The other option is you need to use the molecule to get the bond list
(which is always awkward hence I added these many years ago but it needed a
slow introduction).
public static void main(String[] args) throws Exception {
MDLV2000Reader parser = new MDLV2000Reader(
new FileInputStream("../data/example.mol"),
IChemObjectReader.Mode.RELAXED);
IAtomContainer mol =
parser.read(SilentChemObjectBuilder.getInstance().newAtomContainer());
IAtom atom = mol.getAtom(0);
List<IBond> bonds = mol.getConnectedBondList(atom);
}
On Tue, 28 Jan 2025 at 16:47, John Mayfield <john.wilkinson...@gmail.com>
wrote:
> Hi Tim,
>
> Which version are you using? That should work in CDK 2.10 but before that
> you need to go via the builder. We changed the internals so atoms can know
> about the molecule they belong to... but an atom can still appear in
> multiple molecule at once.
>
> public class MolTest {
>
> public static void main(String[] args) throws Exception {
>
> MDLV2000Reader parser = new MDLV2000Reader(
> new FileInputStream("../data/example.mol"),
> IChemObjectReader.Mode.RELAXED);
> IAtomContainer mol =
> parser.read(SilentChemObjectBuilder.getInstance().newAtomContainer());
> IAtom atom = mol.getAtom(0);
> Iterable<IBond> bonds = atom.bonds();
>
> }
>
> more info: https://github.com/cdk/cdk/wiki/AtomContainer2 (since 7/8
> years ago :p)
>
> On Tue, 28 Jan 2025 at 11:31, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>
>> I've hit a strange problem with org.openscience.cdk.silent.Atom in that
>> several methods just throw a UnsupportedOperationException. This doesn't
>> make much sense to me.
>> I'm reading a molfile which generates that type of Atom, but if lots of
>> its methods are unsupported then that molecule isn't much use. What am I
>> missing?
>> This is using CDK 2.9.
>>
>> package org.squonk.cdk.depict;
>>
>> import org.openscience.cdk.interfaces.IAtom;
>> import org.openscience.cdk.interfaces.IAtomContainer;
>> import org.openscience.cdk.interfaces.IBond;
>> import org.openscience.cdk.io.IChemObjectReader;
>> import org.openscience.cdk.io.MDLV2000Reader;
>> import org.openscience.cdk.silent.AtomContainer;
>>
>> import java.io.FileInputStream;
>>
>> public class MolTest {
>>
>> public static void main(String[] args) throws Exception {
>>
>> MDLV2000Reader parser = new MDLV2000Reader(
>> new FileInputStream("../data/example.mol"),
>> IChemObjectReader.Mode.RELAXED);
>> IAtomContainer mol = parser.read(new AtomContainer());
>> IAtom atom = mol.getAtom(0);
>> Iterable<IBond> bonds = atom.bonds();
>>
>> }
>> }
>> _______________________________________________
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>
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