Re: [Cdk-devel] [Cdk-user] problems in the use of the signature class

[gilleain t. <gil...@gm...>]

Hi Patrik, John, etc

Those lines in the fingerprinter would be one way of doing things, agreed.
>From a quick look at Patrik's code, it seems to be doing something fairly
similar. Also I can't spot any obvious problems - but I will need to take a
more detailed look, probably over the weekend.

I suspect, however, that it is our old nemesis aromaticity. The molecule
has a benzene ring, so maybe different numbering give different results in
the aromatic detection. Of course, it could still be the signature code at
fault, I will check.

gilleain

On Thursday, March 14, 2013, John May wrote:

> Hi Patrik,
>
> This *might* help,
> https://github.com/egonw/cdk/blob/master/src/main/org/openscience/cdk/fingerprint/SignatureFingerprinter.java#L73-L80
>
> I can have a look for if you like, have you got the code?
>
> J
>
> On 14 Mar 2013, at 12:49, Patrik Rydberg <pr...@su...<javascript:_e({}, 'cvml', 'pr...@su...');>>
> wrote:
>
> Hi CDK users,****
>
> Is there anyone who has a working code that creates atomic signatures of
> varying height for a molecule?****
>
> I have made my own code, but for some strange reason it can on occasion
> generate slightly different signatures for the same molecular structure
> (same molecule, but two different mol files with different atom ordering).
> ****
> I’m quite confused in how this can happen and wondering if the error is in
> my code or in the signature class.****
>
> If anyone would be willing to help me find the error I would be very
> grateful.****
>
> Best regards,****
> Patrik Rydberg****
>
>
> --------------------------------------------------------------------------
> ****
> Patrik Rydberg, Associate Professor, Ph.D.****
>
> Biostructural Research Group****
> Department of Drug Design and Pharmacology****
> Faculty of Health and Medical Sciences****
> University of Copenhagen****
> DK-2100 Copenhagen****
>
> http://www.farma.ku.dk/index.php/Patrik-Rydberg/5304/0/****
>
>
>
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