Hi all, I am having some issues with the CDK library.
I have the molecule "glycitein" in the attached file (glycitein.sdf). I am
running the SMARTSQueryTool to perform structure search. The SMARTS
patterns are the following:
P1:
[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-c2ccccc-12)-[c;R1]1[c;R1][c;R1][c;R1][c;R1][c;R1]1
P2:
[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-[#6]-2=[#6]-[#6]=[#6]-[#6]=[#6]-1-2)-[#6;R1]-1=[#6;R1]-[#6;R1]=[#6;R1]-[#6;R1]=[#6;R1]-1
For each of those, the query tool returns false, which is
really surprising. I imagine it still has to do with the Aromaticity
detection or a related issue. I have tried many things and it seems that
they do not always work as they should.
1) I therefore preprocessed the molecule using the code below (from a
previous chat I had on a forum):
SMSDNormalizer.percieveAtomTypesAndConfigureAtoms(molecule);
CDKHydrogenAdder.getInstance(molecule.getBuilder())
.addImplicitHydrogens(molecule);
for (IBond bond : molecule.bonds()) {
if (bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE)) {
bond.setFlag(CDKConstants.ISAROMATIC, true);
bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true);
bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true);
}
}
SMSDNormalizer.aromatizeMolecule(molecule);
I attached the resulting structure in SDF format as returned by CDK
((glycitein_processed.sdf)), which in most editors is shown as in the
attached picture. It seems that all the aromatic bonds (marked as 4) in the
SDF are perceived as single bonds.
Therefore, the result of the structure search is still "FALSE".
By the way, trying a combination of AtomContainerManipulator (to perceive
atom types) and Aromaticity
<http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html>
did not help either
2) Instead of aromatizing, I removed the SMSDNormalizer lines, and added
the following:
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
Kekulization.kekulize(molecule);
The SDF of the resulting molecule is the same. The result also.
How can I process these molecules efficiently?
I am writing a function that will take SDF files, and run
the SMARTSQueryTool to match certain patterns. Therefore, I need an
efficient way to preprocess these molecules.
Can someone help me out here?
Thank you in advance.
Best,
glycitein_processed.sdf
Description: Binary data
glycitein.sdf
Description: Binary data
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