null MDocument after importing MOL structure

The code:

    public LewisMolecule(String molSt) throws VerifyException {

        final String SELF = "LewisMolecule: ";

        try {

            molStr = molSt;

            debugPrint(SELF + "molStr:\n", molStr);

            molecule = MolImporter.importMol(molStr);

            mDoc = molecule.getDocument();

            if (mDoc == null) debugPrint(SELF + "MDocument is null");

            ...

The log output:

Oct 30, 2013 4:33:06 PM org.apache.catalina.core.StandardWrapperValve invoke

INFO: LewisMolecule: molStr:

<?xml version="1.0" ?>

<cml>

<MDocument atomSetRGB="0:N,1:N" atomSetFont="0:SansSerif-PLAIN-12,1:Serif-PLAIN-14">

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray>

        <atom id="a1" elementType="N" x2="202.0" y2="48.0">

          <scalar id="a1:prop1" title="paired electrons" convention="marvin:atomprop" dataType="xsd:integer" value="2"  />

        </atom>

        <atom id="a2" elementType="O" formalCharge="-1"

               x2="248.0" y2="93.0">

          <scalar id="a2:prop1" title="paired electrons" convention="marvin:atomprop" dataType="xsd:integer" value="6"  />

        </atom>

        <atom id="a3" elementType="N" formalCharge="1"

               x2="248.0" y2="48.0" />

        <atom id="a4" elementType="H" x2="157.0" y2="93.0" />

        <atom id="a5" elementType="H" x2="112.0" y2="48.0" />

        <atom id="a6" elementType="C" x2="157.0" y2="48.0" />

        <atom id="a7" elementType="H" x2="157.0" y2="2.0" />

        <atom id="a8" elementType="H" x2="293.0" y2="2.0" />

        <atom id="a9" elementType="H" x2="293.0" y2="93.0" />

        <atom id="a10" elementType="C" x2="293.0" y2="48.0" />

        <atom id="a11" elementType="H" x2="339.0" y2="48.0" />

      </atomArray>

      <bondArray>

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

        <bond atomRefs2="a1 a3" order="2" />

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

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

        <bond atomRefs2="a6 a4" order="1" />

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

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

        <bond atomRefs2="a10 a8" order="1" />

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

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

      </bondArray>

     </molecule>

  </MChemicalStruct>

</MDocument>

</cml>



LewisMolecule: molStr:



  Lewis   122110121158                                           



 11 10  0     0  0             99 V2000

  202.0000  129.0000    0.0000 N   0  0  0  0  0  0

  252.0000  129.0000    0.0000 N   0  0  0  0  0  0

  152.0000  129.0000    0.0000 C   0  0  0  0  0  0

  303.0000  129.0000    0.0000 C   0  0  0  0  0  0

  252.0000  177.0000    0.0000 O   0  0  0  0  0  0

  152.0000  176.0000    0.0000 H   0  0  0  0  0  0

  105.0000  129.0000    0.0000 H   0  0  0  0  0  0

  152.0000   83.0000    0.0000 H   0  0  0  0  0  0

  303.0000   88.0000    0.0000 H   0  0  0  0  0  0

  345.0000  129.0000    0.0000 H   0  0  0  0  0  0

  303.0000  176.0000    0.0000 H   0  0  0  0  0  0

  1  2  1  0     0

  1  3  1  0     0

  2  4  1  0     0

  2  5  1  0     0

  3  6  1  0     0

  3  7  1  0     0

  3  8  1  0     0

  4  9  1  0     0

  4 10  1  0     0

  4 11  1  0     0

M  LNE  1   1   2

M  END



LewisMolecule: MDocument is null

When I import a molecule in MOL format, the MDocument of the resulting Molecule is null.  This seems to me to be a bug.  I am using JChem 6.1.0.

"When I import a molecule in MOL format, the MDocument of the resulting Molecule is null.  This seems to me to be a bug."

Yes the resulting MDocment is null. You may consider this as bug, in my view but the importer imports the smallest molecule object into which the molecule can fit. So if it a reaction you get a RxnMolecule, if it is an MDocument you get a Molecule with MDocument. In this case it is a Molecule which does not have document feature so the MDocument object will be null.

You can create an MDocument from a Molecule(Graph) with the MDocument constructor.

Thanks, that's helpful.  And once I create the MDocument, any time I use MoleculeGraph.getDocument() in the future, it will return the MDocument, correct?

Yes.