[Cdk-user] CML question

Thu, 08 Oct 2009 04:15:31 -0700 


I was testing Save As.. with Jchempaint, saving a structure as CML.
The editor produces a file, see attached called "no.cml".
If I try to open that one in Marvin, I get an error. It expects <cml> as a root tag. 


When I edit the file to be enclosed with <cml>..</cml> (see "yes.cml", 
attached) then it opens up in Marvin all right.


Should the CDK CML writer use these root tags or should Marvin not complain?

thanks,
Mark

<?xml version="1.0" encoding="ISO-8859-1"?>
<list convention="cdk:model" id="model1" xmlns="http://www.xml-cml.org/schema";>
  <moleculeList convention="cdk:moleculeSet" id="molSet1">
    <molecule id="m1">
      <atomArray>
        <atom id="a1" elementType="C" x2="-0.7661" y2="0.7661" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a2" elementType="C" x2="-1.4805" y2="0.3536" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a3" elementType="C" x2="-2.1951" y2="0.7661" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a4" elementType="C" x2="-2.1951" y2="1.5911" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a5" elementType="C" x2="-1.4805" y2="2.0036" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a6" elementType="C" x2="-0.7661" y2="1.5911" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a7" elementType="O" x2="-0.0516" y2="2.0036" formalCharge="0" hydrogenCount="0" isotopeNumber="16"/>
        <atom id="a8" elementType="C" x2="0.6629" y2="1.5911" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a9" elementType="C" x2="0.6629" y2="0.7661" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a10" elementType="C" x2="-0.0516" y2="0.3536" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a11" elementType="C" x2="-0.0516" y2="-0.4714" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a12" elementType="N" x2="-0.0516" y2="-1.2964" formalCharge="0" hydrogenCount="0" isotopeNumber="14"/>
        <atom id="a13" elementType="N" x2="-2.9095" y2="2.0036" formalCharge="0" hydrogenCount="0" isotopeNumber="14"/>
        <atom id="a14" elementType="C" x2="-3.624" y2="1.5911" formalCharge="0" hydrogenCount="2" isotopeNumber="12"/>
        <atom id="a15" elementType="C" x2="-2.9095" y2="2.8286" formalCharge="0" hydrogenCount="2" isotopeNumber="12"/>
        <atom id="a16" elementType="C" x2="-4.3385" y2="2.0036" formalCharge="0" hydrogenCount="3" isotopeNumber="12"/>
        <atom id="a17" elementType="C" x2="-2.1951" y2="3.2411" formalCharge="0" hydrogenCount="3" isotopeNumber="12"/>
        <atom id="a18" elementType="O" x2="1.3774" y2="2.0036" formalCharge="0" hydrogenCount="0" isotopeNumber="16"/>
        <atom id="a19" elementType="C" x2="1.3774" y2="0.3536" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a20" elementType="C" x2="2.1854" y2="-0.7089" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a21" elementType="N" x2="1.3954" y2="-0.4712" formalCharge="0" hydrogenCount="0" isotopeNumber="14"/>
        <atom id="a22" elementType="S" x2="2.1562" y2="0.6256" formalCharge="0" hydrogenCount="0" isotopeNumber="32"/>
        <atom id="a23" elementType="C" x2="2.6556" y2="-0.031" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a24" elementType="C" x2="2.5374" y2="-1.4551" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a25" elementType="C" x2="3.3596" y2="-1.5234" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a26" elementType="C" x2="3.8298" y2="-0.8455" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a27" elementType="C" x2="3.4778" y2="-0.0993" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
      </atomArray>
      <bondArray>
        <bond id="b1" atomRefs2="a1 a2" order="D"/>
        <bond id="b2" atomRefs2="a1 a6" order="S"/>
        <bond id="b3" atomRefs2="a1 a10" order="S"/>
        <bond id="b4" atomRefs2="a2 a3" order="S"/>
        <bond id="b5" atomRefs2="a3 a4" order="D"/>
        <bond id="b6" atomRefs2="a4 a5" order="S"/>
        <bond id="b7" atomRefs2="a5 a6" order="D"/>
        <bond id="b8" atomRefs2="a6 a7" order="S"/>
        <bond id="b9" atomRefs2="a7 a8" order="S"/>
        <bond id="b10" atomRefs2="a8 a9" order="S"/>
        <bond id="b11" atomRefs2="a9 a10" order="D"/>
        <bond id="b12" atomRefs2="a10 a11" order="S"/>
        <bond id="b13" atomRefs2="a11 a12" order="T"/>
        <bond id="b14" atomRefs2="a4 a13" order="S"/>
        <bond id="b15" atomRefs2="a13 a14" order="S"/>
        <bond id="b16" atomRefs2="a13 a15" order="S"/>
        <bond id="b17" atomRefs2="a14 a16" order="S"/>
        <bond id="b18" atomRefs2="a15 a17" order="S"/>
        <bond id="b19" atomRefs2="a8 a18" order="D"/>
        <bond id="b20" atomRefs2="a9 a19" order="S"/>
        <bond id="b21" atomRefs2="a21 a19" order="D"/>
        <bond id="b22" atomRefs2="a19 a22" order="S"/>
        <bond id="b23" atomRefs2="a20 a21" order="S"/>
        <bond id="b24" atomRefs2="a22 a23" order="S"/>
        <bond id="b25" atomRefs2="a23 a27" order="D"/>
        <bond id="b26" atomRefs2="a23 a20" order="S"/>
        <bond id="b27" atomRefs2="a20 a24" order="D"/>
        <bond id="b28" atomRefs2="a24 a25" order="S"/>
        <bond id="b29" atomRefs2="a25 a26" order="D"/>
        <bond id="b30" atomRefs2="a26 a27" order="S"/>
      </bondArray>
    </molecule>
  </moleculeList>
</list>

