On 17/10/2012 02:32, 蓝鱼在嘴里 wrote: > Hi,all, > I know openbabel can generate four kinds of fingerprints,each has an > original > fragement library.If I just want to code a molecule's fingerprint use 0 > or 1 bit to > represent a fragament exist in the molecule or not,how can I do this? Is > there > algorithms for this job?
To specify a particular fragment of a molecule you need to use SMARTS http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html . Edit the file patterns.txt, which is really just a list of SMARTS patterns, to define each bit in the fingerprint (you don't have to define all the bits). This will produce a customized FP3 fingerprint. It is also possible to specify the number of occurrences of a chemical feature in a molecule. The data file format is a little more complicated, see MACCS.txt for an example. Chris ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
