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Detect aromatic rings (using bond order = 4) in a SDF file with CDK

Asked by , Edited by oscar mora

Hi,

I am using CDK. I have some molecules in a SDF with aromatic rings which (mis)use bond order = 4 to represent aromaticity.
I would like to “fix” or transform the bonds with order = 4 (CDK represents them as SINGLE bond order and ISAROMATIC flag enabled) to bond order = SINGLE or DOUBLE.

Reading several resources:

http://chem-bla-ics.blogspot.com.es/2011/10/cdk-file-formats-1-mdl-molfiles-and.html

I guessed that I had to use tools like:

dbst = new DeduceBondSystemTool();
dbst.fixAromaticBondOrders(iAtomContainer);

or

fbot = new FixBondOrdersTool();
fbot.kekuliseAromticRings();


I have tried with the attached SDF (where the first molecule contains bond order = 4) but when I serialize the IAtomContainer object to MDL format using MDLV2000Writer, the bond block of the output still contains bond order = 4. (MDLV2000Writer is configured with default options-> WriteAromaticBondTypes:false)

Maybe I am misunderstanding something? Is it possible to rewrite an input molecule where bond block contains several bond orders = 4 to bond orders = 2 or 1.

thanks in advance!

Oscar







Attached files:
NN comments
jadewicks
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We are often facing the problems while detection of the aromatic rings, now the way about the detection of them with the use of rushanessay com file you shared, its good. With the use of it we can get easy way.

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2 answers

2

johnwilkinsonmay from Craven, United Kingdom

Argh the site ate my first response!


– DeduceBondOrdersTool only handles 5,6,7 member rings and will likely be retired in future
– AtomTypeAwareSaturationChecker is another tool – you can compare the three (here). Put in a SMILES string with aromatic atoms and see what each tool would do.
– Two things to watch out for 
  1. atom typing is required (not sure why)
  2. kekulizeAromaticRings() returns the structure and the input is not modified.
– If you’re using 1.4 instead of 1.5 IteratingSDFReader is named IteratingMDLReader

String input = “/Users/johnmay/Desktop/bo.sdf”;
String output = “/Users/johnmay/Desktop/bo-kekule.sdf”; 
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
IteratingSDFReader sdfr = new IteratingSDFReader(new FileReader(input),
builder);
SDFWriter sdfw = new SDFWriter(new FileWriter(output)); 
FixBondOrdersTool fbot = new FixBondOrdersTool();
while (sdfr.hasNext()) {
IAtomContainer container = sdfr.next();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
container = fbot.kekuliseAromaticRings(container);
sdfw.write(container);
}
sdfr.close();
sdfw.close();
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