On Dec 21, 2010, at 10:55 PM, erapp wrote: > I need to be able > to find all unique fragments for a molecule of a given length (i.e. number > of atoms in fragment) and provide information about what makes it unique.
You might be able to adapt some code I wrote a few weeks ago, at http://www.dalkescientific.com/writings/diary/archive/2011/01/13/faster_subgraph_enumeration.html It's for OEChem but the translation to OpenBabel wouldn't be that hard. Craig James wrote: > If you do find an algorithm that produces a reasonable number of fragments, > the canonical SMILES generator might be useful. It has the ability to > generate fragment SMILES. and if you rewrite the subgraph-to-SMARTS code using that, you might get better performance than OEChem, which doesn't have that feature. As Craig pointed out, the number of subgraphs grows quickly as a function of the number of atoms in the subgraph. I've found that k=6 and k=7 are tractable, but I haven't yet explored larger sizes to judge what the distribution looks like for typical small molecules. Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
