Hi Nick,
Sorry, no - there is no implementation of the InChI canonicalization
routine in the CDK (that I know of!) that doesn't involve actually
generating the InChI using the c-libraries.
The best you can get is to do something like:
public int[] getCanonicalPermutation(IAtomContainer container) {
int atomCount = container.getAtomCount();
try {
CDKInChI cdkInchi = new CDKInChI();
List<INCHI_OPTION> options = new ArrayList<INCHI_OPTION>();
options.add(INCHI_OPTION.DoNotAddH);
cdkInchi.getInChI(container, options); // do nothing with it!
String auxInfo = cdkInchi.getAuxinfo();
int[] permutation = InchiReader.getPermutationFromAuxInfo(auxInfo);
int[] invP = new int[atomCount];
for (int i = 0; i < atomCount; i++) {
invP[permutation[i]] = i;
}
return invP;
} catch (CDKException c) {
int[] permutation = new int[atomCount];
for (int index = 0; index < atomCount; index++) {
permutation[index] = index;
}
return permutation;
}
}
which will give you a permutation of the atoms according to the inchi.
Of course, it generates an inchi at the same time...
gilleain
On 9/10/13, Nick Vandewiele <[email protected]> wrote:
> Hi,
>
>
>
> Imagine I created an IAtomContainer by adding atom after atom. Now I want
> to
> reorder the atoms so that their atom numbers comply to the rules of the
> canonicalization scheme of inchi. I want to do that without actually
> generating the inchi of the atom container and re-using the inchi to create
> a new atom container. Just reshuffling the atom numbers so that they are
> canonical.
>
>
>
> Does CDK have something that does this?
>
>
>
>
>
> regards
>
> Nick
>
>
>
>
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