On Wed, Apr 10, 2019 at 11:56 AM Amber Alley <ara...@georgetown.edu> wrote:
> Hello, > > I have a question about openbabel fingerprints. Although this question > seems straightforward, I am having a hard time finding an answer. Does > openbabel have the capability to produce fingerprints that are binary only? > Aren't all of their fingerprints binary? At least the FP2 ones are. What is the other option you are envisioning? > I ask this because I want to compare openbabel fingerprints with other > fingerprint methods that use binary fingerprints. If not, can I compare > openbabel fingerprints (which are not binary) to fingerprints that are > binary using the Tanimoto coefficient? > You can't meaningfully compute tanimoto coefficients between one fingerprint generated by obabel and another fingerprint generated in something else. You can meaningfully compare the tanimoto coefficient obtained by obabel between two molecules, to the coefficient obtained by some other program with the same two molecules (but you will have to calibrate those distances somehow). Cheers, Jeff
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