Hi Zheng,
Unless the molecule is a query the IteratingSDFReader (using MDLV2000Reader)
will automatically add the implicit hydrogens for you - however your code is
still correct. Do you have an example input molecule?
You are correct in presuming ‘getBond(IAtom, IAtom)’ for the atom container may
be slow. There isn’t a connivence method to do this but a good way is to create
a map with a commutative tuple key. For example...
Map<AtomPair,IBond> bondMap = new HashMap<>();
for (IBond bond : container.bonds())
bondMap.put(new AtomPair(bond.getAtom(0), bond.getAtom(1)),
bond);
// where AtomPair...
class AtomPair {
IAtom a, b;
AtomPair(IAtom a, IAtom b) {
this.a = a, this.b = b;
}
public int hashCode() {
return a.hashCode() ^ b.hashCode();
}
public boolean equals(Object obj) {
// null check etc
AtomPair that = (AtomPair) obj;
return this.a.equals(that.a) && this.b.equal(that.b) ||
this.a.equals(that.b) && this.b.equal(that.a);
}
}
J
> Begin forwarded message:
>
>> From: Zheng Shi <[email protected]>
>> Date: 13 September 2014 22:34:39 BST
>> To: John May <[email protected]>
>> 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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