This question should be send to the cdk-user list (now cc'd).
What do precisely do you mean "compare two molecules"?
- are two molecules the same? : use SMILES/InChI
- how similar are two molecules?: use Fingerprint Tanimoto
- is one molecule part of another?: use Substructure/SMARTS (SmartsPattern
<http://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/smarts/SmartsPattern.html>
)
- find a common part of two molecules?: use SMSD
That class (CDKSubGraphHandler) is internal to the SMSD and IIRC should not
be accessed directly. The first one you mention is from the newer version
of SMSD (GitHub <https://github.com/asad/smsd)> Maven
<http://mvnrepository.com/artifact/uk.ac.ebi.smsd/smsd-core>) the second is
from an old version in the CDK. I'm actually in the process of deprecating
the old version to make it clear to users.
Without seeing your code it's impossible to know why the error is thrown
but I suspect you're doing the wrong thing in the first place.
John
On 16 January 2017 at 16:24, Nuno Manuel Carneiro Osório <
[email protected]> wrote:
> Good afternoon,
>
>
> I'm using this algorithm to compare two molecules.
>
> However, I had already used another (org.openscience.cdk.smsd.
> algorithm.rgraph.CDKSubGraphHandler) which apparently do the same but
> Java throws errors.
>
>
> What are the differences between them?
>
>
> Best regards,
>
> Nuno
>
>
> ----
> *Nuno Osório*
>
> *MSc Bioinformatics **e-mail: [email protected]
> <[email protected]>*
>
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