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 [email protected] ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
