[Cdk-devel] CML markup for fragments (was: [QSAR-devel] MDL keys for drug discovery)

[E.L. W. <eg...@sc...>]

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On Tuesday 27 April 2004 07:52, Egon Willighagen wrote:
> > I think this is the sort of thing we should be making available - in XM=
L,
> > of course!
>
> Of course :)

In CDK Chris and I started (not finished) transforming the templates - whic=
h=20
are fragments - into CML. The result was:

<?xml version=3D"1.0"?>
<molecule id=3D"adamantane" dictRef=3D"cdk:layoutTemplate"
  xmlns=3D"http://www.xml-cml.org/schema/cml2/core">
  <atomArray>
    <atom id=3D"a1" elementType=3D"C" x2=3D"-1.0019" y2=3D"-0.1598"/>
    <atom id=3D"a2" elementType=3D"C" x2=3D"-0.5894" y2=3D"-0.8743"/>
    <atom id=3D"a3" elementType=3D"C" x2=3D"0.2087" y2=3D"-0.6652"/>
    <atom id=3D"a4" elementType=3D"C" x2=3D"1.0019" y2=3D"-0.8743"/>
    <atom id=3D"a5" elementType=3D"C" x2=3D"0.5895" y2=3D"-0.1598"/>
    <atom id=3D"a6" elementType=3D"C" x2=3D"-0.2087" y2=3D"-0.3688"/>
    <atom id=3D"a7" elementType=3D"C" x2=3D"-1.0019" y2=3D"0.6652"/>
    <atom id=3D"a8" elementType=3D"C" x2=3D" 0.5895" y2=3D"0.6652"/>
    <atom id=3D"a9" elementType=3D"C" x2=3D"0.2087" y2=3D"0.1598"/>
    <atom id=3D"a10" elementType=3D"C" x2=3D"-0.2038" y2=3D"0.8743"/>
    <atom id=3D"a11" dictRef=3D"cdk:attachmentPoint"=20
        elementType=3D"Dummy" x2=3D"-4" y2=3D"-5"/>
  </atomArray>
  <bondArray>
    <bond id=3D"b1" atomRefs2=3D"a1 a2" order=3D"1"/>
    <bond id=3D"b2" atomRefs2=3D"a2 a3" order=3D"1"/>
    <bond id=3D"b3" atomRefs2=3D"a3 a4" order=3D"1"/>
    <bond id=3D"b4" atomRefs2=3D"a4 a5" order=3D"1"/>
    <bond id=3D"b5" atomRefs2=3D"a5 a6" order=3D"1"/>
    <bond id=3D"b6" atomRefs2=3D"a6 a1" order=3D"1"/>
    <bond id=3D"b7" atomRefs2=3D"a1 a7" order=3D"1"/>
    <bond id=3D"b8" atomRefs2=3D"a5 a8" order=3D"1"/>
    <bond id=3D"b9" atomRefs2=3D"a3 a9" order=3D"1"/>
    <bond id=3D"b10" atomRefs2=3D"a9 a10" order=3D"1"/>
    <bond id=3D"b11" atomRefs2=3D"a10 a7" order=3D"1"/>
    <bond id=3D"b12" atomRefs2=3D"a10 a8" order=3D"1"/>
    <bond id=3D"b13" atomRefs2=3D"a10 a11" order=3D"1"/>
  </bondArray>
</molecule>

This allows a clear connectivity, clear 2D structure of the attached specie=
s=20
(just rotation required). You'll have noticed that it uses a Dummy element,=
=20
which will be removed when it is attached.

Does this make sense?

Egon

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eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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