Well It's not that big a molecule. I can't remember the exact number but we
can write SMILES for proteins of up to around 1000 AAs. With the correct
algorithm It should be sublinear time to get the framework... however the
fragments and uniquifiing of those would take a while. Unfortunately it
looks like even just requesting the framework takes forever.
Rewriting the code with a better algorithm should do it - a first glance
shows it's doing lots it doesn't need. Curiously you don't need ring
perception to get the framework just iteratively delete degree 1 vertices.
I'll try and find time can you add a feature request/issue on github please.
John
On 11 January 2017 at 12:06, Nikolas Glaser <glase...@gmail.com> wrote:
> Hello guys,
> one question to the murcko fragmenter.
> The fragmenter worked for 15 hours on the following Chembl Compound and
> did not find a result. Is this a bug or is it not possible to get the
> murcko scaffold out of a compound like this?
> I am just fit in the informatics and have not a lot of knowledge for
> chemical compounds. I try to find out if there is a bug in the
> MurckoFragmenter or if it is necessary to change the fragmenter for my
> needs? Or is it just stupid to try fragmentation for a compound like this
> and I should put a filter in front of the fragmenter?
>
> Copmound: https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL529226
>
> Thanks for reply.
>
> Best regards
> Niko
>
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