More than one fragment could hash to the same bit, so why not just do the analysis yourself by hand? Write some code to compare all paths of length 1-7 in the two molecules and see which are different.
- Noel 2009/10/5 erlangener <erlange...@gmail.com>: > Thanks Geoff, > > In FP3, the molecular fingerprint is calculated using a predefined smarts > patterns, which can then be matched by the fingerprint bits. > > However, if FP2, the fingerprint is calculated based on hashing the > fragments with length=1-7. Here is my problem, the hashed bits can not > matched back to the fragments. There is also not (I did not find) file > storing these fragments. So, my question here is how to get the fragments > with length equal to 1 ~7, such as C-C, C=C, C#C, CCC,,,,. > > Yes, after we get the fragment bits, we can use the XOR to get the fragment > difference. > > Thanks, > Er > > > 2009/10/1 Geoffrey Hutchison <ge...@geoffhutchison.net> >>> >>> Anyone knows how to get the fragments (not the bit fingerprints) >>> before the fingerprint hashing? >> >> I do not know of a direct way in the code, although the fingerprints are >> simply a set of SMARTS patterns. You could parse the file and then match the >> SMARTS against your molecules. >> >>> Further, how to get the fragment difference of two molecules? >> >> I'm not sure what you mean. Do you want the difference between the two bit >> fingerprints? You'd take the exclusive or (XOR) of the two bitvectors. That >> will give you the bits which are in one but not both. >> >> Does that help? >> >> -Geoff > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9-12, 2009. Register now! > http://p.sf.net/sfu/devconf > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
