Hello CDK experts, When I take the maximum common substructure of
c1(ccc2c(c1)c(c([nH]2)C(=O)N)S(=O)(=O)N1CCOC(C1)C(=O)N1CCc2c(C1)cccc2)Br and c1(ccc2c(c1)c(c([nH]2)C(=O)N)S(=O)(=O)N1CCOC(C1)C(=O)NCCOc1ccccc1)Br I get a surprising result where some of the atoms in a ring are considered matched to some atoms not in a ring (atoms 25, 26, and 27 in my executions, although I don't know if the numbers will always be consistent). I'd like the maximum common substructure to consider two atoms equivalent only if both (or neither) are in a ring. I'm using the SMSD but it seems (in this case) just to call CDKMCS. I tried specifying different chemical filters but (1) it doesn't solve the problem and (2) this shouldn't be a post facto ordering on matches but rather part of the atom correspondence in the MCS computation. Can anyone point me to a switch I can throw to get MCS to respect ring membership? If that doesn't exist, I'd be willing to write some code (if someone could suggest a better plan than modifying every matches(IAtom atom) method for every class implementing IQueryAtom). Thank you! Cheers, Abe ------------------------------------------------------------------------------ Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
