Someone has previously commented in reply to a question of mine that
the 3D builder is not quite ready for use yet.
2008/5/29 Nicholas FitzGerald <[EMAIL PROTECTED]>:
> Hello all,
> As I've said in past messages, I'm trying to iterate over a large
> database of molecules, calculating the molecular descriptors, and add
> these back to the database. I've experimented with both reading in the
> sdf files or parsing the smiles strings.
>
> First I ensure connectivity like this:
>
> if (!ConnectivityChecker.isConnected(molecule)) {
> IMoleculeSet molSet = ConnectivityChecker
> .partitionIntoMolecules(molecule);
> IMolecule biggest = molSet.getMolecule(0);
> for (int i = 1; i < molSet.getMoleculeCount(); i++) {
> if (molSet.getMolecule(i).getBondCount() > biggest
> .getBondCount()) {
> biggest = molSet.getMolecule(i);
> }
> }
>
> molecule = (Molecule) biggest;
> }
>
> I then pass it through a 3Dcoordinate generator like so:
>
> TemplateHandler3D template = TemplateHandler3D.getInstance();
> ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template,"mm2");
> molecule = (Molecule) mb3d.generate3DCoordinates(molecule, true);
>
> After that, I calculate the descriptors. However, I keep getting two
> separate types of errors which are hindering my progress:
>
> 1. KEYError:Unknown distance key in pSet: O= ;Csp2 take default bon
> length:1.5
>
> 2. WARNING: Maybe RingTemplateError!
> RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be
> layout.
>
> Can someone please explain what these errors are, and what I can do to
> avoid them, or are they bugs? I have noticed these errors turn up on the
> error logs of the nightly builds.
>
> This is CDK 1.0.x
>
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