Just a note on this - in CDK 1.5 the Pattern class is preferred as the
universal isomorphism tester is actually doing MCS (much harder).
Pattern ptrn = Pattern.findIdentical(butane);
for (Mol m : mols)
ptrn.matches(m);
In general though this is the slowest way to do it (n^2) vs (n log n) with
InChI/SMILES.
Regards,
John W May
john.wilkinson...@gmail.com
On 8 July 2015 at 00:03, Egon Willighagen <egon.willigha...@gmail.com>
wrote:
> Dear Zheng Shi,
>
> I think what you are looking for is "isomorphism checking". If the
> chemical graph of two structures is the same, they are called
> isomorphic. The following Groovy code shows a very basic example:
>
> butane = MoleculeFactory.makeAlkane(4);
> isomorphismTester = new UniversalIsomorphismTester()
> println "Is isomorphic: " +
> isomorphismTester.isIsomorph(
> butane, butane
> )
>
> But that can also indeed be done with canonical SMILES or InChI, as
> indicated by John.
>
> Egon
>
> On Mon, Jul 6, 2015 at 11:16 PM, Zheng Shi <zs...@ualberta.ca> wrote:
> > The "compare" means to tell if two molecules are equal. Suppose I have a
> > molecule B, which is generated by molecule A during a reaction: A -> B,
> and
> > I get a molecule C, which is also generated by molecule A during a
> reaction:
> > A->C. I want to tell whether B and C are the same. Usually we can
> visualize
> > the structure of the two structures to see. But if the number of
> molecules
> > is too big, for example, two sdf files contain some molecules, then it's
> not
> > convenient to visualize manually. So is there a reasonable way to do
> that?
> > can we just generate canonical form for molecules (like SMILES, then
> compare
> > the SMILES)? Is it reasonable for this? Or other methods? Thanks.
> >
> > On Mon, Jul 6, 2015 at 3:17 AM, John M <john.wilkinson...@gmail.com>
> wrote:
> >>
> >> Hit send too soon...
> >>
> >> b) Generate hash codes (CDK/InChIKey)
> >> c) Graph-Isomorphism check.
> >>
> >> Normally the best approach is (a) but this might not be the
> >> equality/comparison you want?
> >>
> >> John
> >>
> >>
> >>
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>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
> ImpactStory: https://impactstory.org/EgonWillighagen
>
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