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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