MolFormatException: Parallel bonds: null

The following MRV was generated by our LewisJS program and subjected to MolImporter:

<?xml version="1.0" encoding="UTF-8"?>

<cml>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<propertyList>

<property dictRef="is Lewis Structure?" title="is Lewis Structure?">

<scalar>true</scalar>

</property>

</propertyList>

<atomArray>

<atom id="a1" elementType="C" x2="134" y2="158" />

<atom id="a2" elementType="C" x2="183" y2="126" />

<atom id="a3" elementType="C" x2="241" y2="152" />

<atom id="a4" elementType="O" x2="183" y2="75" />

<atom id="a5" elementType="H" x2="112" y2="129" />

<atom id="a6" elementType="H" x2="108" y2="181" />

<atom id="a7" elementType="H" x2="154" y2="184" />

<atom id="a8" elementType="H" x2="232" y2="182" />

<atom id="a9" elementType="H" x2="274" y2="167" />

<atom id="a10" elementType="H" x2="253" y2="121" />

</atomArray>

<bondArray>

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

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

<bond atomRefs2="a2 a4" order="2" />

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

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

<bond atomRefs2="a1 a7" order="1" />

<bond atomRefs2="a3 a8" order="1" />

<bond atomRefs2="a3 a9" order="1" />

<bond atomRefs2="a3 a9" order="1" />

<bond atomRefs2="a3 a10" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

</cml>

It threw the following exception:

INFO: chemaxon.formats.MolFormatException: Parallel bonds: null

        at chemaxon.marvin.io.formats.cml.BondReader.processBondArrays(BondReader.java:374)

        at chemaxon.marvin.io.formats.cml.CMLImport.readMol0(CMLImport.java:508)

        at chemaxon.marvin.io.formats.cml.CMLImport.readMol00(CMLImport.java:418)

        at chemaxon.marvin.io.formats.cml.CMLImport.readMolecule(CMLImport.java:380)

        at chemaxon.marvin.io.formats.cml.MrvImport.readChemicalStruct(MrvImport.java:352)

        at chemaxon.marvin.io.formats.cml.MrvImport.readMDocument(MrvImport.java:191)

        at chemaxon.marvin.io.formats.cml.MrvImport.readMRV(MrvImport.java:135)

        at chemaxon.marvin.io.formats.cml.MrvImport.readDocument(MrvImport.java:75)

        at chemaxon.marvin.io.formats.cml.CMLImport.readDocument(CMLImport.java:208)

        at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:714)

        at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:686)

        at chemaxon.marvin.io.MRecordImporter.readMol0(MRecordImporter.java:594)

        at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:511)

        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.formats.MolImporter.importMol(MolImporter.java:1465)

        at com.epoch.lewis.LewisMolecule.<init>(LewisMolecule.java:51)

When does the error message mean, and how can we avoid it in the future?

This structure also elicits the error:

<?xml version="1.0" encoding="UTF-8"?>

<cml>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<propertyList>

<property dictRef="is Lewis Structure?" title="is Lewis Structure?">

<scalar>true</scalar>

</property>

</propertyList>

<atomArray>

<atom id="a1" elementType="C" x2="168" y2="158" />

<atom id="a2" elementType="C" x2="217" y2="126" />

<atom id="a3" elementType="C" x2="275" y2="152" />

<atom id="a4" elementType="O" x2="217" y2="75">

<scalar id="a4:prop1" title="paired electrons" convention="marvin:atomprop" dataType="xsd:integer" value="4" />

</atom>

<atom id="a5" elementType="H" x2="146" y2="129" />

<atom id="a6" elementType="H" x2="142" y2="181" />

<atom id="a7" elementType="H" x2="188" y2="184" />

<atom id="a8" elementType="H" x2="266" y2="182" />

<atom id="a9" elementType="H" x2="308" y2="167" />

<atom id="a10" elementType="H" x2="287" y2="121" />

</atomArray>

<bondArray>

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

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

<bond atomRefs2="a2 a4" order="2" />

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

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

<bond atomRefs2="a1 a7" order="1" />

<bond atomRefs2="a3 a8" order="1" />

<bond atomRefs2="a3 a9" order="1" />

<bond atomRefs2="a3 a9" order="1" />

<bond atomRefs2="a3 a10" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

</cml>

Finally, if I just redraw the structure, then the program accepts it. So there's something uniquely wrong with the MRV in these (and a few other) MRVs.

Hi Bob,

There are parallel bonds between a3 and a9 in both mrvs. Parallel bonds are not supported in our API. A solution can be filtering parallel bonds in your exporter.

Janos

Ah, I see, parallel bonds are two separate bonds between the same pair of atoms.

Is there any reason your API can't just ignore the second bond rather than throwing an exception?

Anyway, i modified our code to avoid creating such bonds. Thanks for your explanation.

Hi Bob,

If we would just ignore a request to add a second bond between two atoms then we could hide coding mistakes. I think it would be similar to not throwing AIOBE if someone refers to an element of an array with a negative index.

Regards,

Zsuzsa