Hi Adam, You have to follow these steps:
a) clone a SMSD from Github git clone git://github.com/asad/SMSD.git b) download the patch from the github to restrict the mapping (i.e. ring atoms to ring atoms and linkers to linkers). https://github.com/downloads/asad/SMSD/0001-forced-matching-of-rings-atoms-to-ring-atoms-and-lin.patch c) apply the patch to the current branch by git am -s 0001-forced-matching-of-rings-atoms-to-ring-atoms-and-lin.patch d) compile it. e) Try command line interface java -jar SMSD.jar -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 -b The new outputs looks like http://26.media.tumblr.com/tumblr_lqbf56fklB1r22szco1_500.png Cheers, Asad On 21 Aug 2011, at 21:46, A. Heifets wrote: > Yes, forcing it not to map 23, 24, and 25 is exactly what I was > asking. How is that done? > >> On Sun, Aug 21, 2011 at 10:08 AM, Syed Asad Rahman <a...@ebi.ac.uk> wrote: >>> 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 >>> http://29.media.tumblr.com/tumblr_lqa78hrt8s1r22szco1_500.png >>> 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 >>> ***************************************
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