Problem with conversion to fingerprints

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Problem with conversion to fingerprints

Francesco Napolitano
Hi everybody.

I have a problem. I want to convert a number of smiles to binary
fingerprints using babel. Trying "babel mols.smi -ofpt -xhfFP2" will
also output information about sabstructures and similarities which I did
not expect and don't need. Is there a way to just get the converted
molecules?

Thank you,
Francesco.


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Re: Problem with conversion to fingerprints

Francesco Napolitano
I finally found an answer here:
http://www.dalkescientific.com/writings/diary/archive/2008/06/27/generating_fingerprints_with_openbabel.html

This seems to confirm my idea that there's a problem with babel aim and
actual implementation concerning fpt format. The documentation talks
about a format converter, but when it comes to fingerprints it does
other things (like tanimoto computation) by default, while to have the
actual conversion you must request an hex output and then work on it to
have the final fingerprints. Maybe I'm loosing the whole point of the
babel tool, suggestions and comments appreciated.

Cheers,
Francesco.

Il giorno mar, 06/04/2010 alle 18.05 +0200, Francesco Napolitano ha
scritto:

> Hi everybody.
>
> I have a problem. I want to convert a number of smiles to binary
> fingerprints using babel. Trying "babel mols.smi -ofpt -xhfFP2" will
> also output information about sabstructures and similarities which I did
> not expect and don't need. Is there a way to just get the converted
> molecules?
>
> Thank you,
> Francesco.
>



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Re: Problem with conversion to fingerprints

Chris Morley-3
In reply to this post by Francesco Napolitano
Francesco Napolitano wrote:
> I have a problem. I want to convert a number of smiles to binary
> fingerprints using babel. Trying "babel mols.smi -ofpt -xhfFP2" will
> also output information about sabstructures and similarities which I did
> not expect and don't need. Is there a way to just get the converted
> molecules?

 > I finally found an answer here:
 >
http://www.dalkescientific.com/writings/diary/archive/2008/06/27/generating_fingerprints_with_openbabel.html

 > This seems to confirm my idea that there's a problem with babel aim and
 > actual implementation concerning fpt format. The documentation talks
 > about a format converter, but when it comes to fingerprints it does
 > other things (like tanimoto computation) by default, while to have the
 > actual conversion you must request an hex output and then work on it to
 > have the final fingerprints. Maybe I'm loosing the whole point of the
 > babel tool, suggestions and comments appreciated.


I did not realize the demand there would be for raw fingerprint
output. FingerprintFormat was originally just a debugging aid. I
expected that the boolean operations on fingerprints would be done in
the program that generated them. However I was wrong, so the version
of fingerprint format in the development code now has an option to
provide only hexadecimal output.

Alternatively, the binary file produced by fs format has binary
fingerprints starting at an offset given by the first 32bit word
(currently 0x011c). Eventually I would like to produce fingerprints in
Andrew Dalke's portable binary fpf format.

Babel aims to be more than a format converter, but also a chemical
utility. It is valuable to know what features you find irrelevant, but
suggestions about what is missing are even more useful.

Chris


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