Re: [Cdk-user] Cdk-user Digest, Vol 63, Issue 9

[Syed Asad Rahman]

Hi Abe, I tried the latest SMSD (SMSD20110818.zip) command line option  command: sh SMSD -Q SMI -q "c1(ccc2c(c1)c(c([nH]2)C(=O)N)S(=O)(=O)N1CCOC(C1)C(=O)N1CCc2c(C1)cccc2)Br"  -T SMI -t "c1(ccc2c(c1)c(c([nH]2)C(=O)N)S(=O)(=O)N1CCOC(C1)C(=O)NCCOc1ccccc1)Br" -g and I got this image Do you want to skip mappings 23, 24, and 25 as they match ring vs non ring? For many users this is a valid mapping (eg: in case of atom atom mapping in reactions) but for some like you it's not as your requirements might be different. Let me know and I would let you know the trick..... Asad On 21 Aug 2011, at 13:04, cdk-user-requ...@lists.sourceforge.net wrote: Send Cdk-user mailing list submissions to cdk-user@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/cdk-user or, via email, send a message with subject or body 'help' to cdk-user-requ...@lists.sourceforge.net You can reach the person managing the list at cdk-user-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Cdk-user digest..." Today's Topics:   1. How to get MCS to respect rings? (A. Heifets) ---------------------------------------------------------------------- Message: 1 Date: Sat, 20 Aug 2011 17:47:38 -0400 From: "A. Heifets" <abe...@cs.toronto.edu> Subject: [Cdk-user] How to get MCS to respect rings? To: cdk-user@lists.sourceforge.net Message-ID: <CAHVeH83_Fd5UHt3t9WLTwCTyBD3o=9FNjXSBzdtktGuuWrn=x...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 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 Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user End of Cdk-user Digest, Vol 63, Issue 9 ***************************************

------------------------------------------------------------------------------
EMC VNX: the world's simplest storage, starting under $10K
The only unified storage solution that offers unified management 
Up to 160% more powerful than alternatives and 25% more efficient. 
Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user