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Conversion : CML to SDF

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Conversion : CML to SDF

Sebastien
Hello,

We are converting CML files into SDFiles using this command : cmd>obabel example.cml -O example.sdf

That works fine.

But in a few cases, the conversion is not done. The problem happens when there is data on a atom.

For example,


In this case, the CML looks like :
<?xml version='1.0' encoding='windows-1252'?><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_8_4.xsd" version="ChemAxon file format v14.8.4, generated by v14.9.8.0">
<MDocument>
        <MChemicalStruct>
                <molecule molID="m1">
                        <atomArray atomID="a1 a2 a3 a4 a5 a6 a7" elementType="C C C C C N C" mrvStereoGroup="0 or1 0 0 0 0 0" lonePair="0 0 0 0 0 1 0" sgroupRef="0 sg1 0 0 0 0 0" x2="1.333679121828039 1.3336791218280368 2.6673582436560745 2.6673582436560714 1.3336791218280346 0.0 1.3322676295501878E-15" y2="3.850000000000002 2.310000000000002 1.5399999999999978 -2.220446049250313E-15 -0.77 1.9984014443252818E-15 1.5400000000000018" />
                        <bondArray>
                                <bond id="b1" atomRefs2="a2 a1" order="1">
                                <bondStereo>W</bondStereo>
                                </bond>
                                <bond id="b2" atomRefs2="a2 a3" order="1" />
                                <bond id="b3" atomRefs2="a3 a4" order="1" />
                                <bond id="b4" atomRefs2="a4 a5" order="1" />
                                <bond id="b5" atomRefs2="a5 a6" order="1" />
                                <bond id="b6" atomRefs2="a6 a7" order="1" />
                                <bond id="b7" atomRefs2="a2 a7" order="1" />
                        </bondArray>
                <molecule id="sg1" role="DataSgroup" molID="m2" atomRefs="a2" fieldName="[DUP]" x="0.000000000000000" y="0.000000000000000" placement="Relative" unitsDisplayed="Unit displayed" context="Atom" fieldData="Enantiomer1" />
                </molecule>
        </MChemicalStruct>
        <MElectronContainer id="o2" occupation="0 0" radical="0">
                <MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0" />
                <MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0" />
        </MElectronContainer>
</MDocument>
</cml>


Is there a parameter to add in the command line for making the conversion works in such case ?
Can we ignore the data which is added on the atom ?

Thanks,
Sebastien.
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Re: Conversion : CML to SDF

Chris Morley-3
Sebastian

While reading CML files, OB ignores most elements and attributes it does
not understand. But the <molecule> element (for the SGroup) embedded
within the main <molecule> is not handled properly. I don't think there
is an option to bypass this (see obabel -L cml). It seems this issue was
recognized but not fixed 11 years ago when the code was written.

Chris

On 01/03/2017 10:40, Sebastien wrote:

> <?xml version='1.0' encoding='windows-1252'?><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_8_4.xsd"
> version="ChemAxon file format v14.8.4, generated by v14.9.8.0">
> <MDocument>
> <MChemicalStruct>
> <molecule molID="m1">
> <atomArray atomID="a1 a2 a3 a4 a5 a6 a7" elementType="C C C C C N C"
> mrvStereoGroup="0 or1 0 0 0 0 0" lonePair="0 0 0 0 0 1 0" sgroupRef="0 sg1 0
> 0 0 0 0" x2="1.333679121828039 1.3336791218280368 2.6673582436560745
> 2.6673582436560714 1.3336791218280346 0.0 1.3322676295501878E-15"
> y2="3.850000000000002 2.310000000000002 1.5399999999999978
> -2.220446049250313E-15 -0.77 1.9984014443252818E-15 1.5400000000000018" />
> <bondArray>
> <bond id="b1" atomRefs2="a2 a1" order="1">
> <bondStereo>W</bondStereo>
> </bond>
> <bond id="b2" atomRefs2="a2 a3" order="1" />
> <bond id="b3" atomRefs2="a3 a4" order="1" />
> <bond id="b4" atomRefs2="a4 a5" order="1" />
> <bond id="b5" atomRefs2="a5 a6" order="1" />
> <bond id="b6" atomRefs2="a6 a7" order="1" />
> <bond id="b7" atomRefs2="a2 a7" order="1" />
> </bondArray>
> <molecule id="sg1" role="DataSgroup" molID="m2" atomRefs="a2"
> fieldName="[DUP]" x="0.000000000000000" y="0.000000000000000"
> placement="Relative" unitsDisplayed="Unit displayed" context="Atom"
> fieldData="Enantiomer1" />
> </molecule>
> </MChemicalStruct>
> <MElectronContainer id="o2" occupation="0 0" radical="0">
> <MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0" />
> <MElectron atomRefs="m1.a6" difLoc="0.0 0.0 0.0" />
> </MElectronContainer>
> </MDocument>
> </cml>
Is there a parameter to add in the command line for making the
conversion works in such case ?
Can we ignore the data which is added on the atom ?


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Re: Conversion : CML to SDF

Sebastien
Hi Chris,

Thanks for the reply.

S├ębastien.
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Re: Conversion : CML to SDF

design
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In reply to this post by Sebastien
thank you for sharing this information.I really enjoyable to read your post.thank you so much.I really appreciated for this post.
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