> > From the manual the output format designation of -xN 2048 should do this. > > However, not so. -xf FP2 generates a 1021 bit fingerprint, and is > apparently > > specifically linked to FP2 and cannot be extended to 2048 bits. >
Correct. FP2 is used to generate linear fragments up to length 7 and has a fixed bit length. If anyone has a syntax that works, or if there is a circular format for > specifying 2048 fingerprints, please share the syntax. > $ obabel -L fingerprints ECFP0 Extended-Connectivity Fingerprints (ECFPs) ECFP10 Extended-Connectivity Fingerprints (ECFPs) ECFP2 Extended-Connectivity Fingerprints (ECFPs) ECFP4 Extended-Connectivity Fingerprints (ECFPs) ECFP6 Extended-Connectivity Fingerprints (ECFPs) ECFP8 Extended-Connectivity Fingerprints (ECFPs) FP2 Indexes linear fragments up to 7 atoms. FP3 SMARTS patterns specified in the file patterns.txt FP4 SMARTS patterns specified in the file SMARTS_InteLigand.txt MACCS SMARTS patterns specified in the file MACCS.txt In other words, if you want an extended circular fingerprint, you want ECFP4 or ECFP6, etc. If you want FP2, great, but it has a fixed bit length. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/
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