<?xml version="1.0" encoding="ISO-8859-1"?>
<cml>
<list convention="cdk:model" id="model1" xmlns="http://www.xml-cml.org/schema";>
  <moleculeList convention="cdk:moleculeSet" id="molSet1">
    <molecule id="m1">
      <atomArray>
        <atom id="a1" elementType="C" x2="-0.7661" y2="0.7661" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a2" elementType="C" x2="-1.4805" y2="0.3536" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a3" elementType="C" x2="-2.1951" y2="0.7661" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a4" elementType="C" x2="-2.1951" y2="1.5911" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a5" elementType="C" x2="-1.4805" y2="2.0036" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a6" elementType="C" x2="-0.7661" y2="1.5911" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a7" elementType="O" x2="-0.0516" y2="2.0036" formalCharge="0" hydrogenCount="0" isotopeNumber="16"/>
        <atom id="a8" elementType="C" x2="0.6629" y2="1.5911" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a9" elementType="C" x2="0.6629" y2="0.7661" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a10" elementType="C" x2="-0.0516" y2="0.3536" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a11" elementType="C" x2="-0.0516" y2="-0.4714" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a12" elementType="N" x2="-0.0516" y2="-1.2964" formalCharge="0" hydrogenCount="0" isotopeNumber="14"/>
        <atom id="a13" elementType="N" x2="-2.9095" y2="2.0036" formalCharge="0" hydrogenCount="0" isotopeNumber="14"/>
        <atom id="a14" elementType="C" x2="-3.624" y2="1.5911" formalCharge="0" hydrogenCount="2" isotopeNumber="12"/>
        <atom id="a15" elementType="C" x2="-2.9095" y2="2.8286" formalCharge="0" hydrogenCount="2" isotopeNumber="12"/>
        <atom id="a16" elementType="C" x2="-4.3385" y2="2.0036" formalCharge="0" hydrogenCount="3" isotopeNumber="12"/>
        <atom id="a17" elementType="C" x2="-2.1951" y2="3.2411" formalCharge="0" hydrogenCount="3" isotopeNumber="12"/>
        <atom id="a18" elementType="O" x2="1.3774" y2="2.0036" formalCharge="0" hydrogenCount="0" isotopeNumber="16"/>
        <atom id="a19" elementType="C" x2="1.3774" y2="0.3536" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a20" elementType="C" x2="2.1854" y2="-0.7089" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a21" elementType="N" x2="1.3954" y2="-0.4712" formalCharge="0" hydrogenCount="0" isotopeNumber="14"/>
        <atom id="a22" elementType="S" x2="2.1562" y2="0.6256" formalCharge="0" hydrogenCount="0" isotopeNumber="32"/>
        <atom id="a23" elementType="C" x2="2.6556" y2="-0.031" formalCharge="0" hydrogenCount="0" isotopeNumber="12"/>
        <atom id="a24" elementType="C" x2="2.5374" y2="-1.4551" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a25" elementType="C" x2="3.3596" y2="-1.5234" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a26" elementType="C" x2="3.8298" y2="-0.8455" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
        <atom id="a27" elementType="C" x2="3.4778" y2="-0.0993" formalCharge="0" hydrogenCount="1" isotopeNumber="12"/>
      </atomArray>
      <bondArray>
        <bond id="b1" atomRefs2="a1 a2" order="D"/>
        <bond id="b2" atomRefs2="a1 a6" order="S"/>
        <bond id="b3" atomRefs2="a1 a10" order="S"/>
        <bond id="b4" atomRefs2="a2 a3" order="S"/>
        <bond id="b5" atomRefs2="a3 a4" order="D"/>
        <bond id="b6" atomRefs2="a4 a5" order="S"/>
        <bond id="b7" atomRefs2="a5 a6" order="D"/>
        <bond id="b8" atomRefs2="a6 a7" order="S"/>
        <bond id="b9" atomRefs2="a7 a8" order="S"/>
        <bond id="b10" atomRefs2="a8 a9" order="S"/>
        <bond id="b11" atomRefs2="a9 a10" order="D"/>
        <bond id="b12" atomRefs2="a10 a11" order="S"/>
        <bond id="b13" atomRefs2="a11 a12" order="T"/>
        <bond id="b14" atomRefs2="a4 a13" order="S"/>
        <bond id="b15" atomRefs2="a13 a14" order="S"/>
        <bond id="b16" atomRefs2="a13 a15" order="S"/>
        <bond id="b17" atomRefs2="a14 a16" order="S"/>
        <bond id="b18" atomRefs2="a15 a17" order="S"/>
        <bond id="b19" atomRefs2="a8 a18" order="D"/>
        <bond id="b20" atomRefs2="a9 a19" order="S"/>
        <bond id="b21" atomRefs2="a21 a19" order="D"/>
        <bond id="b22" atomRefs2="a19 a22" order="S"/>
        <bond id="b23" atomRefs2="a20 a21" order="S"/>
        <bond id="b24" atomRefs2="a22 a23" order="S"/>
        <bond id="b25" atomRefs2="a23 a27" order="D"/>
        <bond id="b26" atomRefs2="a23 a20" order="S"/>
        <bond id="b27" atomRefs2="a20 a24" order="D"/>
        <bond id="b28" atomRefs2="a24 a25" order="S"/>
        <bond id="b29" atomRefs2="a25 a26" order="D"/>
        <bond id="b30" atomRefs2="a26 a27" order="S"/>
      </bondArray>
    </molecule>
  </moleculeList>
</cml>
</list>

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