60%15.[Ag]%76%86%93%97%98%100%103%87[Ag]%91%94%104%105.C1CCCCC1 |r,(5.87,1.7,7.18;7.34,.85,9.56;5.87,3.39,9.56;2.94,3.39,9.57;1.47,2.53,11.96;2.93,0,11.97;-0,0,11.97;-1.47,2.54,11.97;-0,5.09,11.96;-1.46,5.93,9.56;.01,6.78,7.18;1.47,4.24,7.18;0,1.7,7.18;2.94,1.7,7.18;2.93,-0,4.79;-0,-0,4.79;-1.46,2.54,4.79;0,3.39,2.39;2.94,3.39,2.39;4.41,5.93,2.39;4.41,4.24,;2.94,1.7,;0,1.7,;-1.46,4.24,;.01,6.78,;1.48,5.93,2.39;-1.46,5.93,2.39;-2.92,6.78,;.01,5.09,4.79;-1.46,4.24,7.18;-2.92,6.78,7.18;.01,3.39,9.57;1.48,5.93,9.57;2.94,6.78,7.18;2.94,5.09,4.79;4.4,2.54,4.79;5.87,3.39,2.39;7.34,.85,2.39;5.87,1.7,;4.4,.85,2.39;1.47,.85,2.39;1.47,2.54,4.79;5.87,-0,4.79;5.87,5.09,4.79;4.41,4.24,7.18;4.41,5.93,9.56;5.87,5.09,11.97;4.41,2.54,11.97;2.95,5.09,11.96;5.87,0,11.97;4.4,.85,9.56;1.47,.85,9.56;1.47,4.24,;2.94,6.78,;.29,4.93,14.91;.29,3.53,14.91;1.5,2.82,14.92;2.72,3.52,14.92;2.72,4.93,14.92;1.51,5.63,14.91)|
at chemaxon.jchem.base.persister.method.SmilesToMolecule.apply(SmilesToMolecule.java:43)
at chemaxon.jchem.base.persister.method.SmilesToMolecule.apply(SmilesToMolecule.java:27)
at chemaxon.jchem.base.persister.method.FunctionBasedPersistencyMethod.read(FunctionBasedPersistencyMethod.java:45)
at chemaxon.jchem.base.persister.method.ValidatingChemicalStructurePersistencyMethod.write(ValidatingChemicalStructurePersistencyMethod.java:48)
at chemaxon.jchem.base.persister.method.ValidatingChemicalStructurePersistencyMethod.write(ValidatingChemicalStructurePersistencyMethod.java:26)
at chemaxon.jchem.base.persister.MoleculePersister.writeMolecule(MoleculePersister.java:95)
at chemaxon.jchem.base.persister.MoleculePersister.<init>(MoleculePersister.java:76)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.init(StructureRecordMaker.java:520)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.initRecord(StructureRecordMaker.java:467)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.initStructureAndMolecule(StructureRecordMaker.java:343)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.createRecord(StructureRecordMaker.java:296)
at chemaxon.jchem.base.search.structurerecord.StructureRecordMaker.insertRecord(StructureRecordMaker.java:160)
at chemaxon.jchem.db.UpdateHandler.createRowData0(UpdateHandler.java:1549)
at chemaxon.jchem.db.ParallelStructTableUpdater$UpdateHandlerAdapter.process(ParallelStructTableUpdater.java:119)
at chemaxon.util.concurrent.util.AbstractWorkUnit.call(AbstractWorkUnit.java:33)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:58)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:50)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(WorkUnitWorker.java:51)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work(WorkUnitWorker.java:36)
at chemaxon.util.concurrent.worker.Worker$1.call(Worker.java:45)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: chemaxon.formats.MolFormatException: Ring (4) formed from two neighboring atoms at smiles [Ag]123456[Ag@]78[Ag]119%10%11%12[Ag]%13%14%15%16%17%18%19%20%21%22[Ag]%23%24%25%26%27%28%29[Ag]%30%31%32%33[Ag@@]%23%23[Ag@@]%24%24[Ag]%25%25%34%35[Ag]%36%37%38%39[Ag]%40%41%42%43%44[Ag]%13%13%45%46%47%48%49%50%51%52[Ag]%53%54%55%56%57%58[Ag]2%14%132%13%14%59%60[Ag]%61%62%63%64%65[Ag]%53%53%66[Ag]%54%54%67%68[Ag]%69%70%71%72%73%74%75%76[Ag]%77%78%79%80%81%82%83%84%85%86[Ag]%87%88%89%90%91[Ag]%77%77%92%93%94[Ag]%78%78%95%96%97[Ag]%69%69%98[Ag]%70%70%99%100[Ag]%101%102%103%104[Ag]%71%79%87%71%79%87%105[Ag]%72%70%101([Ag]%99%102)[Ag]%40%45%54%73%71%40%45[Ag]%36%41%46%55%67([Ag]%37%42)[Ag]%15%26%24%25%38%47%56%15[Ag]%16%34%39%43%48%16%24[Ag]%44%49%25%26[Ag]%50%80%88%79%40%34%36%37[Ag]32%61%8123%38%39%40[Ag]%82%89%77%41%42([Ag@]%43%44[Ag]%92%78%41[Ag]%62%83%952%42%43([Ag]%63%53%74%84%96%69[Ag]%51%57%13%64%66%68%75%85%45%343)[Ag]4%65%38%44)[Ag]%90%36%39[Ag]51%17%52%14%25%37%40[Ag]9%18%16%261[Ag]%102[Ag]%11%19%27%303([Ag]%20%28%35%2412)[Ag@@]7%31[Ag]68%12%21%32%593[Ag]%22%29%33%23%58%60%15.