Dear Users, I would like to apply some biotransformations on a compound. I am using CDK 1.5.6 (I have to stick to this version for compatibility issues). In order to get accurate results, I decided to add all explicit hydrogen atoms in the molecule ( CC would become [H]C([H])([H])C([H])([H])[H] ). After applying the transformation Rx1 on the compound, I would like to remove the explicit atoms from the resulting molecule.
I would like to add hydrogen atom on the molecule test_1 attached below:
For this purpose, I use different methods:
1) I used to CDKHydrogenAdder as follows:
IAtomContainer molecule = (IAtomContainer)reader.next(); //
reading from a SDF file
IChemObjectBuilder builder =
SilentChemObjectBuilder.getInstance();
CDKHydrogenAdder.getInstance(builder).addImplicitHydrogens(molecule);
The raised errors where:
Exception in thread "main" org.openscience.cdk.exception.CDKException:
IAtom is not typed! C
at
org.openscience.cdk.tools.CDKHydrogenAdder.addImplicitHydrogens(CDKHydrogenAdder.java:125)
at
org.openscience.cdk.tools.CDKHydrogenAdder.addImplicitHydrogens(CDKHydrogenAdder.java:109)
.......
2) I used the AtomContainerManipulator from CDK
IAtomContainer molecule = (IAtomContainer)reader.next(); // reading
from a SDF file
AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
The problem here is that the hydrogen atoms are added without coordinates.
When I apply the following transformation on the resulting atom container,
I get a structure with only one hydrogen atom, which is connected to
several hetero atom (which normally implicit H atoms). The molecules
resulting from the transformation are also attached in the file
"transformation_products.sdf"
Reaction SMIRKS: [#6;X4H1,X4H2,X4H3,X4H4:1]>>[#6;X4:1][O][H]
I would like to get help: How can I add explicit hydrogen atoms with
coordinates. I guess this would be the way to correctly add hydrogens.
I tried to remove hydrogen atoms from the transformation products, but
obviously, I received an error message:
"java.lang.IllegalArgumentException: a non-pseudo atom had an unset
hydrogen count"
I used AtomContainerManipulator.removeHydrogens(metabolite), and
AtomContainerManipulator.suppressHydrogens(metabolite). Both did fail.
Thank you for your help.
test.sdf
Description: chemical/mdl-sdfile
transformation_products.sdf
Description: chemical/mdl-sdfile
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