Hi! I am experiencing a problem trying to kekulise a set of molecules with aromatic rings and atoms with formal charge defined.
I use CDK 1.5.5 to read and process a set molecules (SDF/Mol). I would like to kekulise all the aromatic rings in order to transform those bonds which are specified (mis)using bond order = 4 to an alternate set of bonds with order 1 and 2. In order to do this I use the tool 'FixBondOrdersTool'. I use the same piece of code specified in http://blueobelisk.shapado.com/questions/detect-aromatic-rings-using-bond-order-4-in-a-sdf-file-with-cdk#answer52299d9597cfef16df00952f String input = "C:\\Users\\Oscar\\Desktop\\problem.sdf"; String output = "C:\\Users\\Oscar\\Desktop\\problem2.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(); It works fine in most cases. But I have found that when one of the atoms of the ring has a formal charge specified in the input SDF/Mol, the transformation is not performed correctly. Example: Input molecule: 7 7 0 0 0 0 999 V2000 -0.2947 3.3589 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 0.4198 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4198 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2947 1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0091 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0091 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2947 4.1839 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 4 0 0 0 0 1 6 4 0 0 0 0 2 3 4 0 0 0 0 3 4 4 0 0 0 0 4 5 4 0 0 0 0 5 6 4 0 0 0 0 1 7 1 0 0 0 0 M CHG 2 1 1 7 -1 M END $$$$ Processed molecule (using FixBondOrdersTool): CDK 0426141124 7 7 0 0 0 0 0 0 0 0999 V2000 -0.2947 3.3589 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.4198 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4198 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2947 1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0091 2.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0091 2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2947 4.1839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 1 6 0 0 0 0 0 2 3 0 0 0 0 0 3 4 0 0 0 0 0 4 5 0 0 0 0 0 5 6 0 0 0 0 0 1 7 1 0 0 0 0 M CHG 1 1 1 M CHG 1 7 -1 M END > <cdk:Title> null > <cdk:Remark> null $$$$ As you can see the bond type of the bonds which belong to the ring are specified with bond order = 0. Am I doing something wrong ? How could I manage these cases in order to obtain a kekulised structure ? I have attached both SDF files. Thanks in advance Oscar
INPUT.sdf
Description: Binary data
PROCESSED.sdf
Description: Binary data
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