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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