Could someone answer this pls. On holiday.
Sent from my iPhone
Begin forwarded message:
> From: Zheng Shi <zs...@ualberta.ca>
> Date: 13 September 2014 22:34:39 BST
> To: John May <john...@ebi.ac.uk>
> Subject: questions about adding implicit hydrogen and get paths of a certain
> length in a molecule
>
> Hi, John,
>
> Thanks for you help.
>
> I have some questions to ask you again. First is adding implicit hydrogen for
> a given molecule. I write as below, but when I want to see the result, it
> seems the implicit hydrogen is not added. I hope you could help.
> IAtomContainer container = sdfr.next();
> CDKHydrogenAdder adder =
> CDKHydrogenAdder.getInstance(container.getBuilder());
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
> adder.addImplicitHydrogens(container);
> System.out.println(container);
> The other question is that I can use the class of PathTools to get paths of
> given length in a molecule. But the result is a list of atoms along the
> paths. I just wonder how I can get the bonds along the paths. I know using
> getbond() for two atoms. The problem is that I have to use getbond() again
> and again for every two atoms along the path. Is there a efficient way to do
> this? Thank you.
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