[Ag]%76%86%93%97%98%100%103%87[Ag]%91%94%104%105.C1CCCCC1 |r,(5.87,1.7,7.18;7.34,.85,9.56;5.87,3.39,9.56;2.94,3.39,9.57;1.47,2.53,11.96;2.93,0,11.97;-0,0,11.97;-1.47,2.54,11.97;-0,5.09,11.96;-1.46,5.93,9.56;.01,6.78,7.18;1.47,4.24,7.18;0,1.7,7.18;2.94,1.7,7.18;2.93,-0,4.79;-0,-0,4.79;-1.46,2.54,4.79;0,3.39,2.39;2.94,3.39,2.39;4.41,5.93,2.39;4.41,4.24,;2.94,1.7,;0,1.7,;-1.46,4.24,;.01,6.78,;1.48,5.93,2.39;-1.46,5.93,2.39;-2.92,6.78,;.01,5.09,4.79;-1.46,4.24,7.18;-2.92,6.78,7.18;.01,3.39,9.57;1.48,5.93,9.57;2.94,6.78,7.18;2.94,5.09,4.79;4.4,2.54,4.79;5.87,3.39,2.39;7.34,.85,2.39;5.87,1.7,;4.4,.85,2.39;1.47,.85,2.39;1.47,2.54,4.79;5.87,-0,4.79;5.87,5.09,4.79;4.41,4.24,7.18;4.41,5.93,9.56;5.87,5.09,11.97;4.41,2.54,11.97;2.95,5.09,11.96;5.87,0,11.97;4.4,.85,9.56;1.47,.85,9.56;1.47,4.24,;2.94,6.78,;.29,4.93,14.91;.29,3.53,14.91;1.5,2.82,14.92;2.72,3.52,14.92;2.72,4.93,14.92;1.51,5.63,14.91)|
at chemaxon.marvin.io.formats.smiles.SmilesImport.readRingNumber(SmilesImport.java:1539)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol0(SmilesImport.java:913)
at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:622)
at chemaxon.marvin.io.formats.smiles.CxsmilesImport.readMol(CxsmilesImport.java:186)
at chemaxon.jchem.base.persister.method.SmilesToMolecule.apply(SmilesToMolecule.java:41)
... 26 more
Nov 27, 2014 9:44:57 AM chemaxon.jchem.base.persister.MoleculePersister logMolecule
WARNING: <?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_11_17.xsd" version="ChemAxon file format v14.11.17, generated by v14.11.24.0">
<MDocument><MChemicalStruct><molecule molID="m1"><propertyList><property dictRef="mrv_H_3d_coordinates" title="mrv_H_3d_coordinates"><scalar dataType="xsd:ENTITY"><![CDATA[MProp:MHCoords3D:
55 1 -0.660188 2.9848068 14.902826
54 1 -0.65186113 5.4823065 14.90586
59 1 3.6621203 2.974906 14.914598
58 1 3.6706555 5.4728155 14.916926
57 1 1.4958946 1.731153 14.913388
56 1 1.5142885 6.725948 14.906544]]></scalar></property></propertyList><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 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55 a56 a57 a58 a59 a60" elementType="Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag Ag C C C C C C" x3="0.0023661256 -1.4610555 -2.9244332 2.9362197 1.4727981 0.009420395 5.8701615 4.4067397 2.943362 1.4681097 0.0047321464 -1.4586895 4.402052 2.9386742 1.4752525 7.335906 5.872528 4.4091067 -2.0924375E-7 -1.4633778 5.8748503 2.9338534 1.4704758 0.0070543583 5.867795 4.4044175 2.9409957 0.0023658117 -1.4610559 -2.9244335 2.9362195 1.4727978 0.009420081 5.870161 4.406739 2.9433618 1.4680719 0.006217777 -1.4580727 4.4014373 2.9371243 1.4752192 7.33641 5.872467 4.40839 -3.1565467E-4 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</cml>
The file I'm trying to upload is a CML file derived from a VASP calculation I have attached it to this message.
I attach also a CPU benchmark done after cancelling Importer thread, where chemaxon threads are still in execution, such as ParallelStructTableUpdater. I attach too a memory graph with a scaling up Used Heap consumption process (there were no more operations running).
I'm using JChem v6.3.4 libraries included in latest JChem Suite v14.11.24.0.
Thank you in advance.