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 <[email protected]> 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, [email protected] wrote: >> >> Send Cdk-user mailing list submissions to >> [email protected] >> >> 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 >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> 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" <[email protected]> >> Subject: [Cdk-user] How to get MCS to respect rings? >> To: [email protected] >> 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 >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> >> >> End of Cdk-user Digest, Vol 63, Issue 9 >> *************************************** ------------------------------------------------------------------------------ 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
