On May 27, 2011, at 6:01 AM, Greg Landrum wrote: > And now a more philosophical point about this. .. > It seems like it would make a lot more sense for all of us if we had a > truly open definition.
In my followup I said I was working on a fingerprinting tool. It's now available! You can download it from http://code.google.com/p/chem-fingerprints/ or directly at http://code.google.com/p/chem-fingerprints/downloads/detail?name=chemfp-1.0a1.tgz It supports RDKit, OpenBabel, and OEChem, with the command-line programs rdkit2fps, ob2fps, and oe2fps respectively. Support here includes support for the platform-dependent fingerprinters. I've also developed platform-independent definitions for RDKit's MACCS patterns and for substructure patterns heavily based on the published PubChem/CACTVS fingerprints. I've also implemented support for these patterns for each of the toolkits, as well as a validation suite of about 400 structures and expected bits. (And let me say, that alone took about 30 hours of very tedious work!) The distribution includes the command-line tool "sdf2fps" to extract fingerprints from an SD file. It can handle many fingerprint formats, including the --pubchem shortcut to extract the PubChem fingerprints. (Note: this tool does not require a third-pary chemistry toolkit.) Finally, there's the command-line tool "simsearch" which does Tanimoto similarity searching. If the query file is a structure file then it knows how to examine the metadata in the target fingerprint file to get the correct fingerprinter. The code is written in Python, with a C extension for performance. There are no pre-built distributions. I'm looking for feedback about the code. Let me know if it does what you want, and if it doesn't, the let me know what you want. Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
